SMTL ID : 5coq.1

The effect of valine to alanine mutation on InhA enzyme crystallization pattern and substrate binding loop conformation and flexibility

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 26 residues within 4Å: Chain A: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218 Ligands: TCU.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:F.169, A:A.211 Hydrogen bonds: A:G.34, A:I.41, A:D.84, A:D.84, A:V.85, A:I.115, A:G.116, A:K.185, A:I.214, A:I.214, A:A.218 Water bridges: A:G.34, A:A.42, A:F.61, A:I.115, A:L.217 pi-Stacking: A:F.61 NAD.3: 27 residues within 4Å: Chain B: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: TCU.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.41, B:F.169, B:F.169, B:A.211 Hydrogen bonds: B:G.34, B:I.41, B:D.84, B:V.85, B:I.115, B:G.116, B:K.185, B:I.214, B:I.214, B:T.216, B:A.218 Water bridges: B:G.34, B:A.42, B:I.115, B:L.217, B:L.217 NAD.5: 28 residues within 4Å: Chain C: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, F.117, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: TCU.6 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.41, C:F.169, C:A.211 Hydrogen bonds: C:G.34, C:I.41, C:D.84, C:V.85, C:I.115, C:G.116, C:K.185, C:I.214, C:I.214, C:T.216, C:A.218 Water bridges: C:G.34, C:A.42, C:F.61, C:I.115, C:L.217 pi-Stacking: C:F.61 NAD.8: 26 residues within 4Å: Chain D: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218 Ligands: TCU.9 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.41, D:F.169, D:F.169, D:A.211 Hydrogen bonds: D:G.34, D:I.41, D:D.84, D:D.84, D:V.85, D:I.115, D:G.116, D:K.185, D:I.214, D:I.214, D:A.218 Water bridges: D:A.42, D:F.61, D:I.115, D:L.217

4 x TCU: 5-HEXYL-2-(2-METHYLPHENOXY)PHENOL(Non-covalent)

TCU.2: 16 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, K.185, A.218, M.219, I.222, I.235, L.238 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.169, A:F.169, A:F.169, A:A.177, A:Y.178, A:A.218, A:M.219, A:I.222, A:I.235, A:L.238 Hydrogen bonds: A:Y.178, A:Y.178 TCU.4: 16 residues within 4Å: Chain B: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, K.185, A.218, M.219, I.222, I.235, L.238 Ligands: NAD.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.169, B:F.169, B:F.169, B:A.177, B:Y.178, B:Y.178, B:A.218, B:M.219, B:I.222, B:I.235, B:L.238 Hydrogen bonds: B:Y.178 TCU.6: 14 residues within 4Å: Chain C: G.116, F.117, M.118, M.123, F.169, M.175, P.176, Y.178, M.181, K.185, A.218, M.219, I.222 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.169, C:F.169, C:F.169, C:Y.178, C:Y.178, C:A.218, C:I.222 Hydrogen bonds: C:Y.178, C:K.185 TCU.9: 16 residues within 4Å: Chain D: G.116, F.117, M.118, M.123, F.169, M.175, P.176, Y.178, M.181, K.185, P.213, A.218, M.219, I.222, I.235 Ligands: NAD.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.169, D:F.169, D:F.169, D:F.169, D:Y.178, D:Y.178, D:Y.178, D:P.213, D:A.218, D:I.222, D:I.235 Hydrogen bonds: D:Y.178, D:Y.178

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain C: D.243, Q.244, A.246 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, C.T. et al., Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA. Biochemistry (2015)

Release Date

2015-08-05

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Enoyl-[acyl-carrier-protein] reductase [NADH]