4ACF | pdb_00004acf

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE IN COMPLEX WITH IMIDAZOPYRIDINE INHIBITOR ((4-(6-BROMO-3-(BUTYLAMINO)IMIDAZO(1,2-A)PYRIDIN-2-YL)PHENOXY) ACETIC ACID) AND L-METHIONINE-S-SULFOXIMINE PHOSPHATE.

PDB DOI: https://doi.org/10.2210/pdb4ACF/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-12-15 Released: 2012-10-24
Deposition Author(s): Nilsson, M.T., Mowbray, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.165 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Synthesis, Biological Evaluation and X-Ray Crystallographic Studies of Imidazo(1,2-A)Pyridine-Based Mycobacterium Tuberculosis Glutamine Synthetase Inhibitors

Nordqvist, A., Nilsson, M.T., Lagerlund, O., Muthas, D., Gising, J., Yahiaoui, S., Odell, L.R., Srinivasa, B.R., Larhed, M., Mowbray, S.L., Karlen, A.

(2012) Medchemcomm 3: 620

DOI: https://doi.org/10.1039/C2MD00310D

Macromolecule Content

Total Structure Weight: 332.95 kDa
Atom Count: 24,804
Modelled Residue Count: 2,850
Deposited Residue Count: 2,916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMINE SYNTHETASE 1	A, B, C, D, E A, B, C, D, E, F	486	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 EC: 6.3.1.2
UniProt
Find proteins for P9WN39 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN39 Go to UniProtKB: P9WN39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WN39
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
46B Query on 46B Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain MA [auth E] SDF format, chain O [auth B] SDF format, chain UA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain UA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain UA [auth F]	EA [auth D] G [auth A] MA [auth E] O [auth B] UA [auth F] EA [auth D], G [auth A], MA [auth E], O [auth B], UA [auth F], W [auth C]	{4-[6-BROMO-3-(BUTYLAMINO)IMIDAZO[1,2-A]PYRIDIN-2-YL]PHENOXY}ACETIC ACID C₁₉ H₂₀ Br N₃ O₃ OZIYUZINTQIIAN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C]
P3S Query on P3S Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain QA [auth E] SDF format, chain S [auth B] SDF format, chain YA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain YA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain YA [auth F]	AA [auth C] IA [auth D] K [auth A] QA [auth E] S [auth B] AA [auth C], IA [auth D], K [auth A], QA [auth E], S [auth B], YA [auth F]	L-METHIONINE-S-SULFOXIMINE PHOSPHATE C₅ H₁₃ N₂ O₆ P S QQFOFBSCSWFFPB-NMAPHRJESA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain QA [auth E] Focus chain S [auth B] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain QA [auth E] Focus chain S [auth B] Focus chain YA [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain BA [auth C] SDF format, chain RA [auth E] SDF format, chain ZA [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain RA [auth E] MOL2 format, chain ZA [auth F] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain RA [auth E] mmCIF format, chain ZA [auth F]	BA [auth C] JA [auth D] L [auth A] RA [auth E] T [auth B] BA [auth C], JA [auth D], L [auth A], RA [auth E], T [auth B], ZA [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain RA [auth E] Focus chain T [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain RA [auth E] Focus chain T [auth B] Focus chain ZA [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain CA [auth C] SDF format, chain M [auth A] SDF format, chain KA [auth D] SDF format, chain SA [auth E] SDF format, chain U [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain U [auth B]	AB [auth F] CA [auth C] KA [auth D] M [auth A] SA [auth E] AB [auth F], CA [auth C], KA [auth D], M [auth A], SA [auth E], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth F] Focus chain CA [auth C] Focus chain KA [auth D] Focus chain M [auth A] Focus chain SA [auth E] Focus chain U [auth B] Interactions & Density Focus chain AB [auth F] Focus chain CA [auth C] Focus chain KA [auth D] Focus chain M [auth A] Focus chain SA [auth E] Focus chain U [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain LA [auth D] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain R [auth B] SDF format, chain TA [auth E] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain LA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C]	BB [auth F] DA [auth C] FA [auth D] GA [auth D] H [auth A] BB [auth F], DA [auth C], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], LA [auth D], N [auth A], NA [auth E], OA [auth E], P [auth B], PA [auth E], Q [auth B], R [auth B], TA [auth E], V [auth B], VA [auth F], WA [auth F], X [auth C], XA [auth F], Y [auth C], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth F] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.165 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.59	α = 90
b = 227.39	β = 90
c = 202.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

Nilsson, M.T.

Mowbray, S.L.

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2019-05-15
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description