SMTL ID : 5v7g.2 (1 other biounit)

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADPH and oxalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x OXL: OXALATE ION(Non-covalent)

OXL.1: 7 residues within 4Å: Chain A: G.72, V.73, G.74, L.97, R.231, H.278 Ligands: NDP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.73, A:G.74 Water bridges: A:N.70, A:R.231 Salt bridges: A:R.231, A:R.231, A:H.278 OXL.5: 7 residues within 4Å: Chain B: G.72, V.73, G.74, L.97, R.231, H.278 Ligands: NDP.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.73, B:G.74 Salt bridges: B:R.231, B:R.231, B:H.278

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 26 residues within 4Å: Chain A: V.73, G.74, V.101, F.149, G.150, L.151, G.152, R.153, I.154, H.172, T.173, R.174, T.175, I.201, V.202, P.203, S.207, T.208, V.229, G.230, R.231, D.255, V.256, H.278, A.280 Ligands: OXL.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.73, A:V.101, A:I.154 Hydrogen bonds: A:L.151, A:L.151, A:R.153, A:I.154, A:R.174, A:T.175, A:S.207, A:V.229, A:A.280 Water bridges: A:Y.75, A:D.76, A:G.152, A:R.153, A:R.153, A:R.153, A:R.153, A:G.155, A:T.175, A:G.204, A:S.281 Salt bridges: A:R.153, A:R.153, A:R.174 NDP.6: 26 residues within 4Å: Chain B: V.73, G.74, V.101, F.149, G.150, L.151, G.152, R.153, I.154, H.172, T.173, R.174, T.175, I.201, V.202, P.203, S.207, T.208, V.229, G.230, R.231, D.255, V.256, H.278, A.280 Ligands: OXL.5 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:V.73, B:V.101, B:I.154 Hydrogen bonds: B:L.151, B:L.151, B:R.153, B:I.154, B:R.174, B:T.175, B:S.207, B:V.229, B:D.255, B:A.280, B:S.281 Water bridges: B:Y.75, B:D.76, B:G.152, B:R.153, B:R.153, B:G.155, B:T.173, B:T.173, B:G.204, B:T.205 Salt bridges: B:R.153, B:R.153, B:R.174

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: N.14, R.287 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: N.14, F.71, R.287 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: A.192, E.193, V.195, A.219, L.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.195, A:V.195 Water bridges: A:E.193 NA.9: 5 residues within 4Å: Chain B: A.192, E.193, V.195, A.219, L.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.195, B:A.219

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: R.142 Chain B: V.96, T.286, A.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kutner, J. et al., Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry (2018)

Release Date

2017-03-29

Peptides

NADPH-dependent glyoxylate/hydroxypyruvate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

NADPH-dependent glyoxylate/hydroxypyruvate reductase

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