SMTL ID : 6vly.1

Crystal structure of FabI-NADH complex from Alistipes finegoldii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.127, L.177, Y.178, G.179, Y.180, N.181 Chain B: Y.199 Chain C: D.296 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:D.296, C:D.296, A:G.179, A:G.179, A:Y.180, A:N.181 Water bridges: A:L.177 GOL.3: 4 residues within 4Å: Chain B: Q.40, T.220, S.223 Ligands: GOL.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.40, B:Q.40, B:S.223 Water bridges: B:S.223, B:S.223, B:S.223 GOL.4: 6 residues within 4Å: Chain B: L.37, N.38, M.68, G.69, T.220 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.38 GOL.5: 10 residues within 4Å: Chain A: Y.199, I.200 Chain B: Y.127, T.176, L.177, Y.178, G.179, Y.180, N.181 Chain D: D.296 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.179, B:G.179, B:Y.180, B:N.181, D:D.296 Water bridges: B:L.177, B:N.181 GOL.8: 7 residues within 4Å: Chain C: M.117, S.118, V.121, M.183, A.221, G.224, V.225 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.118, C:S.118, C:G.224 Water bridges: C:Y.180 GOL.9: 9 residues within 4Å: Chain A: D.296 Chain C: Y.127, L.177, Y.178, G.179, Y.180, N.181 Chain D: Y.199, I.200 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.179, C:G.179, C:Y.180, C:N.181, A:D.296, A:D.296 Water bridges: C:N.181 GOL.11: 7 residues within 4Å: Chain D: M.117, S.118, V.121, M.183, A.221, G.224, V.225 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.118, D:G.224 Water bridges: D:R.122, D:Y.180, D:T.220 GOL.12: 10 residues within 4Å: Chain B: D.296 Chain C: Y.199, I.200 Chain D: Y.127, T.176, L.177, Y.178, G.179, Y.180, N.181 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.179, D:G.179, D:Y.180, D:N.181, B:D.296 Water bridges: D:L.177

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 28 residues within 4Å: Chain A: G.35, A.36, L.37, S.41, I.42, N.61, T.62, S.65, A.85, D.86, A.87, S.114, I.115, G.116, I.141, L.168, S.169, Y.170, K.187, Q.214, S.215, P.216, T.217, T.219, T.220, A.221, G.222, M.228 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.170, A:Y.170, A:Q.214 Hydrogen bonds: A:G.35, A:S.41, A:I.42, A:N.61, A:S.65, A:S.65, A:D.86, A:D.86, A:A.87, A:I.115, A:I.115, A:G.116, A:K.187, A:T.217, A:T.217, A:T.219, A:A.221 Water bridges: A:T.88, A:S.114, A:S.114, A:T.220 NAI.6: 28 residues within 4Å: Chain B: G.35, A.36, L.37, S.41, I.42, N.61, T.62, S.65, A.85, D.86, A.87, S.114, I.115, G.116, I.141, L.168, S.169, Y.170, K.187, Q.214, S.215, P.216, T.217, T.219, T.220, A.221, G.222, M.228 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.170, B:Y.170, B:Q.214 Hydrogen bonds: B:G.35, B:S.41, B:I.42, B:N.61, B:S.65, B:S.65, B:D.86, B:A.87, B:I.115, B:I.115, B:G.116, B:K.187, B:T.217, B:T.217, B:T.219, B:T.219, B:T.220, B:A.221, B:G.222 Water bridges: B:N.38, B:A.43 NAI.10: 27 residues within 4Å: Chain C: G.35, L.37, S.41, I.42, N.61, T.62, S.65, A.85, D.86, A.87, S.114, I.115, G.116, I.141, L.168, S.169, Y.170, K.187, Q.214, S.215, P.216, T.217, T.219, T.220, A.221, G.222, M.228 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.170, C:Y.170, C:Q.214 Hydrogen bonds: C:G.35, C:S.41, C:I.42, C:N.61, C:S.65, C:S.65, C:D.86, C:D.86, C:A.87, C:I.115, C:I.115, C:G.116, C:K.187, C:T.217, C:T.217, C:T.219, C:A.221 Water bridges: C:N.38, C:T.88, C:S.114, C:S.114, C:Y.180, C:T.220 NAI.13: 28 residues within 4Å: Chain D: G.35, A.36, L.37, S.41, I.42, N.61, T.62, S.65, A.85, D.86, A.87, S.114, I.115, G.116, I.141, L.168, S.169, Y.170, K.187, Q.214, S.215, P.216, T.217, T.219, T.220, A.221, G.222, M.228 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.170, D:Y.170, D:Q.214 Hydrogen bonds: D:G.35, D:S.41, D:I.42, D:N.61, D:S.65, D:S.65, D:D.86, D:A.87, D:I.115, D:I.115, D:G.116, D:K.187, D:T.217, D:T.217, D:T.219, D:T.219, D:A.221, D:G.222 Water bridges: D:N.38, D:A.43, D:Y.180, D:T.220

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain B: S.281, R.282, R.283, F.294 Chain C: Y.199 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Radka, C.D. et al., The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI). J.Biol.Chem. (2020)

Release Date

2020-04-29

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]

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