SMTL ID : 7nn8.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1H-indole-3-carbonitrile.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 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 SO4.2: 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 SO4.5: 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 SO4.6: 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 SO4.9: 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 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 SO4.13: 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 SO4.14: 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 SO4.17: 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 SO4.18: 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 SO4.21: 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 SO4.22: 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

6 x 98Z: 1~{H}-indole-3-carbonitrile(Non-covalent)

98Z.3: 8 residues within 4Å: Chain A: V.128, I.130, L.171 Chain F: V.128, G.129, I.130, L.171 Ligands: 98Z.23 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:V.128, A:L.171, F:I.130, F:L.171 Hydrogen bonds: F:G.129 98Z.7: 8 residues within 4Å: Chain B: V.128, I.130, L.171 Chain E: V.128, G.129, I.130, L.171 Ligands: 98Z.19 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:V.128, B:L.171, E:I.130, E:L.171 Hydrogen bonds: E:G.129 98Z.11: 8 residues within 4Å: Chain C: V.128, I.130, L.171 Chain D: V.128, G.129, I.130, L.171 Ligands: 98Z.15 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.128, C:L.171, D:I.130, D:L.171 98Z.15: 8 residues within 4Å: Chain C: V.128, G.129, I.130, L.171 Chain D: V.128, I.130, L.171 Ligands: 98Z.11 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.130, C:L.171, D:V.128, D:L.171 98Z.19: 8 residues within 4Å: Chain B: V.128, G.129, I.130, L.171 Chain E: V.128, I.130, L.171 Ligands: 98Z.7 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:V.128, E:L.171, B:I.130, B:L.171 Hydrogen bonds: B:G.129 98Z.23: 8 residues within 4Å: Chain A: V.128, G.129, I.130, L.171 Chain F: V.128, I.130, L.171 Ligands: 98Z.3 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:V.128, F:L.171, A:I.130, A:L.171 Hydrogen bonds: A:G.129

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: R.105, G.189, V.191 Chain F: E.115, N.118 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:E.115, F:N.118, A:R.105, A:R.105, A:V.191 Water bridges: A:V.191 EDO.8: 5 residues within 4Å: Chain B: R.105, G.189, V.191 Chain E: E.115, N.118 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.105, B:R.105, B:V.191, E:E.115, E:N.118 Water bridges: B:V.191 EDO.12: 5 residues within 4Å: Chain C: R.105, G.189, V.191 Chain D: E.115, N.118 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.115, D:N.118, C:R.105, C:R.105, C:V.191 Water bridges: C:V.191 EDO.16: 5 residues within 4Å: Chain C: E.115, N.118 Chain D: R.105, G.189, V.191 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.105, D:R.105, D:V.191, C:E.115, C:N.118 Water bridges: D:V.191 EDO.20: 5 residues within 4Å: Chain B: E.115, N.118 Chain E: R.105, G.189, V.191 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:R.105, E:R.105, E:V.191, B:E.115, B:N.118 Water bridges: E:V.191 EDO.24: 5 residues within 4Å: Chain A: E.115, N.118 Chain F: R.105, G.189, V.191 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain F Hydrogen bonds: A:E.115, A:N.118, F:R.105, F:R.105, F:V.191 Water bridges: F:V.191

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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