SMTL ID : 5aov.1

Ternary Crystal Structure of Pyrococcus furiosus Glyoxylate Hydroxypyruvate Reductase in presence of glyoxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 30 residues within 4Å: Chain A: V.76, G.77, L.100, T.104, G.157, F.158, G.159, R.160, I.161, G.162, Y.179, S.180, R.181, T.182, K.184, A.211, V.212, P.213, L.214, E.217, T.218, I.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: GLV.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.76, A:T.104, A:I.161 Hydrogen bonds: A:F.158, A:F.158, A:R.160, A:I.161, A:S.180, A:R.181, A:T.182, A:K.184, A:D.265, A:G.290, A:S.291 Water bridges: A:G.159, A:G.162, A:R.181, A:R.181, A:R.181, A:R.181, A:L.214, A:L.214 Salt bridges: A:R.160, A:R.181, A:K.184 NAP.26: 30 residues within 4Å: Chain B: V.76, G.77, L.100, T.104, G.157, F.158, G.159, R.160, I.161, G.162, Y.179, S.180, R.181, T.182, K.184, A.211, V.212, P.213, L.214, E.217, T.218, I.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: GLV.27 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.76, B:T.104, B:I.161 Hydrogen bonds: B:F.158, B:F.158, B:R.160, B:I.161, B:S.180, B:R.181, B:T.182, B:K.184, B:D.265, B:G.290, B:S.291 Water bridges: B:G.159, B:G.162, B:R.181, B:R.181, B:R.181, B:R.181, B:L.214, B:L.214 Salt bridges: B:R.160, B:R.181, B:K.184

4 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.2: 9 residues within 4Å: Chain A: L.53, A.75, V.76, G.77, L.100, R.241, H.288 Ligands: NAP.1, GLV.22 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.76, A:G.77, A:R.241, A:R.241 Salt bridges: A:R.241 GLV.22: 7 residues within 4Å: Chain A: M.52, L.53, Y.74, A.75, M.300 Chain B: W.138 Ligands: GLV.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.53, A:Y.74 Water bridges: A:S.54, A:S.291, A:R.297 GLV.27: 9 residues within 4Å: Chain B: L.53, A.75, V.76, G.77, L.100, R.241, H.288 Ligands: NAP.26, GLV.47 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.76, B:G.77, B:R.241, B:R.241 Salt bridges: B:R.241 GLV.47: 7 residues within 4Å: Chain A: W.138 Chain B: M.52, L.53, Y.74, A.75, M.300 Ligands: GLV.27 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.53, B:Y.74 Water bridges: B:S.54, B:S.291, B:R.297

30 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 6 residues within 4Å: Chain A: R.56, D.58, D.79, N.80, I.81, D.82 Ligand excluded by PLIP 1PE.4: 5 residues within 4Å: Chain A: S.128, G.129, K.132, R.133 Chain B: Y.273 Ligand excluded by PLIP 1PE.5: 6 residues within 4Å: Chain A: F.294, E.295 Chain B: Y.146, K.151, T.233 Ligands: 1PE.38 Ligand excluded by PLIP 1PE.6: 5 residues within 4Å: Chain A: M.219, Y.220, M.221, N.223, R.226 Ligand excluded by PLIP 1PE.7: 3 residues within 4Å: Chain A: R.183, Y.195, P.197 Ligand excluded by PLIP 1PE.8: 4 residues within 4Å: Chain A: G.150, N.173, M.174, R.175 Ligand excluded by PLIP 1PE.9: 14 residues within 4Å: Chain A: A.114, T.115, A.116, H.118, K.121, G.145, Y.146, I.235, A.260, G.261, D.281, N.282, V.284 Ligands: 1PE.25 Ligand excluded by PLIP 1PE.10: 6 residues within 4Å: Chain A: F.278, S.279, D.281 Chain B: K.124, R.127, S.128 Ligand excluded by PLIP 1PE.11: 6 residues within 4Å: Chain A: D.79, L.214, T.215, K.216, M.219 Ligands: 1PE.15 Ligand excluded by PLIP 1PE.12: 6 residues within 4Å: Chain A: D.98, T.101, N.102, R.167 Chain B: Y.149 Ligands: 1PE.38 Ligand excluded by PLIP 1PE.13: 10 residues within 4Å: Chain A: Y.146, Y.149, G.150, K.151, D.206, K.231, T.233 Chain B: E.295 Ligands: 1PE.30, 1PE.37 Ligand excluded by PLIP 1PE.14: 4 residues within 4Å: Chain A: E.199, E.200, K.203, L.229 Ligand excluded by PLIP 1PE.15: 7 residues within 4Å: Chain A: M.219, Y.220, K.243, E.268, E.269 Ligands: 1PE.11, EDO.17 Ligand excluded by PLIP 1PE.21: 4 residues within 4Å: Chain A: E.269, Y.272, Y.273, N.274 Ligand excluded by PLIP 1PE.25: 11 residues within 4Å: Chain A: H.118, K.121, F.125, K.134, W.142, F.143, L.144, G.145, Y.146 Chain B: F.294 Ligands: 1PE.9 Ligand excluded by PLIP 1PE.28: 6 residues within 4Å: Chain B: R.56, D.58, D.79, N.80, I.81, D.82 Ligand excluded by PLIP 1PE.29: 5 residues within 4Å: Chain A: Y.273 Chain B: S.128, G.129, K.132, R.133 Ligand excluded by PLIP 1PE.30: 6 residues within 4Å: Chain A: Y.146, K.151, T.233 Chain B: F.294, E.295 Ligands: 1PE.13 Ligand excluded by PLIP 1PE.31: 5 residues within 4Å: Chain B: M.219, Y.220, M.221, N.223, R.226 Ligand excluded by PLIP 1PE.32: 3 residues within 4Å: Chain B: R.183, Y.195, P.197 Ligand excluded by PLIP 1PE.33: 4 residues within 4Å: Chain B: G.150, N.173, M.174, R.175 Ligand excluded by PLIP 1PE.34: 14 residues within 4Å: Chain B: A.114, T.115, A.116, H.118, K.121, G.145, Y.146, I.235, A.260, G.261, D.281, N.282, V.284 Ligands: 1PE.50 Ligand excluded by PLIP 1PE.35: 6 residues within 4Å: Chain A: K.124, R.127, S.128 Chain B: F.278, S.279, D.281 Ligand excluded by PLIP 1PE.36: 6 residues within 4Å: Chain B: D.79, L.214, T.215, K.216, M.219 Ligands: 1PE.40 Ligand excluded by PLIP 1PE.37: 6 residues within 4Å: Chain A: Y.149 Chain B: D.98, T.101, N.102, R.167 Ligands: 1PE.13 Ligand excluded by PLIP 1PE.38: 10 residues within 4Å: Chain A: E.295 Chain B: Y.146, Y.149, G.150, K.151, D.206, K.231, T.233 Ligands: 1PE.5, 1PE.12 Ligand excluded by PLIP 1PE.39: 4 residues within 4Å: Chain B: E.199, E.200, K.203, L.229 Ligand excluded by PLIP 1PE.40: 7 residues within 4Å: Chain B: M.219, Y.220, K.243, E.268, E.269 Ligands: 1PE.36, EDO.42 Ligand excluded by PLIP 1PE.46: 4 residues within 4Å: Chain B: E.269, Y.272, Y.273, N.274 Ligand excluded by PLIP 1PE.50: 11 residues within 4Å: Chain A: F.294 Chain B: H.118, K.121, F.125, K.134, W.142, F.143, L.144, G.145, Y.146 Ligands: 1PE.34 Ligand excluded by PLIP

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

EDO.16: 4 residues within 4Å: Chain A: E.31 Chain B: H.139, K.141, W.142 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.31, B:W.142 EDO.17: 3 residues within 4Å: Chain A: Y.220, D.246 Ligands: 1PE.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.246 Water bridges: A:D.246 EDO.18: 6 residues within 4Å: Chain A: G.314, E.315, I.316, I.326, K.330, P.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.314 Water bridges: A:I.316 EDO.19: 3 residues within 4Å: Chain A: K.44, N.64, P.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.20: 6 residues within 4Å: Chain A: R.329, K.330, P.331, G.332, F.333, N.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.333, A:N.334 Water bridges: A:R.329, A:R.329 EDO.41: 4 residues within 4Å: Chain A: H.139, K.141, W.142 Chain B: E.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.142, B:E.31 EDO.42: 3 residues within 4Å: Chain B: Y.220, D.246 Ligands: 1PE.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.246 Water bridges: B:D.246 EDO.43: 6 residues within 4Å: Chain B: G.314, E.315, I.316, I.326, K.330, P.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.314 Water bridges: B:I.316 EDO.44: 3 residues within 4Å: Chain B: K.44, N.64, P.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.44 EDO.45: 6 residues within 4Å: Chain B: R.329, K.330, P.331, G.332, F.333, N.334 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.333, B:N.334 Water bridges: B:R.329, B:R.329

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.23: 5 residues within 4Å: Chain A: Y.78, R.181, P.213, T.215 Ligands: ACY.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.213, A:T.215 Water bridges: A:R.181 Salt bridges: A:R.181 ACY.24: 4 residues within 4Å: Chain A: R.181, T.215, E.217 Ligands: ACY.23 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.217, A:E.217 Salt bridges: A:R.181 ACY.48: 5 residues within 4Å: Chain B: Y.78, R.181, P.213, T.215 Ligands: ACY.49 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.213, B:T.215 Water bridges: B:R.181 Salt bridges: B:R.181 ACY.49: 4 residues within 4Å: Chain B: R.181, T.215, E.217 Ligands: ACY.48 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.217, B:E.217 Salt bridges: B:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lassalle, L. et al., New Insights Into the Mechanism of Substrates Trafficking in Glyoxylate/Hydroxypyruvate Reductases. Sci.Rep. (2016)

Release Date

2016-03-02

Peptides

GLYOXYLATE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYOXYLATE REDUCTASE