SMTL ID : 3ai3.1

The crystal structure of L-Sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: G.14, S.15, S.16, S.17, G.18, I.19, A.38, R.39, Q.40, R.43, V.64, D.65, V.66, N.92, A.93, G.94, L.115, N.142, A.143, S.144, Y.157, K.161, P.187, G.188, I.190, T.192, P.193, W.195 Ligands: SOL.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.19, A:P.187 Hydrogen bonds: A:G.14, A:S.16, A:S.16, A:S.16, A:S.17, A:I.19, A:R.39, A:Q.40, A:R.43, A:D.65, A:V.66, A:N.92, A:N.92, A:N.142, A:Y.157, A:K.161, A:I.190, A:T.192 Water bridges: A:G.20, A:T.192, A:T.192 Salt bridges: A:R.39, A:R.43 pi-Cation interactions: A:R.39 NDP.3: 30 residues within 4Å: Chain B: G.14, S.15, S.16, S.17, G.18, I.19, A.38, R.39, Q.40, R.43, V.64, D.65, V.66, N.92, A.93, G.94, L.115, N.142, A.143, S.144, Y.157, K.161, P.187, G.188, L.189, I.190, T.192, P.193, W.195 Ligands: SOL.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.19, B:P.187 Hydrogen bonds: B:S.16, B:S.17, B:S.17, B:I.19, B:R.39, B:Q.40, B:R.43, B:D.65, B:D.65, B:V.66, B:A.67, B:N.92, B:N.92, B:N.142, B:K.161, B:I.190, B:I.190, B:T.192 Water bridges: B:S.17, B:S.17, B:G.20, B:R.39 Salt bridges: B:R.39, B:R.43 NDP.5: 29 residues within 4Å: Chain C: G.14, S.15, S.16, S.17, G.18, I.19, A.38, R.39, Q.40, R.43, V.64, D.65, V.66, N.92, A.93, G.94, L.115, N.142, A.143, S.144, Y.157, K.161, P.187, G.188, I.190, T.192, P.193, W.195 Ligands: SOL.6 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:I.19, C:P.187 Hydrogen bonds: C:G.14, C:S.16, C:S.17, C:I.19, C:R.39, C:Q.40, C:Q.40, C:D.65, C:V.66, C:A.67, C:N.92, C:N.92, C:G.94, C:N.142, C:Y.157, C:K.161, C:I.190, C:T.192 Water bridges: C:S.16, C:S.17, C:G.20, C:R.39, C:R.43, C:R.43 Salt bridges: C:R.39, C:R.43 NDP.9: 29 residues within 4Å: Chain D: G.14, S.15, S.16, S.17, G.18, I.19, A.38, R.39, Q.40, R.43, V.64, D.65, V.66, N.92, A.93, G.94, L.115, N.142, A.143, S.144, Y.157, K.161, P.187, G.188, I.190, T.192, P.193, W.195 Ligands: SOL.10 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.19, D:P.187 Hydrogen bonds: D:S.16, D:S.16, D:S.17, D:S.17, D:I.19, D:R.39, D:Q.40, D:R.43, D:D.65, D:D.65, D:V.66, D:N.92, D:N.92, D:N.142, D:K.161, D:I.190, D:T.192, D:T.192 Water bridges: D:G.20 Salt bridges: D:R.39, D:R.43

5 x SOL: L-sorbose(Non-covalent)

SOL.2: 12 residues within 4Å: Chain A: G.96, S.144, I.145, C.146, L.151, Y.153, E.154, Y.157, P.187, G.188, W.195 Ligands: NDP.1 Protein-ligand interaction information (PLIP) not available SOL.4: 11 residues within 4Å: Chain B: T.95, G.96, S.144, I.145, L.151, Y.153, E.154, Y.157, G.188, W.195 Ligands: NDP.3 Protein-ligand interaction information (PLIP) not available SOL.6: 9 residues within 4Å: Chain C: G.96, S.144, I.145, L.151, Y.153, E.154, Y.157, G.188 Ligands: NDP.5 Protein-ligand interaction information (PLIP) not available SOL.8: 8 residues within 4Å: Chain A: V.148, M.165, A.252, F.254, L.263 Chain C: A.252, F.254, L.263 Protein-ligand interaction information (PLIP) not available SOL.10: 12 residues within 4Å: Chain D: G.96, S.144, I.145, C.146, L.151, Y.153, E.154, Y.157, P.187, G.188, W.195 Ligands: NDP.9 Protein-ligand interaction information (PLIP) not available

4 x SOE: alpha-L-sorbopyranose(Non-covalent)

SOE.7: 9 residues within 4Å: Chain C: G.4, I.5, K.8, I.88, G.137, N.179, R.181, C.241, E.243 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.8, C:N.179, C:R.181, C:R.181, C:E.243, C:E.243 SOE.11: 6 residues within 4Å: Chain D: H.45, A.48, R.49, K.52, V.59, E.61 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.59, D:V.59, D:E.61 Water bridges: D:V.59 SOE.12: 9 residues within 4Å: Chain D: G.4, I.5, K.8, I.88, G.137, N.179, R.181, C.241, E.243 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.8, D:N.179, D:R.181, D:R.181 Water bridges: D:K.8 SOE.13: 7 residues within 4Å: Chain B: A.252, F.254, L.263 Chain D: A.252, F.254, L.260, L.263 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Water bridges: B:A.252, B:A.252, B:A.252, B:F.254, D:A.252, D:A.252, D:A.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubota, K. et al., The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose. J.Mol.Biol. (2011)

Release Date

2011-02-09

Peptides

NADPH-sorbose reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

NADPH-sorbose reductase