SMTL ID : 1ryd.1

Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: T.139, R.209, G.213, Q.363, Y.366 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.366 ACT.2: 2 residues within 4Å: Chain A: P.31, M.325 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.325 ACT.5: 4 residues within 4Å: Chain B: R.360, W.379, G.380, Y.381 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.360 Salt bridges: B:R.360 ACT.8: 5 residues within 4Å: Chain C: T.139, R.209, G.213, Q.363, Y.366 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.366 ACT.9: 2 residues within 4Å: Chain C: P.31, M.325 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.325 ACT.12: 4 residues within 4Å: Chain D: R.360, W.379, G.380, Y.381 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.360 Salt bridges: D:R.360

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

NDP.3: 33 residues within 4Å: Chain A: G.44, L.45, G.46, K.47, Y.48, S.70, G.71, N.72, K.75, Y.93, I.111, L.112, P.113, N.114, L.116, H.117, E.134, K.135, P.136, G.161, R.163, A.202, W.205, R.206, Y.223, Y.302 Chain C: V.16, P.17, T.19, P.20, A.21, G.22, R.23 31 PLIP interactions: 27 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.48, A:Y.48, A:Y.48 Hydrogen bonds: A:L.45, A:K.47, A:Y.48, A:G.71, A:N.72, A:K.75, A:Y.93, A:Y.93, A:L.112, A:N.114, A:E.134, A:K.135, A:R.163, A:P.201, A:Y.223, C:P.17, C:A.21, C:R.23 Water bridges: A:G.46, A:A.49, A:K.75, A:R.163, A:R.163, A:A.202, A:R.206, C:R.23 Salt bridges: A:K.75, A:R.206 NDP.6: 32 residues within 4Å: Chain B: G.44, L.45, G.46, K.47, Y.48, S.70, G.71, K.75, Y.93, I.111, L.112, P.113, N.114, L.116, H.117, E.134, K.135, P.136, G.161, R.163, A.202, W.205, R.206, Y.223, Y.302 Chain D: V.16, P.17, T.19, P.20, A.21, G.22, R.23 31 PLIP interactions: 3 interactions with chain D, 28 interactions with chain B Hydrogen bonds: D:T.19, D:A.21, D:R.23, B:L.45, B:K.47, B:Y.48, B:G.71, B:N.72, B:Y.93, B:L.112, B:N.114, B:E.134, B:K.135, B:R.163, B:Y.302 Hydrophobic interactions: B:Y.48, B:Y.48 Water bridges: B:G.46, B:A.49, B:K.75, B:K.75, B:Y.109, B:R.163, B:P.201, B:R.206, B:R.206, B:D.219, B:Y.223, B:Y.223 Salt bridges: B:K.75, B:R.206 NDP.10: 33 residues within 4Å: Chain A: V.16, P.17, T.19, P.20, A.21, G.22, R.23 Chain C: G.44, L.45, G.46, K.47, Y.48, S.70, G.71, N.72, K.75, Y.93, I.111, L.112, P.113, N.114, L.116, H.117, E.134, K.135, P.136, G.161, R.163, A.202, W.205, R.206, Y.223, Y.302 31 PLIP interactions: 4 interactions with chain A, 27 interactions with chain C Hydrogen bonds: A:P.17, A:A.21, A:R.23, C:L.45, C:K.47, C:Y.48, C:G.71, C:N.72, C:K.75, C:Y.93, C:Y.93, C:L.112, C:N.114, C:E.134, C:K.135, C:R.163, C:P.201, C:Y.223 Water bridges: A:R.23, C:G.46, C:A.49, C:K.75, C:R.163, C:R.163, C:A.202, C:R.206 Hydrophobic interactions: C:Y.48, C:Y.48, C:Y.48 Salt bridges: C:K.75, C:R.206 NDP.13: 32 residues within 4Å: Chain B: V.16, P.17, T.19, P.20, A.21, G.22, R.23 Chain D: G.44, L.45, G.46, K.47, Y.48, S.70, G.71, K.75, Y.93, I.111, L.112, P.113, N.114, L.116, H.117, E.134, K.135, P.136, G.161, R.163, A.202, W.205, R.206, Y.223, Y.302 31 PLIP interactions: 3 interactions with chain B, 28 interactions with chain D Hydrogen bonds: B:T.19, B:A.21, B:R.23, D:L.45, D:K.47, D:Y.48, D:G.71, D:N.72, D:Y.93, D:L.112, D:N.114, D:E.134, D:K.135, D:R.163, D:Y.302 Hydrophobic interactions: D:Y.48, D:Y.48 Water bridges: D:G.46, D:A.49, D:K.75, D:K.75, D:Y.109, D:R.163, D:P.201, D:R.206, D:R.206, D:D.219, D:Y.223, D:Y.223 Salt bridges: D:K.75, D:R.206

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.4: 10 residues within 4Å: Chain A: R.240, A.241, Y.242, I.260, Q.262 Chain B: R.240, A.241, Y.242, I.260, Q.262 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.260, A:I.260 Water bridges: B:A.241, B:A.368, A:R.240 GLC.11: 10 residues within 4Å: Chain C: R.240, A.241, Y.242, I.260, Q.262 Chain D: R.240, A.241, Y.242, I.260, Q.262 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.260, C:I.260 Water bridges: D:A.241, D:A.368, C:R.240

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.7: 4 residues within 4Å: Chain B: A.28, P.31, M.32, Q.61 No protein-ligand interaction detected (PLIP) BME.14: 4 residues within 4Å: Chain D: A.28, P.31, M.32, Q.61 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis. To be Published

Release Date

2005-02-15

Peptides

glucose-fructose oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

glucose-fructose oxidoreductase

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