7CZ9 | pdb_00007cz9

Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7CZ9/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-09-07 Released: 2021-09-22
Deposition Author(s): Murakami, S., Okada, U., Yamashita, E.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae.

Bharatham, N., Bhowmik, P., Aoki, M., Okada, U., Sharma, S., Yamashita, E., Shanbhag, A.P., Rajagopal, S., Thomas, T., Sarma, M., Narjari, R., Nagaraj, S., Ramachandran, V., Katagihallimath, N., Datta, S., Murakami, S.

(2021) Nat Commun 12: 5400-5400

PubMed: 34518546 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-25679-0
Primary Citation Related Structures:
7CZ9

PubMed Abstract:
OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.

Organizational Affiliation

Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka, India.

Macromolecule Content

Total Structure Weight: 722.46 kDa
Atom Count: 53,422
Modeled Residue Count: 6,243
Deposited Residue Count: 6,252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Efflux pump membrane transporter	A, B, C, D, E A, B, C, D, E, F	1,042	Klebsiella pneumoniae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for U5U6L7 (Klebsiella pneumoniae) Explore U5U6L7 Go to UniProtKB: U5U6L7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5U6L7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain LD [auth F] SDF format, chain MA [auth B] SDF format, chain PC [auth E] SDF format, chain R [auth A] SDF format, chain WB [auth D] SDF format, chain OC [auth E] SDF format, chain MD [auth F] SDF format, chain LA [auth B] SDF format, chain CB [auth C] MOL2 format, chain LD [auth F] MOL2 format, chain MA [auth B] MOL2 format, chain PC [auth E] MOL2 format, chain R [auth A] MOL2 format, chain WB [auth D] MOL2 format, chain OC [auth E] MOL2 format, chain MD [auth F] MOL2 format, chain LA [auth B] MOL2 format, chain CB [auth C] mmCIF format, chain LD [auth F] mmCIF format, chain MA [auth B] mmCIF format, chain PC [auth E] mmCIF format, chain R [auth A] mmCIF format, chain WB [auth D] mmCIF format, chain OC [auth E] mmCIF format, chain MD [auth F] mmCIF format, chain LA [auth B] mmCIF format, chain CB [auth C]	CB [auth C] LA [auth B] LD [auth F] MA [auth B] MD [auth F] CB [auth C], LA [auth B], LD [auth F], MA [auth B], MD [auth F], OC [auth E], PC [auth E], R [auth A], WB [auth D]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain CB [auth C] Focus chain LA [auth B] Focus chain LD [auth F] Focus chain MA [auth B] Focus chain MD [auth F] Focus chain OC [auth E] Focus chain PC [auth E] Focus chain R [auth A] Focus chain WB [auth D] Interactions & Density Focus chain CB [auth C] Focus chain LA [auth B] Focus chain LD [auth F] Focus chain MA [auth B] Focus chain MD [auth F] Focus chain OC [auth E] Focus chain PC [auth E] Focus chain R [auth A] Focus chain WB [auth D]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AD [auth F] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain BC [auth E] SDF format, chain CA [auth B] SDF format, chain CD [auth F] SDF format, chain DA [auth B] SDF format, chain DD [auth F] SDF format, chain EA [auth B] SDF format, chain ED [auth F] SDF format, chain FA [auth B] SDF format, chain FC [auth E] SDF format, chain FD [auth F] SDF format, chain G [auth A] SDF format, chain GC [auth E] SDF format, chain H [auth A] SDF format, chain HC [auth E] SDF format, chain HD [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JC [auth E] SDF format, chain JD [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain KD [auth F] SDF format, chain LB [auth D] SDF format, chain LC [auth E] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain NC [auth E] SDF format, chain O [auth A] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain QB [auth D] SDF format, chain RA [auth C] SDF format, chain RB [auth D] SDF format, chain SA [auth C] SDF format, chain SB [auth D] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain YC [auth F] SDF format, chain ZA [auth C] SDF format, chain ZC [auth F] SDF format, chain VB [auth D] SDF format, chain UB [auth D] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain NB [auth D] SDF format, chain MC [auth E] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KC [auth E] SDF format, chain ID [auth F] SDF format, chain IC [auth E] SDF format, chain HA [auth B] SDF format, chain GD [auth F] SDF format, chain GA [auth B] SDF format, chain EC [auth E] SDF format, chain DC [auth E] SDF format, chain CC [auth E] SDF format, chain BD [auth F] MOL2 format, chain AB [auth C] MOL2 format, chain AD [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain CD [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain DD [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain ED [auth F] MOL2 format, chain FA [auth B] MOL2 format, chain FC [auth E] MOL2 format, chain FD [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GC [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HC [auth E] MOL2 format, chain HD [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JC [auth E] MOL2 format, chain JD [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain KD [auth F] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth E] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NC [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain YC [auth F] MOL2 format, chain ZA [auth C] MOL2 format, chain ZC [auth F] MOL2 format, chain VB [auth D] MOL2 format, chain UB [auth D] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain MC [auth E] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth E] MOL2 format, chain ID [auth F] MOL2 format, chain IC [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain GD [auth F] MOL2 format, chain GA [auth B] MOL2 format, chain EC [auth E] MOL2 format, chain DC [auth E] MOL2 format, chain CC [auth E] MOL2 format, chain BD [auth F] mmCIF format, chain AB [auth C] mmCIF format, chain AD [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain BC [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain CD [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain DD [auth F] mmCIF format, chain EA [auth B] mmCIF format, chain ED [auth F] mmCIF format, chain FA [auth B] mmCIF format, chain FC [auth E] mmCIF format, chain FD [auth F] mmCIF format, chain G [auth A] mmCIF format, chain GC [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HC [auth E] mmCIF format, chain HD [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain JC [auth E] mmCIF format, chain JD [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain KD [auth F] mmCIF format, chain LB [auth D] mmCIF format, chain LC [auth E] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NC [auth E] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain QB [auth D] mmCIF format, chain RA [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth D] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain YC [auth F] mmCIF format, chain ZA [auth C] mmCIF format, chain ZC [auth F] mmCIF format, chain VB [auth D] mmCIF format, chain UB [auth D] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain MC [auth E] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth E] mmCIF format, chain ID [auth F] mmCIF format, chain IC [auth E] mmCIF format, chain HA [auth B] mmCIF format, chain GD [auth F] mmCIF format, chain GA [auth B] mmCIF format, chain EC [auth E] mmCIF format, chain DC [auth E] mmCIF format, chain CC [auth E] mmCIF format, chain BD [auth F]	AB [auth C] AD [auth F] BA [auth B] BB [auth C] BC [auth E] AB [auth C], AD [auth F], BA [auth B], BB [auth C], BC [auth E], BD [auth F], CA [auth B], CC [auth E], CD [auth F], DA [auth B], DC [auth E], DD [auth F], EA [auth B], EC [auth E], ED [auth F], FA [auth B], FC [auth E], FD [auth F], G [auth A], GA [auth B], GC [auth E], GD [auth F], H [auth A], HA [auth B], HC [auth E], HD [auth F], I [auth A], IA [auth B], IC [auth E], ID [auth F], J [auth A], JA [auth B], JC [auth E], JD [auth F], K [auth A], KA [auth B], KB [auth D], KC [auth E], KD [auth F], L [auth A], LB [auth D], LC [auth E], M [auth A], MB [auth D], MC [auth E], N [auth A], NB [auth D], NC [auth E], O [auth A], OB [auth D], P [auth A], PB [auth D], Q [auth A], QA [auth C], QB [auth D], RA [auth C], RB [auth D], SA [auth C], SB [auth D], TA [auth C], TB [auth D], UA [auth C], UB [auth D], VA [auth C], VB [auth D], WA [auth C], XA [auth C], YA [auth C], YC [auth F], ZA [auth C], ZC [auth F]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AB [auth C] Focus chain AD [auth F] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain BD [auth F] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain CD [auth F] Focus chain DA [auth B] Focus chain DC [auth E] Focus chain DD [auth F] Focus chain EA [auth B] Focus chain EC [auth E] Focus chain ED [auth F] Focus chain FA [auth B] Focus chain FC [auth E] Focus chain FD [auth F] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GC [auth E] Focus chain GD [auth F] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HC [auth E] Focus chain HD [auth F] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain ID [auth F] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JC [auth E] Focus chain JD [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain KD [auth F] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain MC [auth E] Focus chain N [auth A] Focus chain NB [auth D] Focus chain NC [auth E] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain YC [auth F] Focus chain ZA [auth C] Focus chain ZC [auth F] Interactions & Density Focus chain AB [auth C] Focus chain AD [auth F] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain BD [auth F] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain CD [auth F] Focus chain DA [auth B] Focus chain DC [auth E] Focus chain DD [auth F] Focus chain EA [auth B] Focus chain EC [auth E] Focus chain ED [auth F] Focus chain FA [auth B] Focus chain FC [auth E] Focus chain FD [auth F] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GC [auth E] Focus chain GD [auth F] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HC [auth E] Focus chain HD [auth F] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain ID [auth F] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JC [auth E] Focus chain JD [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain KD [auth F] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain MC [auth E] Focus chain N [auth A] Focus chain NB [auth D] Focus chain NC [auth E] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain YC [auth F] Focus chain ZA [auth C] Focus chain ZC [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain FB [auth C] SDF format, chain JB [auth C] SDF format, chain ND [auth F] SDF format, chain OA [auth B] SDF format, chain OD [auth F] SDF format, chain PA [auth B] SDF format, chain PD [auth F] SDF format, chain QC [auth E] SDF format, chain QD [auth F] SDF format, chain RD [auth F] SDF format, chain SC [auth E] SDF format, chain TC [auth E] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WC [auth E] SDF format, chain X [auth A] SDF format, chain XC [auth E] SDF format, chain YB [auth D] SDF format, chain Z [auth A] SDF format, chain ZB [auth D] SDF format, chain Y [auth A] SDF format, chain XB [auth D] SDF format, chain VC [auth E] SDF format, chain UC [auth E] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain RC [auth E] SDF format, chain NA [auth B] SDF format, chain IB [auth C] SDF format, chain HB [auth C] SDF format, chain GB [auth C] SDF format, chain EB [auth C] SDF format, chain DB [auth C] SDF format, chain AA [auth A] MOL2 format, chain AC [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain ND [auth F] MOL2 format, chain OA [auth B] MOL2 format, chain OD [auth F] MOL2 format, chain PA [auth B] MOL2 format, chain PD [auth F] MOL2 format, chain QC [auth E] MOL2 format, chain QD [auth F] MOL2 format, chain RD [auth F] MOL2 format, chain SC [auth E] MOL2 format, chain TC [auth E] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WC [auth E] MOL2 format, chain X [auth A] MOL2 format, chain XC [auth E] MOL2 format, chain YB [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain VC [auth E] MOL2 format, chain UC [auth E] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain RC [auth E] MOL2 format, chain NA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain AC [auth D] mmCIF format, chain FB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain ND [auth F] mmCIF format, chain OA [auth B] mmCIF format, chain OD [auth F] mmCIF format, chain PA [auth B] mmCIF format, chain PD [auth F] mmCIF format, chain QC [auth E] mmCIF format, chain QD [auth F] mmCIF format, chain RD [auth F] mmCIF format, chain SC [auth E] mmCIF format, chain TC [auth E] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WC [auth E] mmCIF format, chain X [auth A] mmCIF format, chain XC [auth E] mmCIF format, chain YB [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain XB [auth D] mmCIF format, chain VC [auth E] mmCIF format, chain UC [auth E] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain RC [auth E] mmCIF format, chain NA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain AA [auth A]	AA [auth A] AC [auth D] DB [auth C] EB [auth C] FB [auth C] AA [auth A], AC [auth D], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], NA [auth B], ND [auth F], OA [auth B], OD [auth F], PA [auth B], PD [auth F], QC [auth E], QD [auth F], RC [auth E], RD [auth F], S [auth A], SC [auth E], T [auth A], TC [auth E], U [auth A], UC [auth E], V [auth A], VC [auth E], W [auth A], WC [auth E], X [auth A], XB [auth D], XC [auth E], Y [auth A], YB [auth D], Z [auth A], ZB [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AC [auth D] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain NA [auth B] Focus chain ND [auth F] Focus chain OA [auth B] Focus chain OD [auth F] Focus chain PA [auth B] Focus chain PD [auth F] Focus chain QC [auth E] Focus chain QD [auth F] Focus chain RC [auth E] Focus chain RD [auth F] Focus chain S [auth A] Focus chain SC [auth E] Focus chain T [auth A] Focus chain TC [auth E] Focus chain U [auth A] Focus chain UC [auth E] Focus chain V [auth A] Focus chain VC [auth E] Focus chain W [auth A] Focus chain WC [auth E] Focus chain X [auth A] Focus chain XB [auth D] Focus chain XC [auth E] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth D] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain NA [auth B] Focus chain ND [auth F] Focus chain OA [auth B] Focus chain OD [auth F] Focus chain PA [auth B] Focus chain PD [auth F] Focus chain QC [auth E] Focus chain QD [auth F] Focus chain RC [auth E] Focus chain RD [auth F] Focus chain S [auth A] Focus chain SC [auth E] Focus chain T [auth A] Focus chain TC [auth E] Focus chain U [auth A] Focus chain UC [auth E] Focus chain V [auth A] Focus chain VC [auth E] Focus chain W [auth A] Focus chain WC [auth E] Focus chain X [auth A] Focus chain XB [auth D] Focus chain XC [auth E] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.180 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.947	α = 91.28
b = 128.78	β = 90.01
c = 137.262	γ = 103.57

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Murakami, S.

Okada, U.

Yamashita, E.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02386
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05396
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06079