SMTL ID : 4iql.1

Crystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase II (FabK) with cofactors NADPH and FMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: G.37, G.38, M.39, V.40, N.88, P.90, S.114, E.156, A.160, G.161, A.189, G.190, G.191, Q.210, V.211, G.212, T.213, I.286, E.297, I.298, G.299 Ligands: NA.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:M.39, A:V.40, A:I.286, A:E.297 Hydrogen bonds: A:G.38, A:V.40, A:N.88, A:N.88, A:S.114, A:G.161, A:G.161, A:G.191, A:Q.210, A:G.212, A:T.213, A:T.213, A:G.299 Water bridges: A:G.38, A:G.190, A:I.192, A:Q.210 FMN.8: 20 residues within 4Å: Chain B: G.37, G.38, M.39, V.40, N.88, S.114, E.156, E.159, A.160, G.161, A.189, G.190, G.191, Q.210, G.212, T.213, E.297, I.298, G.299 Ligands: NA.13 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:M.39, B:E.297, B:I.298 Hydrogen bonds: B:G.38, B:V.40, B:N.88, B:N.88, B:S.114, B:G.161, B:G.161, B:G.191, B:Q.210, B:G.212, B:T.213, B:G.299 Water bridges: B:G.38, B:G.190, B:I.192, B:Q.210

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 14 residues within 4Å: Chain A: W.41, C.42, S.43, G.44, W.45, K.46, S.64, M.65, N.69, H.72, H.73, S.222, F.287 Ligands: GOL.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:W.41, A:W.45, A:S.64, A:N.69, A:S.222, A:S.222 Water bridges: A:C.42, A:S.43 Salt bridges: A:K.46, A:K.46, A:H.72, A:H.73 pi-Stacking: A:H.73 NDP.3: 12 residues within 4Å: Chain A: W.41, G.63, S.64, M.65, H.66, P.67, Y.93, P.94, E.95, R.279, G.280, K.283 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.93, A:E.95, A:G.280 Water bridges: A:W.41, A:H.66, A:G.278, A:R.279, A:R.281, A:A.282 Salt bridges: A:H.66, A:K.283 pi-Stacking: A:H.66, A:H.66 NDP.9: 12 residues within 4Å: Chain B: W.41, C.42, S.43, G.44, W.45, S.64, M.65, N.69, H.72, H.73, S.222, F.287 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:W.41, B:S.64, B:N.69, B:S.222, B:S.222 Water bridges: B:C.42, B:S.43, B:H.73, B:S.222 Salt bridges: B:H.72, B:H.72, B:H.73 pi-Stacking: B:H.73 NDP.10: 12 residues within 4Å: Chain B: W.41, G.63, S.64, M.65, H.66, P.67, Y.93, P.94, E.95, R.279, G.280, K.283 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.93, B:Y.93, B:G.280 Water bridges: B:W.41, B:H.66, B:G.278, B:R.279, B:A.282 Salt bridges: B:H.66, B:K.283 pi-Stacking: B:H.66, B:H.66

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.222, A.223, H.224, F.287 Ligands: NDP.2 No protein-ligand interaction detected (PLIP)

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

NA.5: 2 residues within 4Å: Chain A: V.179, V.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.182 NA.6: 4 residues within 4Å: Chain A: R.232, S.234, I.305, S.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.234 NA.7: 7 residues within 4Å: Chain A: E.156, A.160, G.161, G.162, H.163, N.164 Ligands: FMN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.161 NA.11: 2 residues within 4Å: Chain B: V.179, V.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.182 NA.12: 4 residues within 4Å: Chain B: R.232, S.234, I.305, S.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.303 NA.13: 7 residues within 4Å: Chain B: E.156, A.160, G.161, G.162, H.163, N.164 Ligands: FMN.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hevener, K.E. et al., Structural characterization of Porphyromonas gingivalis enoyl-ACP reductase II (FabK). Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2014-01-29

Peptides

Enoyl-(Acyl-carrier-protein) reductase II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Enoyl-(Acyl-carrier-protein) reductase II