SMTL ID : 1vl8.2 (1 other biounit)

Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: R.124, E.128, F.132 Chain B: R.124, E.128, F.132 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.128, A:E.128, A:E.128, B:E.128 Water bridges: B:R.124 PO4.5: 6 residues within 4Å: Chain C: R.124, E.128, F.132 Chain D: R.124, E.128, F.132 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.128, D:E.128, C:E.128, C:E.128 Water bridges: D:R.124

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

NAP.2: 29 residues within 4Å: Chain A: G.28, S.30, R.31, G.32, L.33, S.52, R.53, N.54, C.78, D.79, V.80, A.106, A.107, G.108, I.109, V.129, I.156, G.157, S.158, Y.172, K.176, P.202, G.203, W.204, Y.205, T.207, K.208, M.209, T.210 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.33, A:P.202, A:P.202 Hydrogen bonds: A:G.28, A:S.30, A:S.30, A:R.31, A:L.33, A:R.53, A:R.53, A:N.54, A:D.79, A:V.80, A:A.106, A:G.108, A:K.176, A:Y.205, A:Y.205, A:K.208, A:M.209 Water bridges: A:R.31, A:G.34, A:N.54 Salt bridges: A:R.31, A:R.31, A:R.53 NAP.4: 30 residues within 4Å: Chain B: G.28, S.30, R.31, G.32, L.33, S.52, R.53, N.54, E.57, C.78, D.79, V.80, A.106, A.107, G.108, I.109, V.129, I.156, G.157, S.158, Y.172, K.176, P.202, G.203, W.204, Y.205, T.207, K.208, M.209, T.210 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:L.33, B:P.202 Hydrogen bonds: B:G.28, B:S.30, B:S.30, B:R.31, B:L.33, B:R.53, B:R.53, B:N.54, B:D.79, B:V.80, B:A.106, B:G.108, B:K.176, B:Y.205, B:Y.205, B:T.207, B:M.209 Water bridges: B:R.31, B:R.31, B:R.31, B:G.34, B:S.52, B:S.52, B:K.208 Salt bridges: B:R.31, B:R.31, B:R.53 NAP.6: 29 residues within 4Å: Chain C: G.28, S.30, R.31, G.32, L.33, S.52, R.53, N.54, C.78, D.79, V.80, A.106, A.107, G.108, I.109, V.129, I.156, G.157, S.158, Y.172, K.176, P.202, G.203, W.204, Y.205, T.207, K.208, M.209, T.210 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:L.33, C:P.202, C:P.202 Hydrogen bonds: C:G.28, C:S.30, C:S.30, C:R.31, C:L.33, C:R.53, C:R.53, C:N.54, C:D.79, C:D.79, C:V.80, C:A.106, C:G.108, C:Y.172, C:K.176, C:Y.205, C:Y.205, C:T.207, C:K.208, C:M.209 Water bridges: C:R.31, C:G.34, C:N.54 Salt bridges: C:R.31, C:R.31, C:R.53 NAP.8: 30 residues within 4Å: Chain D: G.28, S.30, R.31, G.32, L.33, S.52, R.53, N.54, E.57, C.78, D.79, V.80, A.106, A.107, G.108, I.109, V.129, I.156, G.157, S.158, Y.172, K.176, P.202, G.203, W.204, Y.205, T.207, K.208, M.209, T.210 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:L.33, D:P.202 Hydrogen bonds: D:G.28, D:S.30, D:S.30, D:R.31, D:L.33, D:R.53, D:R.53, D:N.54, D:E.57, D:D.79, D:D.79, D:V.80, D:A.106, D:G.108, D:Y.172, D:K.176, D:Y.205, D:Y.205, D:M.209 Water bridges: D:R.31, D:R.31, D:R.31, D:G.34, D:S.52, D:S.52, D:K.208 Salt bridges: D:R.31, D:R.31, D:R.53

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: E.163 Chain C: E.163 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: C:E.163, B:E.163, H2O.8, H2O.8, H2O.8, H2O.13 MG.7: 2 residues within 4Å: Chain A: E.163 Chain D: E.163 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: A:E.163, D:E.163, H2O.1, H2O.20, H2O.20, H2O.20

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution. To be published

Release Date

2004-08-17

Peptides

Gluconate 5-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Gluconate 5-dehydrogenase

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