6X9F | pdb_00006x9f

Pseudomonas aeruginosa MurC with AZ8074

PDB DOI: https://doi.org/10.2210/pdb6X9F/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-06-02 Released: 2020-09-02
Deposition Author(s): Horanyi, P.S., Mayclin, S.J., Durand-Reville, T.F., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.183 (Depositor), 0.185 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Pseudomonas aeruginosa MurC with AZ8074

Horanyi, P.S., Mayclin, S.J., Durand-Reville, T.F., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 409.25 kDa
Atom Count: 18,978
Modeled Residue Count: 2,434
Deposited Residue Count: 3,728
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate--L-alanine ligase	A, B, C, D, E A, B, C, D, E, F, G, H	466	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: murC, PA4411 EC: 6.3.2.8
UniProt
Find proteins for Q9HW02 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HW02 Go to UniProtKB: Q9HW02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HW02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UXP (Subject of Investigation/LOI) Query on UXP Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain XA [auth F] SDF format, chain PA [auth E] SDF format, chain P [auth B] SDF format, chain IB [auth H] SDF format, chain I [auth A] SDF format, chain DB [auth G] SDF format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain XA [auth F] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain IB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain DB [auth G] MOL2 format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain XA [auth F] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain IB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain DB [auth G] mmCIF format, chain BA [auth C]	BA [auth C] DB [auth G] HA [auth D] I [auth A] IB [auth H] BA [auth C], DB [auth G], HA [auth D], I [auth A], IB [auth H], P [auth B], PA [auth E], XA [auth F]	[(2R)-1-{4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-2H-pyrazolo[3,4-d]pyrimidin-6-yl}piperidin-2-yl]methanol C₁₇ H₂₂ N₈ O YKDFQYJWKSLGGG-LLVKDONJSA-N		Interactions Focus chain BA [auth C] Focus chain DB [auth G] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IB [auth H] Focus chain P [auth B] Focus chain PA [auth E] Focus chain XA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain DB [auth G] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IB [auth H] Focus chain P [auth B] Focus chain PA [auth E] Focus chain XA [auth F]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain UA [auth E] SDF format, chain O [auth A] SDF format, chain NA [auth D] SDF format, chain MB [auth H] SDF format, chain MA [auth D] SDF format, chain GB [auth G] SDF format, chain AA [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain MB [auth H] MOL2 format, chain MA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain BB [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain MB [auth H] mmCIF format, chain MA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain AA [auth B]	AA [auth B] BB [auth F] GB [auth G] MA [auth D] MB [auth H] AA [auth B], BB [auth F], GB [auth G], MA [auth D], MB [auth H], NA [auth D], O [auth A], UA [auth E], VA [auth E], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth F] Focus chain GB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain NA [auth D] Focus chain O [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth F] Focus chain GB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain NA [auth D] Focus chain O [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain ZA [auth F] SDF format, chain YA [auth F] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain T [auth B] SDF format, chain SA [auth E] SDF format, chain S [auth B] SDF format, chain RA [auth E] SDF format, chain R [auth B] SDF format, chain QA [auth E] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LB [auth H] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KB [auth H] SDF format, chain KA [auth D] SDF format, chain JB [auth H] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain GA [auth C] SDF format, chain FB [auth G] SDF format, chain EB [auth G] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain AB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain ZA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth H] MOL2 format, chain KA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain AB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain ZA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth H] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth H] mmCIF format, chain KA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain AB [auth F]	AB [auth F] CA [auth C] DA [auth C] EA [auth C] EB [auth G] AB [auth F], CA [auth C], DA [auth C], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], IA [auth D], J [auth A], JA [auth D], JB [auth H], K [auth A], KA [auth D], KB [auth H], L [auth A], LA [auth D], LB [auth H], M [auth A], N [auth A], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], V [auth B], YA [auth F], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain NB [auth H] SDF format, chain WA [auth E] SDF format, chain OA [auth D] SDF format, chain HB [auth G] SDF format, chain CB [auth F] MOL2 format, chain NB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain OA [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain CB [auth F] mmCIF format, chain NB [auth H] mmCIF format, chain WA [auth E] mmCIF format, chain OA [auth D] mmCIF format, chain HB [auth G] mmCIF format, chain CB [auth F]	CB [auth F], HB [auth G], NB [auth H], OA [auth D], WA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CB [auth F] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain OA [auth D] Focus chain WA [auth E] Interactions & Density Focus chain CB [auth F] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain OA [auth D] Focus chain WA [auth E]