SMTL ID : 7nlf.1

Crystal structure of Mycobacterium tuberculosis ArgB in apo form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 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 SO4.2: 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: 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 SO4.6: 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: 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 SO4.10: 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: 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 SO4.14: 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: 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 SO4.18: 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: 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 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

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

EDO.3: 3 residues within 4Å: Chain A: R.94, T.96, N.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 EDO.4: 4 residues within 4Å: Chain A: P.125, R.176 Chain F: N.164, A.167 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:R.176, A:R.176, F:N.164 EDO.7: 3 residues within 4Å: Chain B: R.94, T.96, N.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.193 EDO.8: 4 residues within 4Å: Chain B: P.125, R.176 Chain E: N.164, A.167 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:N.164, B:R.176, B:R.176 EDO.11: 3 residues within 4Å: Chain C: R.94, T.96, N.193 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.193 EDO.12: 4 residues within 4Å: Chain C: P.125, R.176 Chain D: N.164, A.167 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.176, C:R.176, D:N.164 EDO.15: 3 residues within 4Å: Chain D: R.94, T.96, N.193 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.96, D:N.193 EDO.16: 4 residues within 4Å: Chain C: N.164, A.167 Chain D: P.125, R.176 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.176, D:R.176, C:N.164 EDO.19: 3 residues within 4Å: Chain E: R.94, T.96, N.193 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.96, E:N.193 EDO.20: 4 residues within 4Å: Chain B: N.164, A.167 Chain E: P.125, R.176 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:R.176, E:R.176, B:N.164 EDO.23: 3 residues within 4Å: Chain F: R.94, T.96, N.193 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.96, F:N.193 EDO.24: 4 residues within 4Å: Chain A: N.164, A.167 Chain F: P.125, R.176 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:N.164, F:R.176, F:R.176

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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