SMTL ID : 7nnq.1

Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.8, S.10, G.11, Y.12, A.13, A.39, A.40, T.41, S.42, T.65, A.79, L.80, P.81, H.82, H.84, C.101, G.102, R.106, C.150, S.181, G.182, G.184, R.185, A.186, N.312, L.313, G.316, T.317 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.317 Hydrogen bonds: A:G.8, A:S.10, A:S.10, A:S.10, A:Y.12, A:A.13, A:A.40, A:T.41, A:S.42, A:S.42, A:L.80, A:H.82, A:H.84, A:S.181, A:R.185, A:A.186, A:N.312 Water bridges: A:G.11, A:G.14, A:A.103 NAP.2: 28 residues within 4Å: Chain B: G.8, S.10, G.11, Y.12, A.13, A.39, A.40, T.41, S.42, T.65, A.79, L.80, P.81, H.82, H.84, C.101, G.102, R.106, C.150, S.181, G.182, G.184, R.185, A.186, N.312, L.313, G.316, T.317 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.317 Hydrogen bonds: B:G.8, B:S.10, B:S.10, B:Y.12, B:A.13, B:A.40, B:A.40, B:S.42, B:S.42, B:L.80, B:H.84, B:R.106, B:S.181, B:R.185, B:A.186, B:N.312, B:T.317 Water bridges: B:S.10, B:G.11, B:G.14, B:T.41, B:T.41, B:H.82, B:A.103, B:R.106 NAP.4: 27 residues within 4Å: Chain C: G.8, S.10, G.11, Y.12, A.13, A.39, A.40, T.41, S.42, T.65, A.79, L.80, P.81, H.84, C.101, G.102, R.106, C.150, S.181, G.182, G.184, R.185, A.186, N.312, L.313, G.316, T.317 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.317 Hydrogen bonds: C:G.8, C:S.10, C:S.10, C:G.11, C:Y.12, C:A.13, C:A.40, C:S.42, C:S.42, C:S.42, C:T.65, C:L.80, C:S.181, C:R.185, C:A.186, C:N.312 Water bridges: C:T.41, C:T.41, C:A.103, C:R.106 NAP.6: 27 residues within 4Å: Chain D: G.8, S.10, G.11, Y.12, A.13, A.39, A.40, T.41, S.42, T.65, A.79, L.80, P.81, H.84, C.101, G.102, R.106, C.150, S.181, G.182, G.184, R.185, A.186, N.312, L.313, G.316, T.317 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:T.317 Hydrogen bonds: D:G.8, D:S.10, D:S.10, D:G.11, D:Y.12, D:A.13, D:A.40, D:T.41, D:S.42, D:S.42, D:T.65, D:L.80, D:H.82, D:H.84, D:R.106, D:S.181, D:R.185, D:A.186, D:N.312 Water bridges: D:G.14, D:A.103 pi-Stacking: D:H.84

3 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 8 residues within 4Å: Chain B: H.24, P.25, A.26, D.29, R.31, W.331, P.332, D.335 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.26, B:D.29, B:W.331, B:D.335, B:D.335 Salt bridges: B:D.29 BTB.5: 8 residues within 4Å: Chain C: H.24, P.25, A.26, D.29, R.31, W.331, P.332, D.335 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.26, C:D.29, C:W.331, C:D.335 Salt bridges: C:D.29 BTB.7: 8 residues within 4Å: Chain D: H.24, P.25, A.26, D.29, R.31, W.331, P.332, D.335 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.26, D:D.29, D:W.331, D:D.335, D:D.335 Salt bridges: D:D.29

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

N-acetyl-gamma-glutamyl-phosphate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

N-acetyl-gamma-glutamyl-phosphate reductase

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