SMTL ID : 2cdb.1

Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: D.83, L.84, K.137, I.138, P.139, K.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.84, A:L.84, A:I.138, A:K.140 EDO.6: 5 residues within 4Å: Chain B: D.83, L.84, K.137, I.138, K.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.84, B:L.84, B:I.138 Water bridges: B:K.140 EDO.11: 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.16: 5 residues within 4Å: Chain D: D.83, L.84, K.137, I.138, K.140 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.84, D:I.138, D:K.140 Water bridges: D:D.83

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.2: 13 residues within 4Å: Chain A: C.39, A.41, H.66, N.89, R.90, E.114, Q.150, D.154, F.279, N.307 Chain C: H.297 Ligands: NAP.3, ZN.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.89, A:R.90, A:Q.150, A:Q.150, A:D.154, A:N.307, C:H.297 Water bridges: A:A.41, A:D.154, A:G.308 Salt bridges: A:H.66 BGC.7: 11 residues within 4Å: Chain B: C.39, A.41, H.66, N.89, R.90, E.114, Q.150, D.154, N.307 Ligands: NAP.8, ZN.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.89, B:R.90, B:R.90, B:Q.150, B:Q.150, B:D.154, B:N.307 Water bridges: B:A.41, B:G.308 Salt bridges: B:H.66 BGC.12: 13 residues within 4Å: Chain A: H.297 Chain C: C.39, A.41, H.66, N.89, R.90, E.114, Q.150, D.154, F.279, N.307 Ligands: NAP.13, ZN.14 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.89, C:R.90, C:Q.150, C:Q.150, C:D.154, C:N.307, A:H.297 Water bridges: C:A.41, C:R.90, C:G.308 Salt bridges: C:H.66 BGC.17: 12 residues within 4Å: Chain D: C.39, A.41, H.66, N.89, R.90, E.114, I.117, Q.150, D.154, N.307 Ligands: NAP.18, ZN.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.89, D:R.90, D:Q.150, D:Q.150, D:D.154, D:N.307 Water bridges: D:A.41, D:N.89, D:E.114 Salt bridges: D:H.66

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

NAP.3: 25 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, F.277, G.278, F.279, L.305, V.306, N.307, K.354, H.356 Chain C: V.296 Ligands: BGC.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.277, A:F.279 Hydrogen bonds: A:T.189, A:T.189, A:T.189, A:T.189, A:I.192, A:N.211, A:R.212, A:R.213, A:F.277, A:F.279, A:N.307 Water bridges: A:G.40, A:G.40, A:E.44, A:G.193, A:N.211, A:R.213, A:S.233, A:T.254, A:K.354, A:K.354, A:K.354, A:K.354, A:H.356, A:H.356 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, I.260, F.277, G.278, F.279, L.305, V.306, N.307, K.354 Chain D: V.296 Ligands: BGC.7 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.192, B:F.277, B:F.279 Hydrogen bonds: B:T.189, B:G.190, 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:G.40, B:E.44, B:G.193, B:S.233, B:T.254, B:K.354, B:K.354, B:K.354 Salt bridges: B:R.213, B:K.354, B:H.356 NAP.13: 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: BGC.12 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:I.192, C:F.277, C:F.279 Hydrogen bonds: C:T.189, C:T.189, C:I.192, 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.190, C:G.193, C:N.211, C:R.213, C:S.233, C:T.254, C:K.354, C:K.354, C:K.354, C:K.354, C:H.356, C:H.356 Salt bridges: C:R.213, C:K.354, C:K.354, C:H.356 NAP.18: 24 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, F.277, G.278, F.279, L.305, V.306, N.307, K.354 Ligands: BGC.17 25 PLIP interactions: 25 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:R.213, D:F.277, D:F.279, D:N.307 Water bridges: D:E.44, D:G.193, D:N.211, D:S.233, D:T.254, D:K.354, D:K.354, D:K.354, D:K.354 Salt bridges: D:R.213, D:K.354, D:K.354, D:H.356

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.39, H.66, E.67, Q.150 Ligands: BGC.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.39, A:H.66, A:E.67, H2O.13 ZN.5: 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.9: 5 residues within 4Å: Chain B: C.39, H.66, E.67, Q.150 Ligands: BGC.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.39, B:H.66, B:E.67, H2O.24 ZN.10: 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.14: 5 residues within 4Å: Chain C: C.39, H.66, E.67, Q.150 Ligands: BGC.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.39, C:H.66, C:E.67, H2O.36 ZN.15: 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.19: 5 residues within 4Å: Chain D: C.39, H.66, E.67, Q.150 Ligands: BGC.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.39, D:H.66, D:E.67, H2O.50 ZN.20: 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

Links

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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 1-DEHYDROGENASE (DHG-1): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLUCOSE 1-DEHYDROGENASE (DHG-1)

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