SMTL ID : 4weq.1

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

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: 30 residues within 4Å: Chain A: A.96, G.97, R.114, M.124, G.168, M.169, G.170, V.171, L.172, W.190, S.191, R.192, S.193, R.195, L.221, L.222, P.223, D.227, T.228, A.254, G.255, R.256, D.280, V.281, H.304, A.306, A.307, Y.341 Ligands: SO4.2, SO4.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.96, A:L.172 Hydrogen bonds: A:M.169, A:M.169, A:V.171, A:L.172, A:R.192, A:S.193, A:R.195, A:D.280, A:A.306, A:A.307, A:Y.341, A:Y.341 Water bridges: A:V.98, A:R.114, A:R.114, A:R.114, A:G.170, A:G.173, A:R.192, A:R.192, A:L.224, A:L.224 Salt bridges: A:R.114, A:R.114, A:R.195 NAP.8: 30 residues within 4Å: Chain B: A.96, G.97, R.114, M.124, G.168, M.169, G.170, V.171, L.172, W.190, S.191, R.192, S.193, R.195, L.221, L.222, P.223, D.227, T.228, A.254, G.255, R.256, D.280, V.281, H.304, A.306, A.307, Y.341 Ligands: SO4.9, SO4.10 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.96, B:L.172 Hydrogen bonds: B:M.169, B:M.169, B:V.171, B:L.172, B:R.192, B:S.193, B:R.195, B:D.280, B:D.280, B:A.306, B:A.307, B:Y.341 Water bridges: B:V.98, B:R.114, B:R.114, B:R.114, B:G.170, B:G.173, B:R.192, B:R.192, B:L.224, B:L.224, B:Y.341 Salt bridges: B:R.114, B:R.114, B:R.195

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: W.75, G.95, A.96, G.97, R.256, H.304 Ligands: NAP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.96, A:G.97, A:G.97 Salt bridges: A:R.256, A:H.304 SO4.3: 4 residues within 4Å: Chain A: R.114, V.171, H.333 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.333 Water bridges: A:R.114, A:R.114, A:V.171, A:H.333 Salt bridges: A:R.114, A:H.333 SO4.4: 9 residues within 4Å: Chain A: H.139, R.140, E.143, Y.300 Chain B: H.139, R.140, E.143, Y.300 Ligands: SO4.11 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.143, A:E.143 Water bridges: B:R.140, B:R.140, A:R.140, A:R.140 Salt bridges: B:H.139, B:R.140, A:H.139, A:R.140 SO4.9: 7 residues within 4Å: Chain B: W.75, G.95, A.96, G.97, R.256, H.304 Ligands: NAP.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.96, B:G.97, B:G.97 Salt bridges: B:R.256, B:H.304 SO4.10: 4 residues within 4Å: Chain B: R.114, V.171, H.333 Ligands: NAP.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.333 Water bridges: B:R.114, B:R.114, B:V.171 Salt bridges: B:R.114, B:H.333 SO4.11: 9 residues within 4Å: Chain A: H.139, R.140, E.143, Y.300 Chain B: H.139, R.140, E.143, Y.300 Ligands: SO4.4 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.143, B:E.143 Water bridges: B:R.140, B:R.140, A:R.140, A:R.140 Salt bridges: B:H.139, B:R.140, A:H.139, A:R.140

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: P.49, G.50, R.51, E.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.50 PEG.12: 4 residues within 4Å: Chain B: P.49, G.50, R.51, E.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.50

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: H.135, Q.138, V.250, G.275, G.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.135, A:H.135, A:Q.138, A:N.298 Water bridges: A:R.140, A:R.140 GOL.13: 5 residues within 4Å: Chain B: H.135, Q.138, V.250, G.275, G.276 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.135, B:H.135, B:Q.138, B:N.298 Water bridges: B:R.140, B:R.140

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

CL.7: 3 residues within 4Å: Chain A: M.296, P.297, N.298 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: M.296, P.297, N.298 Ligand excluded by PLIP

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

2014-09-24

Peptides

NAD-dependent dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD-dependent dehydrogenase