SMTL ID : 7nly.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-Chlorobenzimidazole.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Salt bridges: A:R.81 SO4.2: 5 residues within 4Å: Chain A: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28 Salt bridges: A:K.211, A:H.270 SO4.4: 3 residues within 4Å: Chain B: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Salt bridges: B:R.81 SO4.5: 5 residues within 4Å: Chain B: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28 Salt bridges: B:K.211, B:H.270 SO4.7: 3 residues within 4Å: Chain C: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.94 Salt bridges: C:R.81 SO4.8: 5 residues within 4Å: Chain C: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.28 Salt bridges: C:K.211, C:H.270 SO4.10: 3 residues within 4Å: Chain D: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.94 Salt bridges: D:R.81 SO4.11: 5 residues within 4Å: Chain D: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.28 Salt bridges: D:K.211, D:H.270 SO4.13: 3 residues within 4Å: Chain E: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.94 Salt bridges: E:R.81 SO4.14: 5 residues within 4Å: Chain E: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.28 Salt bridges: E:K.211, E:H.270 SO4.16: 3 residues within 4Å: Chain F: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.94 Salt bridges: F:R.81 SO4.17: 5 residues within 4Å: Chain F: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.28 Salt bridges: F:K.211, F:H.270

6 x 98K: 2-chloranyl-1~{H}-benzimidazole(Non-covalent)

98K.3: 9 residues within 4Å: Chain A: V.128, I.130, L.171, R.176 Chain F: V.128, A.135, L.137, L.171 Ligands: 98K.18 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:A.135, F:L.137, F:L.171, A:V.128, A:V.128 98K.6: 9 residues within 4Å: Chain B: V.128, I.130, L.171, R.176 Chain E: V.128, A.135, L.137, L.171 Ligands: 98K.15 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:A.135, E:L.137, E:L.171, B:V.128, B:V.128 98K.9: 9 residues within 4Å: Chain C: V.128, I.130, L.171, R.176 Chain D: V.128, A.135, L.137, L.171 Ligands: 98K.12 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.135, D:L.137, D:L.171, C:V.128, C:V.128 98K.12: 9 residues within 4Å: Chain C: V.128, A.135, L.137, L.171 Chain D: V.128, I.130, L.171, R.176 Ligands: 98K.9 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.135, C:L.137, C:L.171, D:V.128, D:V.128 98K.15: 9 residues within 4Å: Chain B: V.128, A.135, L.137, L.171 Chain E: V.128, I.130, L.171, R.176 Ligands: 98K.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:A.135, B:L.137, B:L.171, E:V.128, E:V.128 98K.18: 9 residues within 4Å: Chain A: V.128, A.135, L.137, L.171 Chain F: V.128, I.130, L.171, R.176 Ligands: 98K.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:A.135, A:L.137, A:L.171, F:V.128, F:V.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, P. et al., A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis. Comput Struct Biotechnol J (2021)

Release Date

2021-06-30

Peptides

Acetylglutamate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Acetylglutamate kinase

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