6X9N | pdb_00006x9n

Pseudomonas aeruginosa MurC with AZ5595

PDB DOI: https://doi.org/10.2210/pdb6X9N/pdb

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

Deposited: 2020-06-03 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)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.222 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (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 1.1 of the entry. See complete history.

Literature

Pseudomonas aeruginosa MurC with AZ5595

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

To be published.

Macromolecule Content

Total Structure Weight: 410.09 kDa
Atom Count: 19,389
Modeled Residue Count: 2,439
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UYD (Subject of Investigation/LOI) Query on UYD Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain I [auth A] SDF format, chain IB [auth G] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain PB [auth H] SDF format, chain RA [auth E] SDF format, chain ZA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain ZA [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PB [auth H] mmCIF format, chain RA [auth E] mmCIF format, chain ZA [auth F]	CA [auth C] I [auth A] IB [auth G] JA [auth D] P [auth B] CA [auth C], I [auth A], IB [auth G], JA [auth D], P [auth B], PB [auth H], RA [auth E], ZA [auth F]	(2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethan-1-ol C₂₁ H₂₆ N₈ O MOLGZLFXZJMRCB-HNNXBMFYSA-N		Interactions Focus chain CA [auth C] Focus chain I [auth A] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain P [auth B] Focus chain PB [auth H] Focus chain RA [auth E] Focus chain ZA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain I [auth A] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain P [auth B] Focus chain PB [auth H] Focus chain RA [auth E] Focus chain ZA [auth F]
VAL Query on VAL Download:Ideal Coordinates CCD File SDF format, chain OB [auth H] MOL2 format, chain OB [auth H] mmCIF format, chain OB [auth H]	OB [auth H]	VALINE C₅ H₁₁ N O₂ KZSNJWFQEVHDMF-BYPYZUCNSA-N		Interactions Focus chain OB [auth H] Interactions & Density Focus chain OB [auth H]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HA [auth C] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain TB [auth H] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain TB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain FB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain MB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain TB [auth H] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] FB [auth F] GB [auth F] HA [auth C] MB [auth G] AA [auth B], FB [auth F], GB [auth F], HA [auth C], MB [auth G], N [auth A], OA [auth D], PA [auth D], TB [auth H], WA [auth E], X [auth B], XA [auth E], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain MB [auth G] Focus chain N [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain TB [auth H] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain MB [auth G] Focus chain N [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain TB [auth H] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain J [auth A] SDF format, chain JB [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain QB [auth H] SDF format, chain R [auth B] SDF format, chain RB [auth H] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QB [auth H] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth H] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QB [auth H] mmCIF format, chain R [auth B] mmCIF format, chain RB [auth H] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B]	AB [auth F] BB [auth F] CB [auth F] DA [auth C] DB [auth F] AB [auth F], BB [auth F], CB [auth F], DA [auth C], DB [auth F], EA [auth C], EB [auth F], FA [auth C], GA [auth C], J [auth A], JB [auth G], K [auth A], KA [auth D], KB [auth G], L [auth A], LA [auth D], LB [auth G], M [auth A], MA [auth D], NA [auth D], Q [auth B], QB [auth H], R [auth B], RB [auth H], S [auth B], SA [auth E], SB [auth H], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain J [auth A] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain J [auth A] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain HB [auth F] SDF format, chain IA [auth C] SDF format, chain NB [auth G] SDF format, chain O [auth A] SDF format, chain QA [auth D] SDF format, chain UB [auth H] SDF format, chain YA [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain HB [auth F] MOL2 format, chain IA [auth C] MOL2 format, chain NB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain UB [auth H] MOL2 format, chain YA [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain HB [auth F] mmCIF format, chain IA [auth C] mmCIF format, chain NB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain UB [auth H] mmCIF format, chain YA [auth E]	BA [auth B] HB [auth F] IA [auth C] NB [auth G] O [auth A] BA [auth B], HB [auth F], IA [auth C], NB [auth G], O [auth A], QA [auth D], UB [auth H], YA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain HB [auth F] Focus chain IA [auth C] Focus chain NB [auth G] Focus chain O [auth A] Focus chain QA [auth D] Focus chain UB [auth H] Focus chain YA [auth E] Interactions & Density Focus chain BA [auth B] Focus chain HB [auth F] Focus chain IA [auth C] Focus chain NB [auth G] Focus chain O [auth A] Focus chain QA [auth D] Focus chain UB [auth H] Focus chain YA [auth E]