SMTL ID : 5ha5.1

Crystal structure of an NAD-bound oxidoreductase from Brucella ovis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 6 residues within 4Å: Chain A: L.8, R.32, F.81, G.83, D.85, A.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32, A:D.85 IMD.11: 5 residues within 4Å: Chain B: L.8, R.32, F.81, G.83, D.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:G.83 Water bridges: B:R.32 IMD.16: 5 residues within 4Å: Chain C: L.8, R.32, F.81, G.83, D.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.83 IMD.22: 6 residues within 4Å: Chain D: L.8, R.32, F.81, G.83, D.85, A.133 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.32

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: L.8, R.32, V.33, V.56, A.57, E.58, F.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.57 Water bridges: A:A.57 EDO.3: 4 residues within 4Å: Chain A: K.44, E.58, G.59, H.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.44, A:E.58, A:G.59, A:R.80 EDO.4: 3 residues within 4Å: Chain A: A.94, S.151, Y.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.191 Water bridges: A:Y.155 EDO.5: 5 residues within 4Å: Chain A: D.100, Q.101, P.102 Chain B: H.124, P.128 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.101, B:H.124 Water bridges: B:H.124 EDO.6: 2 residues within 4Å: Chain A: P.128, K.131 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: N.208 Chain D: W.205, N.208, R.209 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.208, D:R.209, D:R.209 EDO.8: 9 residues within 4Å: Chain A: G.145, F.146, G.160, R.163, S.164 Chain B: G.160, R.163, S.164, Q.167 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.163, B:Q.167, B:Q.167, A:G.160, A:R.163 Water bridges: A:R.163 EDO.10: 6 residues within 4Å: Chain B: G.92, V.93, A.94, Y.155, E.191 Ligands: NAD.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.92 EDO.12: 3 residues within 4Å: Chain A: K.131 Chain B: D.100, P.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.131, A:K.131 EDO.13: 7 residues within 4Å: Chain B: L.8, R.32, V.33, V.56, A.57, E.58, F.81 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.32, B:E.58 Water bridges: B:A.57, B:A.57, B:R.80, B:R.80 EDO.14: 5 residues within 4Å: Chain B: A.174, G.177, I.178, R.179 Chain D: M.212 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.174 Water bridges: D:R.214, D:R.214 EDO.17: 7 residues within 4Å: Chain C: L.8, R.32, V.33, V.56, A.57, E.58, F.81 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.57 Water bridges: C:R.32, C:A.57 EDO.18: 6 residues within 4Å: Chain C: R.67, V.70, A.71, N.121, H.124, A.125 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.67, C:A.71, C:H.124 EDO.19: 2 residues within 4Å: Chain C: F.146, L.248 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.240 EDO.20: 4 residues within 4Å: Chain C: I.38, V.93, V.114 Ligands: NAD.15 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.63, C:T.65

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

NAD.9: 26 residues within 4Å: Chain B: G.13, R.16, G.17, L.18, D.37, I.38, L.62, D.63, V.64, N.90, A.91, G.92, V.93, V.114, L.140, C.141, S.142, Y.155, K.159, P.185, G.186, I.187, M.188, S.190, E.191 Ligands: EDO.10 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.185 Hydrogen bonds: B:G.13, B:G.15, B:R.16, B:L.18, B:I.38, B:D.63, B:V.64, B:N.90, B:G.92, B:K.159, B:M.188, B:S.190, B:S.190, B:S.190 Water bridges: B:G.19, B:G.19, B:D.37, B:D.37, B:E.191, B:E.191 Salt bridges: B:R.16 NAD.15: 25 residues within 4Å: Chain C: G.13, R.16, G.17, L.18, D.37, I.38, L.62, D.63, V.64, N.90, A.91, G.92, V.93, V.114, L.140, C.141, S.142, Y.155, K.159, P.185, G.186, I.187, M.188, S.190 Ligands: EDO.20 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.185 Hydrogen bonds: C:G.13, C:G.15, C:R.16, C:L.18, C:I.38, C:D.63, C:D.63, C:V.64, C:N.90, C:G.92, C:Y.155, C:K.159, C:M.188, C:S.190, C:S.190, C:S.190 Water bridges: C:R.16, C:G.19, C:D.37, C:D.37, C:N.90 Salt bridges: C:R.16 NAD.21: 25 residues within 4Å: Chain D: G.13, R.16, G.17, L.18, D.37, I.38, L.62, D.63, V.64, T.65, N.90, A.91, G.92, V.93, V.114, L.140, S.142, Y.155, K.159, P.185, G.186, I.187, M.188, S.190, E.191 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.13, D:R.16, D:R.16, D:L.18, D:I.38, D:D.63, D:V.64, D:N.90, D:G.92, D:Y.155, D:Y.155, D:K.159, D:S.190, D:S.190, D:E.191 Water bridges: D:G.19, D:N.90 Salt bridges: D:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal structure of an NAD-bound oxidoreductase from Brucella ovis. to be published

Release Date

2016-02-10

Peptides

Brucella ovis oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Brucella ovis oxidoreductase