SMTL ID : 6ep8.1

InhA Y158F mutant in complex with NADH from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: D.226, Q.227, A.229 Ligand excluded by PLIP NA.3: 4 residues within 4Å: Chain A: S.22, H.27, I.197, A.238 Ligand excluded by PLIP NA.4: 5 residues within 4Å: Chain A: Q.33, A.37, Q.38, L.39, K.60 Ligand excluded by PLIP NA.5: 5 residues within 4Å: Chain A: E.71, L.74, Y.128, S.132 Ligands: GOL.10 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain B: D.226, Q.227, A.229 Ligand excluded by PLIP NA.15: 4 residues within 4Å: Chain B: S.22, H.27, I.197, A.238 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain B: Q.33, A.37, Q.38, L.39, K.60 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain B: E.71, L.74, Y.128, S.132 Ligands: GOL.22 Ligand excluded by PLIP NA.25: 3 residues within 4Å: Chain C: D.226, Q.227, A.229 Ligand excluded by PLIP NA.27: 4 residues within 4Å: Chain C: S.22, H.27, I.197, A.238 Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain C: Q.33, A.37, Q.38, L.39, K.60 Ligand excluded by PLIP NA.29: 5 residues within 4Å: Chain C: E.71, L.74, Y.128, S.132 Ligands: GOL.34 Ligand excluded by PLIP NA.37: 3 residues within 4Å: Chain D: D.226, Q.227, A.229 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain D: S.22, H.27, I.197, A.238 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain D: Q.33, A.37, Q.38, L.39, K.60 Ligand excluded by PLIP NA.41: 5 residues within 4Å: Chain D: E.71, L.74, Y.128, S.132 Ligands: GOL.46 Ligand excluded by PLIP

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

NAD.2: 24 residues within 4Å: Chain A: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, M.202 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.24, A:F.152, A:A.194 Hydrogen bonds: A:G.17, A:S.23, A:I.24, A:D.67, A:D.67, A:V.68, A:I.98, A:G.99, A:K.168, A:I.197, A:I.197 Water bridges: A:G.17, A:A.25, A:F.44, A:F.44, A:I.98, A:L.200 pi-Stacking: A:F.44 NAD.14: 24 residues within 4Å: Chain B: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, M.202 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.24, B:F.152, B:A.194 Hydrogen bonds: B:G.17, B:S.23, B:I.24, B:D.67, B:D.67, B:V.68, B:I.98, B:G.99, B:K.168, B:I.197, B:I.197 Water bridges: B:G.17, B:A.25, B:F.44, B:F.44, B:I.98, B:L.200 pi-Stacking: B:F.44 NAD.26: 24 residues within 4Å: Chain C: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, M.202 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.24, C:F.152, C:A.194 Hydrogen bonds: C:G.17, C:S.23, C:I.24, C:D.67, C:V.68, C:I.98, C:G.99, C:K.168, C:I.197, C:I.197, C:T.199 Water bridges: C:G.17, C:A.25, C:F.44, C:F.44, C:I.98, C:L.200 pi-Stacking: C:F.44 NAD.38: 24 residues within 4Å: Chain D: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, M.202 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.24, D:F.152, D:A.194 Hydrogen bonds: D:G.17, D:S.23, D:I.24, D:D.67, D:V.68, D:I.98, D:G.99, D:K.168, D:I.197, D:I.197, D:T.199 Water bridges: D:G.17, D:A.25, D:F.44, D:F.44, D:I.98, D:L.200 pi-Stacking: D:F.44

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Q.33, E.34, P.58 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: T.5, L.7, Q.35 Chain D: T.5, L.7, W.252 Ligands: GOL.43 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: L.63, L.64, E.65, R.80 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: G.144, G.186, R.188, P.254 Chain D: I.231 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: E.71, Y.128, K.135 Chain C: F.112, D.113, A.114, P.115 Ligands: NA.5 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: D.45, R.46, L.47, R.48, L.49 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: Q.33, E.34, P.58 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: T.5, L.7, Q.35 Chain C: T.5, L.7, W.252 Ligands: GOL.31 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: L.63, L.64, E.65, R.80 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: G.144, G.186, R.188, P.254 Chain C: I.231 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: E.71, Y.128, K.135 Chain D: F.112, D.113, A.114, P.115 Ligands: NA.17 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: D.45, R.46, L.47, R.48, L.49 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain C: Q.33, E.34, P.58 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain B: T.5, L.7, W.252 Chain C: T.5, L.7, Q.35 Ligands: GOL.19 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: L.63, L.64, E.65, R.80 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain B: I.231 Chain C: G.144, G.186, R.188, P.254 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain A: F.112, D.113, A.114, P.115 Chain C: E.71, Y.128, K.135 Ligands: NA.29 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain C: D.45, R.46, L.47, R.48, L.49 Ligand excluded by PLIP GOL.42: 3 residues within 4Å: Chain D: Q.33, E.34, P.58 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain A: T.5, L.7, W.252 Chain D: T.5, L.7, Q.35 Ligands: GOL.7 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: L.63, L.64, E.65, R.80 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain A: I.231 Chain D: G.144, G.186, R.188, P.254 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain B: F.112, D.113, A.114, P.115 Chain D: E.71, Y.128, K.135 Ligands: NA.41 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain D: D.45, R.46, L.47, R.48, L.49 Ligand excluded by PLIP

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 2 residues within 4Å: Chain A: K.184, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.184, A:Y.185 Hydrogen bonds: A:Y.185 MPD.24: 2 residues within 4Å: Chain B: K.184, Y.185 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.184, B:Y.185 Hydrogen bonds: B:Y.185 MPD.36: 2 residues within 4Å: Chain C: K.184, Y.185 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.184, C:Y.185 Hydrogen bonds: C:Y.185 MPD.48: 2 residues within 4Å: Chain D: K.184, Y.185 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.184, D:Y.185 Hydrogen bonds: D:Y.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogeli, B. et al., InhA, the enoyl-thioester reductase fromMycobacterium tuberculosisforms a covalent adduct during catalysis. J. Biol. Chem. (2018)

Release Date

2018-09-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

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