SMTL ID : 3r3s.1

Structure of the YghA Oxidoreductase from Salmonella enterica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 32 residues within 4Å: Chain A: G.56, D.58, S.59, G.60, I.61, N.79, Y.80, L.81, E.84, G.107, D.108, L.109, V.135, A.136, G.137, V.159, T.184, S.185, S.186, Y.199, K.203, P.229, G.230, P.231, I.232, T.234, A.235, L.236, Q.237, F.250 Ligands: FMT.2, MG.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.229 Hydrogen bonds: A:S.59, A:S.59, A:S.59, A:I.61, A:L.81, A:E.84, A:D.108, A:D.108, A:L.109, A:V.135, A:G.137, A:I.232, A:I.232, A:L.236, A:Q.237 Water bridges: A:G.56, A:G.62, A:G.62, A:Q.155, A:K.203, A:A.235 NAD.4: 32 residues within 4Å: Chain B: G.56, D.58, S.59, G.60, I.61, N.79, Y.80, L.81, E.84, G.107, D.108, L.109, V.135, A.136, G.137, V.159, T.184, S.185, S.186, Y.199, K.203, P.229, G.230, P.231, I.232, T.234, A.235, L.236, Q.237, F.250 Ligands: FMT.5, MG.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.229 Hydrogen bonds: B:S.59, B:S.59, B:S.59, B:I.61, B:L.81, B:E.84, B:D.108, B:L.109, B:V.135, B:G.137, B:Y.199, B:I.232, B:I.232, B:T.234, B:T.234, B:L.236, B:Q.237 Water bridges: B:G.56, B:G.62, B:G.62, B:E.84, B:Q.155, B:Q.155, B:K.203, B:A.235 NAD.8: 32 residues within 4Å: Chain C: G.56, D.58, S.59, G.60, I.61, N.79, Y.80, L.81, E.84, G.107, D.108, L.109, V.135, A.136, G.137, V.159, T.184, S.185, S.186, Y.199, K.203, P.229, G.230, P.231, I.232, T.234, A.235, L.236, Q.237, F.250 Ligands: FMT.9, MG.10 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.229 Hydrogen bonds: C:S.59, C:S.59, C:S.59, C:I.61, C:L.81, C:E.84, C:D.108, C:L.109, C:V.135, C:G.137, C:I.232, C:I.232, C:T.234, C:T.234, C:L.236, C:Q.237 Water bridges: C:G.56, C:G.62, C:G.62, C:E.84, C:Q.155, C:K.203, C:A.235 NAD.11: 31 residues within 4Å: Chain D: G.56, D.58, S.59, G.60, I.61, Y.80, L.81, E.84, G.107, D.108, L.109, V.135, A.136, G.137, V.159, T.184, S.185, S.186, Y.199, K.203, P.229, G.230, P.231, I.232, T.234, A.235, L.236, Q.237, F.250 Ligands: FMT.12, MG.13 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:P.229 Hydrogen bonds: D:S.59, D:S.59, D:S.59, D:I.61, D:L.81, D:E.84, D:D.108, D:D.108, D:L.109, D:V.135, D:G.137, D:Y.199, D:I.232, D:I.232, D:L.236, D:Q.237 Water bridges: D:G.56, D:G.62, D:G.62, D:Q.155, D:K.203, D:A.235

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: Q.139, S.186, Q.188, Y.199 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.186, A:Y.199, A:Y.199 Water bridges: A:Q.242, A:Q.242 FMT.5: 5 residues within 4Å: Chain B: Q.139, S.186, Q.188, Y.199 Ligands: NAD.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.186, B:Y.199 Water bridges: B:Q.242, B:Q.242 FMT.9: 5 residues within 4Å: Chain C: Q.139, S.186, Q.188, Y.199 Ligands: NAD.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.186, C:Y.199, C:Y.199 Water bridges: C:Q.242, C:Q.242 FMT.12: 5 residues within 4Å: Chain D: Q.139, S.186, Q.188, Y.199 Ligands: NAD.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.186 Water bridges: D:Q.237, D:Q.242, D:Q.242

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.58, S.59, E.84 Ligands: NAD.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.58, A:S.59, A:E.84, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.58, S.59, E.84 Ligands: NAD.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.58, B:S.59, B:E.84, H2O.19, H2O.19 MG.10: 4 residues within 4Å: Chain C: D.58, S.59, E.84 Ligands: NAD.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.58, C:S.59, C:E.84, H2O.38, H2O.38 MG.13: 4 residues within 4Å: Chain D: D.58, S.59, E.84 Ligands: NAD.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.58, D:S.59, D:E.84, H2O.57, H2O.57

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 1 residues within 4Å: Chain B: Q.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, S.M. et al., Structure of the YghA Oxidoreductase from Salmonella enterica. TO BE PUBLISHED

Release Date

2011-03-30

Peptides

oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

oxidoreductase