SMTL ID : 2cdc.1

Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and Xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: D.154, V.187, G.188, T.189, G.190, P.191, I.192, A.210, N.211, R.212, R.213, A.253, T.254, G.255, A.256, I.260, F.277, G.278, F.279, L.305, V.306, N.307, K.354, H.356 Chain C: V.296 Ligands: XYS.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.277, A:F.279 Hydrogen bonds: A:T.189, A:T.189, A:I.192, A:N.211, A:N.211, A:R.212, A:R.213, A:F.277, A:F.279, A:N.307 Water bridges: A:G.40, A:E.44, A:G.193, A:S.233, A:G.255, A:G.255, A:K.354, A:K.354, A:K.354 Salt bridges: A:R.213, A:K.354, A:K.354, A:H.356 NAP.8: 25 residues within 4Å: Chain B: D.154, V.187, G.188, T.189, G.190, P.191, I.192, A.210, N.211, R.212, R.213, A.253, T.254, G.255, A.256, F.277, G.278, F.279, L.305, V.306, N.307, K.354, H.356 Chain D: V.296 Ligands: XYP.9 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:F.277, B:F.279 Hydrogen bonds: B:T.189, B:T.189, B:I.192, B:N.211, B:R.212, B:R.213, B:F.277, B:F.279, B:N.307 Water bridges: B:G.40, B:E.44, B:E.44, B:E.44, B:G.193, B:R.212, B:R.212, B:S.233, B:G.255, B:G.255, B:K.354, B:K.354, B:K.354, B:H.356 Salt bridges: B:R.213, B:K.354, B:K.354, B:H.356 NAP.14: 26 residues within 4Å: Chain A: V.296 Chain C: D.154, V.187, G.188, T.189, G.190, P.191, I.192, A.210, N.211, R.212, R.213, A.253, T.254, G.255, A.256, I.260, F.277, G.278, F.279, L.305, V.306, N.307, K.354, H.356 Ligands: XYP.15 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:F.277, C:F.279 Hydrogen bonds: C:T.189, C:T.189, C:G.190, C:I.192, C:N.211, C:N.211, C:R.212, C:R.213, C:F.277, C:F.279, C:N.307 Water bridges: C:G.40, C:E.44, C:E.44, C:E.44, C:G.193, C:Y.237, C:T.254, C:D.257, C:K.354, C:K.354, C:K.354, C:K.354 Salt bridges: C:R.213, C:K.354, C:K.354, C:H.356 NAP.20: 25 residues within 4Å: Chain B: V.296 Chain D: D.154, V.187, G.188, T.189, G.190, P.191, I.192, A.210, N.211, R.212, R.213, A.253, T.254, G.255, A.256, I.260, F.277, G.278, F.279, L.305, V.306, N.307, K.354 Ligands: XYS.21 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:I.192, D:F.277, D:F.279 Hydrogen bonds: D:T.189, D:T.189, D:G.190, D:I.192, D:N.211, D:N.211, D:R.212, D:R.213, D:F.277, D:F.279, D:N.307 Water bridges: D:G.40, D:G.193, D:S.233, D:S.233, D:G.255, D:G.255, D:K.354, D:K.354, D:E.358 Salt bridges: D:R.213, D:K.354, D:H.356

6 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.2: 9 residues within 4Å: Chain A: N.89, R.90, E.114, I.117, Q.150, D.154, N.307 Ligands: NAP.1, XYP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.89, A:R.90, A:Q.150, A:Q.150, A:D.154, A:D.154, A:N.307 Salt bridges: A:H.66 XYS.4: 7 residues within 4Å: Chain A: K.137, Q.314, V.317, V.318 Chain B: R.201, T.202, G.204 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.201 Water bridges: B:R.201, B:G.204, A:K.137 XYS.10: 7 residues within 4Å: Chain A: R.201, T.202, G.204 Chain B: K.137, Q.314, V.317, V.318 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.201 Water bridges: A:Y.327, B:K.137 XYS.16: 7 residues within 4Å: Chain C: K.137, Q.314, V.317, V.318 Chain D: R.201, T.202, G.204 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:K.137 Hydrogen bonds: D:R.201 XYS.21: 8 residues within 4Å: Chain D: N.89, R.90, E.114, Q.150, D.154, N.307 Ligands: NAP.20, XYP.22 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.89, D:R.90, D:R.90, D:Q.150, D:Q.150, D:D.154, D:D.154, D:N.307 Water bridges: D:G.308 XYS.23: 7 residues within 4Å: Chain C: R.201, T.202, G.204 Chain D: K.137, Q.314, V.317, V.318 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:K.137, C:R.201, C:G.204 Hydrogen bonds: C:R.201

4 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.3: 12 residues within 4Å: Chain A: C.39, A.41, H.66, N.89, R.90, E.114, I.117, Q.150, D.154, N.307 Ligands: XYS.2, ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.89, A:R.90, A:Q.150, A:Q.150, A:D.154, A:N.307 Water bridges: A:A.41 Salt bridges: A:H.66 XYP.9: 10 residues within 4Å: Chain B: C.39, A.41, H.66, N.89, R.90, Q.150, D.154, N.307 Ligands: NAP.8, ZN.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.89, B:R.90, B:Q.150, B:Q.150, B:D.154, B:N.307 Water bridges: B:D.154 Salt bridges: B:H.66 XYP.15: 12 residues within 4Å: Chain C: C.39, A.41, H.66, N.89, R.90, E.114, I.117, Q.150, D.154, N.307 Ligands: NAP.14, ZN.17 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.89, C:R.90, C:Q.150, C:Q.150, C:D.154, C:N.307 Water bridges: C:A.41, C:H.66 Salt bridges: C:H.66 XYP.22: 11 residues within 4Å: Chain D: C.39, A.41, H.66, N.89, R.90, E.114, Q.150, D.154, N.307 Ligands: XYS.21, ZN.24 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.89, D:R.90, D:R.90, D:Q.150, D:Q.150, D:D.154, D:N.307 Water bridges: D:A.41, D:G.308 Salt bridges: D:H.66

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.39, H.66, E.67, Q.150 Ligands: XYP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.39, A:H.66, A:E.67, H2O.15 ZN.6: 6 residues within 4Å: Chain A: C.93, C.96, C.99, C.107, E.108, T.109 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.93, A:C.96, A:C.99, A:C.107 ZN.11: 5 residues within 4Å: Chain B: C.39, H.66, E.67, Q.150 Ligands: XYP.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.39, B:H.66, B:E.67, H2O.30 ZN.12: 6 residues within 4Å: Chain B: C.93, C.96, C.99, C.107, E.108, T.109 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.93, B:C.96, B:C.99, B:C.107 ZN.17: 5 residues within 4Å: Chain C: C.39, H.66, E.67, Q.150 Ligands: XYP.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.39, C:H.66, C:E.67, H2O.46 ZN.18: 6 residues within 4Å: Chain C: C.93, C.96, C.99, C.107, E.108, T.109 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.93, C:C.96, C:C.99, C:C.107 ZN.24: 5 residues within 4Å: Chain D: C.39, H.66, E.67, Q.150 Ligands: XYP.22 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.39, D:H.66, D:E.67, H2O.61 ZN.25: 6 residues within 4Å: Chain D: C.93, C.96, C.99, C.107, E.108, T.109 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.93, D:C.96, D:C.99, D:C.107

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

EDO.7: 4 residues within 4Å: Chain B: D.83, L.84, K.137, I.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.84, B:I.138, B:K.140 EDO.13: 5 residues within 4Å: Chain C: D.83, L.84, K.137, I.138, K.140 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.84, C:I.138, C:K.140 EDO.19: 5 residues within 4Å: Chain D: D.83, L.84, K.137, I.138, K.140 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.84, D:I.138, D:K.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milburn, C.C. et al., The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. J. Biol. Chem. (2006)

Release Date

2006-03-22

Peptides

GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1

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