SMTL ID : 5tsd.1

Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 30 residues within 4Å: Chain A: A.77, G.78, R.95, L.101, M.105, G.149, L.150, G.151, I.152, L.153, W.171, S.172, R.173, T.174, K.176, L.202, L.203, P.204, E.208, T.209, A.235, G.236, R.237, D.261, V.262, H.285, A.287, A.288, Y.322 Ligands: OXD.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.77, A:L.101, A:L.153 Hydrogen bonds: A:L.150, A:L.150, A:I.152, A:L.153, A:R.173, A:T.174, A:T.174, A:D.261, A:D.261, A:A.287, A:A.288, A:Y.322 Water bridges: A:D.80, A:R.95, A:R.95, A:R.95, A:G.151, A:G.154, A:R.173, A:L.205, A:E.208, A:E.208 Salt bridges: A:R.95, A:R.95, A:K.176 NDP.3: 30 residues within 4Å: Chain B: A.77, G.78, R.95, L.101, M.105, G.149, L.150, G.151, I.152, L.153, W.171, S.172, R.173, T.174, K.176, L.202, L.203, P.204, E.208, T.209, A.235, G.236, R.237, D.261, V.262, H.285, A.287, A.288, Y.322 Ligands: OXD.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:A.77, B:L.101, B:L.153, B:A.288 Hydrogen bonds: B:L.150, B:L.150, B:I.152, B:L.153, B:R.173, B:T.174, B:T.174, B:D.261, B:A.287, B:A.288 Water bridges: B:G.151, B:G.151, B:R.173, B:L.205, B:L.205 Salt bridges: B:R.95, B:R.95, B:K.176

2 x OXD: OXALIC ACID(Non-covalent)

OXD.2: 7 residues within 4Å: Chain A: W.56, G.76, A.77, G.78, R.237, H.285 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.77, A:G.78 Salt bridges: A:R.237, A:R.237, A:H.285 OXD.4: 7 residues within 4Å: Chain B: W.56, G.76, A.77, G.78, R.237, H.285 Ligands: NDP.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.77, B:G.78 Water bridges: B:G.75, B:A.288 Salt bridges: B:R.237, B:R.237, B:H.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matelska, D. et al., Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate. to be published

Release Date

2016-11-16

Peptides

Probable hydroxyacid dehydrogenase protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable hydroxyacid dehydrogenase protein

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