SMTL ID : 7nln.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with N-acetyl-glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-hexamer

Ligands

6 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)

NLG.1: 11 residues within 4Å: Chain A: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.93, A:V.157 Hydrogen bonds: A:G.72, A:G.73, A:R.94, A:N.193, A:N.193, A:A.196 Water bridges: A:N.195, A:D.197 Salt bridges: A:K.37, A:R.94 NLG.4: 11 residues within 4Å: Chain B: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.93, B:V.157 Hydrogen bonds: B:G.72, B:G.73, B:R.94, B:N.193, B:N.193, B:N.193, B:A.196 Water bridges: B:N.195, B:D.197 Salt bridges: B:K.37, B:R.94 NLG.6: 11 residues within 4Å: Chain C: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.93, C:V.157 Hydrogen bonds: C:G.72, C:G.73, C:R.94, C:N.193, C:N.193, C:A.196 Water bridges: C:N.195, C:D.197 Salt bridges: C:K.37, C:R.94 NLG.9: 11 residues within 4Å: Chain D: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.93, D:V.157 Hydrogen bonds: D:G.72, D:G.73, D:R.94, D:N.193, D:N.193, D:N.193, D:A.196 Water bridges: D:N.195, D:D.197 Salt bridges: D:K.37, D:R.94 NLG.11: 11 residues within 4Å: Chain E: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:F.93, E:V.157 Hydrogen bonds: E:G.72, E:G.73, E:R.94, E:N.193, E:N.193, E:A.196 Water bridges: E:N.195, E:D.197 Salt bridges: E:K.37, E:R.94 NLG.14: 11 residues within 4Å: Chain F: G.71, G.72, G.73, I.76, F.93, R.94, V.157, N.193, I.194, N.195, A.196 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:F.93, F:V.157 Hydrogen bonds: F:G.72, F:G.73, F:R.94, F:N.193, F:N.193, F:N.193, F:A.196 Water bridges: F:N.195, F:D.197 Salt bridges: F:K.37, F:R.94

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

EDO.2: 5 residues within 4Å: Chain A: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.37, A:L.215, A:K.254 EDO.3: 3 residues within 4Å: Chain A: L.171, R.176 Chain B: A.167 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.167, A:R.176 EDO.5: 5 residues within 4Å: Chain B: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.37, B:L.215, B:K.254 EDO.7: 5 residues within 4Å: Chain C: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.37, C:L.215, C:K.254 EDO.8: 3 residues within 4Å: Chain C: L.171, R.176 Chain D: A.167 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.176, D:A.167 EDO.10: 5 residues within 4Å: Chain D: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.37, D:L.215, D:K.254 EDO.12: 5 residues within 4Å: Chain E: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.37, E:L.215, E:K.254 EDO.13: 3 residues within 4Å: Chain E: L.171, R.176 Chain F: A.167 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.176, F:A.167 EDO.15: 5 residues within 4Å: Chain F: K.37, G.39, G.40, L.215, K.254 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.37, F:L.215, F:K.254

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
B

C
A

D
B

E
A

F
B

Acetylglutamate kinase

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