SMTL ID : 3uuw.1

1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: N.262, I.263 Chain C: N.262, I.263 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: G.258, A.259, W.260, V.261 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: R.127, W.177, A.287 Ligands: GOL.5 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.39, P.40, N.41, K.44 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: N.262, I.263 Chain D: N.262, I.263 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: G.258, A.259, W.260, V.261 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: T.39, P.40, N.41, K.44 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: G.258, A.259, W.260, V.261 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: N.138, Q.236, I.246 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: T.39, P.40, N.41 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain D: G.258, A.259, W.260, V.261 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: T.39, P.40, N.41 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: R.127, W.177, A.287 Ligands: GOL.22 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.127, F.128, K.133, W.177 Ligands: CL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.133, A:W.177 GOL.11: 4 residues within 4Å: Chain B: R.127, F.128, K.133, W.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.133, B:W.177 Water bridges: B:K.136 GOL.16: 4 residues within 4Å: Chain C: R.127, F.128, K.133, W.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.133, C:W.177 GOL.22: 5 residues within 4Å: Chain D: R.127, F.128, K.133, W.177 Ligands: CL.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.133, D:W.177 Water bridges: D:K.136, D:K.136

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 10 residues within 4Å: Chain A: C.148, H.150, S.215, L.224 Chain B: S.144, N.146, E.228, L.230, R.237 Ligands: 1PE.7 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.144, B:S.144, B:N.146, B:R.237, A:S.215 PEG.12: 6 residues within 4Å: Chain B: I.17, S.74, T.76, H.79, D.96, K.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.76, B:K.97 Water bridges: B:H.170 PEG.18: 11 residues within 4Å: Chain C: F.200, S.202, H.203, K.204, N.213, T.214, S.215 Chain D: S.144, N.146, N.213 Ligands: PEG.23 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.144, D:N.146, C:S.215 Water bridges: C:H.203 PEG.23: 9 residues within 4Å: Chain C: N.146, K.204, N.213 Chain D: N.146, S.202, H.203, N.213, T.214 Ligands: PEG.18 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.146, D:H.203, D:N.213, C:K.204 Water bridges: C:N.146

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 15 residues within 4Å: Chain A: N.146, S.202, H.203, K.204, N.213, T.214, S.215 Chain B: N.146, S.202, H.203, K.204, N.213, T.214, S.215 Ligands: PEG.6 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.146, A:K.204, A:K.204, A:K.204 Water bridges: B:S.215, A:N.146, A:N.213

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.17: 9 residues within 4Å: Chain A: W.260 Chain C: I.17, D.96, K.97, N.125, R.126, H.170, K.267, F.269 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.96, C:K.97, C:N.125, C:R.126, C:R.126 Water bridges: C:D.96, C:K.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile. TO BE PUBLISHED

Release Date

2011-12-21

Peptides

Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain