SMTL ID : 6bii.1

Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: V.76, G.77, T.104, G.157, F.158, G.159, R.160, I.161, A.180, R.181, S.182, K.184, A.211, V.212, P.213, E.217, T.218, V.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: MLI.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:G.159, A:R.160, A:I.161, A:R.181, A:S.182, A:E.217, A:E.217, A:D.265, A:G.290, A:S.291 Water bridges: A:D.79, A:R.160, A:R.160, A:R.160, A:R.160, A:G.162, A:L.214 Salt bridges: A:R.160, A:R.160, A:K.184 NAP.6: 26 residues within 4Å: Chain B: V.76, G.77, T.104, G.157, F.158, G.159, R.160, I.161, A.180, R.181, S.182, K.184, A.211, V.212, P.213, E.217, T.218, V.239, A.240, R.241, D.265, V.266, H.288, G.290, S.291 Ligands: MLI.7 29 PLIP interactions: 29 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:R.181, B:S.182, B:S.182, B:D.265, B:G.290, B:S.291 Water bridges: B:G.159, B:R.160, B:R.160, B:R.160, B:R.160, B:G.162, B:R.181, B:R.181, B:R.181, B:L.214, B:L.214, B:E.217 Salt bridges: B:R.160, B:R.160, B:R.181, B:K.184

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 10 residues within 4Å: Chain A: L.53, A.75, V.76, G.77, L.100, R.241, H.288, S.291 Chain B: W.138 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.53, A:A.75 Hydrogen bonds: A:V.76, A:G.77, A:S.291 Salt bridges: A:R.241, A:R.241, A:H.288 MLI.7: 10 residues within 4Å: Chain A: W.138 Chain B: L.53, A.75, V.76, G.77, L.100, R.241, H.288, S.291 Ligands: NAP.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.53, B:A.75 Hydrogen bonds: B:V.76, B:G.77 Water bridges: B:R.297 Salt bridges: B:R.241, B:R.241, B:H.288

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.78, N.95, R.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.78, A:N.95, A:R.160, A:R.160 GOL.4: 3 residues within 4Å: Chain A: H.30, E.31, H.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.30, A:E.31, A:H.32, A:H.32 GOL.5: 5 residues within 4Å: Chain A: Q.163, K.184, P.185, E.186, A.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.163, A:Q.163, A:K.184, A:E.186 GOL.8: 3 residues within 4Å: Chain B: Y.78, N.95, R.160 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.78, B:Y.78, B:N.95, B:R.160, B:R.160 Water bridges: B:Y.78 GOL.9: 4 residues within 4Å: Chain B: K.184, P.185, E.186, A.187 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.186, B:A.187 Water bridges: B:Q.163, B:Q.163, B:Q.163, B:E.190

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

2018-01-17

Peptides

Glyoxylate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glyoxylate reductase