SMTL ID : 7nnb.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2,8-bis(trifluoromethyl)quinolin-4-ol.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-hexamer

Ligands

6 x 97Q: 2,8-bis(trifluoromethyl)quinolin-4-ol(Non-covalent)

97Q.1: 10 residues within 4Å: Chain A: V.128, I.130, A.167, D.170, L.171 Chain F: V.128, L.171, A.174, R.176 Ligands: 97Q.26 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:V.128, A:L.171, F:V.128, F:L.171 Hydrogen bonds: A:R.176 97Q.6: 10 residues within 4Å: Chain B: V.128, I.130, A.167, D.170, L.171 Chain E: V.128, L.171, A.174, R.176 Ligands: 97Q.21 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:V.128, B:L.171, E:V.128, E:L.171 Hydrogen bonds: B:R.176 97Q.11: 10 residues within 4Å: Chain C: V.128, I.130, A.167, D.170, L.171 Chain D: V.128, L.171, A.174, R.176 Ligands: 97Q.16 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.128, D:L.171, C:V.128, C:L.171 Hydrogen bonds: C:R.176 97Q.16: 10 residues within 4Å: Chain C: V.128, L.171, A.174, R.176 Chain D: V.128, I.130, A.167, D.170, L.171 Ligands: 97Q.11 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.128, C:L.171, D:V.128, D:L.171 Hydrogen bonds: D:R.176 97Q.21: 10 residues within 4Å: Chain B: V.128, L.171, A.174, R.176 Chain E: V.128, I.130, A.167, D.170, L.171 Ligands: 97Q.6 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:V.128, E:L.171, B:V.128, B:L.171 Hydrogen bonds: E:R.176 97Q.26: 10 residues within 4Å: Chain A: V.128, L.171, A.174, R.176 Chain F: V.128, I.130, A.167, D.170, L.171 Ligands: 97Q.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:V.128, A:L.171, F:V.128, F:L.171 Hydrogen bonds: F:R.176

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

EDO.2: 4 residues within 4Å: Chain A: R.105, V.191 Chain F: E.115, N.118 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:R.105, A:R.105, A:V.191, F:N.118 Water bridges: A:V.191 EDO.3: 1 residues within 4Å: Chain A: A.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.122 EDO.7: 4 residues within 4Å: Chain B: R.105, V.191 Chain E: E.115, N.118 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:N.118, B:R.105, B:R.105, B:V.191 Water bridges: B:V.191 EDO.8: 1 residues within 4Å: Chain B: A.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.122 EDO.12: 4 residues within 4Å: Chain C: R.105, V.191 Chain D: E.115, N.118 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.118, C:R.105, C:R.105, C:V.191 Water bridges: C:V.191 EDO.13: 1 residues within 4Å: Chain C: A.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.122 EDO.17: 4 residues within 4Å: Chain C: E.115, N.118 Chain D: R.105, V.191 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.105, D:R.105, D:V.191, C:N.118 Water bridges: D:V.191 EDO.18: 1 residues within 4Å: Chain D: A.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.122 EDO.22: 4 residues within 4Å: Chain B: E.115, N.118 Chain E: R.105, V.191 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:N.118, E:R.105, E:R.105, E:V.191 Water bridges: E:V.191 EDO.23: 1 residues within 4Å: Chain E: A.122 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.122 EDO.27: 4 residues within 4Å: Chain A: E.115, N.118 Chain F: R.105, V.191 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:R.105, F:R.105, F:V.191, A:N.118 Water bridges: F:V.191 EDO.28: 1 residues within 4Å: Chain F: A.122 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.122

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

SO4.4: 2 residues within 4Å: Chain A: R.81, F.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Salt bridges: A:R.81 SO4.5: 4 residues within 4Å: Chain A: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28 Salt bridges: A:K.211, A:H.270 SO4.9: 2 residues within 4Å: Chain B: R.81, F.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Salt bridges: B:R.81 SO4.10: 4 residues within 4Å: Chain B: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28 Salt bridges: B:K.211, B:H.270 SO4.14: 2 residues within 4Å: Chain C: R.81, F.89 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.94 Salt bridges: C:R.81 SO4.15: 4 residues within 4Å: Chain C: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.28 Salt bridges: C:K.211, C:H.270 SO4.19: 2 residues within 4Å: Chain D: R.81, F.89 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.94 Salt bridges: D:R.81 SO4.20: 4 residues within 4Å: Chain D: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.28 Salt bridges: D:K.211, D:H.270 SO4.24: 2 residues within 4Å: Chain E: R.81, F.89 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.94 Salt bridges: E:R.81 SO4.25: 4 residues within 4Å: Chain E: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.28 Salt bridges: E:K.211, E:H.270 SO4.29: 2 residues within 4Å: Chain F: R.81, F.89 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.94 Salt bridges: F:R.81 SO4.30: 4 residues within 4Å: Chain F: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.28 Salt bridges: F:K.211, F:H.270

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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