SMTL ID : 5j23.2 (1 other biounit)

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: V.96, T.286, A.289 Chain B: R.142 No protein-ligand interaction detected (PLIP)

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

CL.2: 4 residues within 4Å: Chain A: N.14, F.71, R.287 Chain B: L.136 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: R.231, H.278 Ligands: A2R.4 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.136 Chain B: N.14, R.287 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: R.231, H.278 Ligands: A2R.7 Ligand excluded by PLIP

2 x A2R: [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

A2R.4: 19 residues within 4Å: Chain A: V.73, G.74, F.149, L.151, G.152, R.153, I.154, T.173, R.174, T.175, I.201, V.202, P.203, S.207, T.208, V.229, G.230, R.231 Ligands: CL.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:L.151, A:R.153, A:I.154, A:R.174, A:T.175, A:T.175, A:S.207, A:G.230 Water bridges: A:D.76, A:R.153, A:T.173, A:T.173, A:R.174, A:G.204 Salt bridges: A:R.153, A:R.153, A:R.174, A:R.231 pi-Cation interactions: A:R.174 A2R.7: 21 residues within 4Å: Chain B: V.73, G.74, 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 Ligands: CL.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:L.151, B:R.153, B:I.154, B:R.174, B:T.175, B:T.175, B:S.207, B:G.230 Water bridges: B:D.76, B:L.151, B:G.152, B:R.153, B:R.153, B:G.155, B:G.204 Salt bridges: B:R.153, B:R.153, B:R.174, B:R.231

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

2016-04-13

Peptides

2-hydroxyacid dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

2-hydroxyacid dehydrogenase

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