SMTL ID : 2dbq.1

Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (I41)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: Y.78, N.95, R.160, V.321 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.78, A:N.95 Water bridges: A:Y.78, A:R.160, A:L.320, A:V.321 Salt bridges: A:R.160 SO4.2: 9 residues within 4Å: Chain A: L.53, A.75, V.76, G.77, L.100, R.241, H.288 Ligands: NAP.3, GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.76, A:G.77 Water bridges: A:H.288 Salt bridges: A:R.241, A:H.288 SO4.9: 4 residues within 4Å: Chain B: Y.78, N.95, R.160, V.321 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.78, B:N.95 Water bridges: B:Y.78, B:R.160, B:L.320, B:V.321 Salt bridges: B:R.160 SO4.10: 9 residues within 4Å: Chain B: L.53, A.75, V.76, G.77, L.100, R.241, H.288 Ligands: NAP.11, GOL.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.76, B:G.77 Water bridges: B:H.288 Salt bridges: B:R.241, B:H.288

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

NAP.3: 27 residues within 4Å: Chain A: V.76, G.77, T.104, G.157, L.158, G.159, R.160, I.161, Y.179, S.180, R.181, T.182, K.184, A.211, V.212, P.213, E.217, T.218, I.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: SO4.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.76, A:T.104, A:I.161 Hydrogen bonds: A:L.158, A:R.160, A:I.161, A:S.180, A:R.181, A:T.182, A:I.239, A:G.290, A:S.291 Water bridges: A:D.79, A:G.159, A:R.160, A:R.160, A:G.162, A:R.181, A:T.182, A:T.182, A:K.184, A:K.184, A:L.214, A:E.217, A:E.217 Salt bridges: A:R.160, A:R.160, A:R.181, A:K.184 NAP.11: 27 residues within 4Å: Chain B: V.76, G.77, T.104, G.157, L.158, G.159, R.160, I.161, Y.179, S.180, R.181, T.182, K.184, A.211, V.212, P.213, E.217, T.218, I.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: SO4.10 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:V.76, B:T.104, B:I.161 Hydrogen bonds: B:L.158, B:R.160, B:I.161, B:S.180, B:R.181, B:T.182, B:I.239, B:G.290, B:S.291 Water bridges: B:D.79, B:G.159, B:R.160, B:R.160, B:G.162, B:R.181, B:T.182, B:T.182, B:K.184, B:K.184, B:L.214, B:E.217, B:E.217 Salt bridges: B:R.160, B:R.160, B:R.181, B:K.184

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: M.52, L.53, Y.74, A.75, H.288, M.300 Chain B: W.138 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.53 GOL.5: 3 residues within 4Å: Chain A: P.35, R.36, E.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.37 Water bridges: A:R.36 GOL.6: 7 residues within 4Å: Chain A: D.79, L.214, K.243, F.267, E.268, E.269, E.270 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.79, A:D.79, A:E.268, A:E.270 Water bridges: A:K.243, A:E.270, A:E.270 GOL.7: 3 residues within 4Å: Chain A: Y.146, K.151, D.206 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:D.147, A:K.151, A:D.206, A:K.231, B:G.295 GOL.8: 4 residues within 4Å: Chain A: F.125, R.134, W.142, F.143 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.134 Water bridges: A:K.121, A:K.121, A:K.121, B:E.31, B:E.31 GOL.12: 8 residues within 4Å: Chain A: W.138 Chain B: M.52, L.53, Y.74, A.75, H.288, M.300 Ligands: SO4.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.53 GOL.13: 3 residues within 4Å: Chain B: P.35, R.36, E.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.37 Water bridges: B:R.36 GOL.14: 7 residues within 4Å: Chain B: D.79, L.214, K.243, F.267, E.268, E.269, E.270 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.79, B:D.79, B:E.268, B:E.270 Water bridges: B:K.243, B:E.270, B:E.270 GOL.15: 3 residues within 4Å: Chain B: Y.146, K.151, D.206 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:D.147, B:K.151, B:D.206, B:K.231, A:G.295 GOL.16: 4 residues within 4Å: Chain B: F.125, R.134, W.142, F.143 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.31, A:E.31, B:K.121, B:K.121, B:K.121 Hydrogen bonds: B:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikawa, S. et al., Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate. Acta Crystallogr.,Sect.D (2007)

Release Date

2006-06-16

Peptides

Glyoxylate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glyoxylate reductase

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