SMTL ID : 4z0p.1

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: M.275, P.276, N.277, V.278 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: M.275, P.276, N.277, V.278 Ligand excluded by PLIP

4 x OXD: OXALIC ACID(Non-covalent)

OXD.2: 7 residues within 4Å: Chain A: W.54, G.74, A.75, G.76, R.235, H.283 Ligands: NDP.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.75, A:G.76 Salt bridges: A:R.235, A:R.235, A:H.283 OXD.3: 9 residues within 4Å: Chain A: H.118, R.119, E.122, Y.279 Chain B: H.118, R.119, E.122, Y.279 Ligands: OXD.10 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Water bridges: A:E.122, B:E.122 Salt bridges: A:H.118, A:H.118, A:R.119, B:H.118, B:H.118, B:R.119 Hydrogen bonds: B:E.122 OXD.9: 7 residues within 4Å: Chain B: W.54, G.74, A.75, G.76, R.235, H.283 Ligands: NDP.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.75, B:G.76 Salt bridges: B:R.235, B:R.235, B:H.283 OXD.10: 9 residues within 4Å: Chain A: H.118, R.119, E.122, Y.279 Chain B: H.118, R.119, E.122, Y.279 Ligands: OXD.3 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Water bridges: A:E.122, B:E.122 Salt bridges: A:H.118, A:H.118, A:R.119, B:H.118, B:H.118, B:R.119 Hydrogen bonds: B:E.122

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 2 residues within 4Å: Chain A: G.47, D.66 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.46, A:S.46 Salt bridges: A:D.66 EPE.11: 2 residues within 4Å: Chain B: G.47, D.66 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.46, B:S.46 Salt bridges: B:D.66

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: V.240, A.242 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.243 GOL.6: 4 residues within 4Å: Chain A: H.114, Q.117, V.229, G.254 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.114, A:Q.117 Water bridges: A:Q.117, A:H.118, A:R.119, A:F.225 GOL.12: 2 residues within 4Å: Chain B: V.240, A.242 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.243 GOL.13: 4 residues within 4Å: Chain B: H.114, Q.117, V.229, G.254 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.114, B:Q.117 Water bridges: B:Q.117, B:H.118, B:R.119, B:F.225

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

NDP.7: 29 residues within 4Å: Chain A: A.75, G.76, R.93, M.103, G.147, M.148, G.149, V.150, L.151, W.169, S.170, R.171, S.172, R.174, L.200, L.201, P.202, D.206, T.207, A.233, G.234, R.235, D.259, V.260, H.283, A.285, A.286, Y.320 Ligands: OXD.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:A.75, A:L.151, A:A.286 Hydrogen bonds: A:M.148, A:M.148, A:V.150, A:L.151, A:S.170, A:R.171, A:S.172, A:R.174, A:D.259, A:A.285, A:A.286, A:Y.320 Water bridges: A:V.77, A:V.77, A:D.78, A:R.93, A:R.93, A:G.149, A:G.152, A:R.171, A:R.171, A:R.171, A:R.171, A:L.203, A:D.206 Salt bridges: A:R.93, A:R.93, A:R.174 NDP.14: 29 residues within 4Å: Chain B: A.75, G.76, R.93, M.103, G.147, M.148, G.149, V.150, L.151, W.169, S.170, R.171, S.172, R.174, L.200, L.201, P.202, D.206, T.207, A.233, G.234, R.235, D.259, V.260, H.283, A.285, A.286, Y.320 Ligands: OXD.9 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:A.75, B:L.151, B:A.286 Hydrogen bonds: B:M.148, B:M.148, B:V.150, B:L.151, B:S.170, B:R.171, B:S.172, B:R.174, B:D.259, B:D.259, B:A.285, B:A.286 Water bridges: B:V.77, B:V.77, B:D.78, B:R.93, B:R.93, B:G.149, B:G.152, B:R.171, B:R.171, B:R.171, B:L.203, B:D.206, B:Y.320 Salt bridges: B:R.93, B:R.93, B:R.174

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

2015-04-08

Peptides

NAD-dependent dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD-dependent dehydrogenase