SMTL ID : 3bio.2 (1 other biounit)

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: N.19, I.20, M.157, P.259 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.259 Hydrogen bonds: A:N.19 Water bridges: A:I.20 ACT.5: 4 residues within 4Å: Chain C: N.19, I.20, M.157, P.259 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.259 Hydrogen bonds: C:N.19 Water bridges: C:I.20 ACT.9: 4 residues within 4Å: Chain E: N.19, I.20, M.157, P.259 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:P.259 Hydrogen bonds: E:N.19 Water bridges: E:I.20

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 11 residues within 4Å: Chain A: D.97, G.125, W.126, D.127, P.128, F.151, S.156, T.176, R.186, H.232, T.262 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.126, A:D.127, A:R.186, A:T.262 Water bridges: A:G.125, A:R.186 Salt bridges: A:D.97, A:H.232 EPE.4: 11 residues within 4Å: Chain B: D.97, G.125, W.126, D.127, P.128, F.151, M.155, S.156, T.176, H.232, T.262 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.126, B:D.127, B:T.176, B:T.262 Water bridges: B:G.125, B:S.156 Salt bridges: B:D.97, B:H.232 EPE.6: 11 residues within 4Å: Chain C: D.97, G.125, W.126, D.127, P.128, F.151, S.156, T.176, R.186, H.232, T.262 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.126, C:D.127, C:R.186, C:T.262 Water bridges: C:G.125, C:R.186 Salt bridges: C:D.97, C:H.232 EPE.8: 11 residues within 4Å: Chain D: D.97, G.125, W.126, D.127, P.128, F.151, M.155, S.156, T.176, H.232, T.262 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:W.126, D:D.127, D:T.176, D:T.262 Water bridges: D:G.125, D:S.156 Salt bridges: D:D.97, D:H.232 EPE.10: 11 residues within 4Å: Chain E: D.97, G.125, W.126, D.127, P.128, F.151, S.156, T.176, R.186, H.232, T.262 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:W.126, E:D.127, E:R.186, E:T.262 Water bridges: E:G.125, E:R.186 Salt bridges: E:D.97, E:H.232 EPE.12: 11 residues within 4Å: Chain F: D.97, G.125, W.126, D.127, P.128, F.151, M.155, S.156, T.176, H.232, T.262 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:W.126, F:D.127, F:T.176, F:T.262 Water bridges: F:G.125, F:S.156 Salt bridges: F:D.97, F:H.232

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.99, D.127, R.135, T.149, F.151 Chain B: K.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.127 GOL.7: 6 residues within 4Å: Chain C: H.99, D.127, R.135, T.149, F.151 Chain D: K.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.127 GOL.11: 6 residues within 4Å: Chain E: H.99, D.127, R.135, T.149, F.151 Chain F: K.302 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83. To be Published

Release Date

2007-12-25

Peptides

Oxidoreductase, Gfo/Idh/MocA family: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Oxidoreductase, Gfo/Idh/MocA family

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