SMTL ID : 5bqf.1

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

EPE.1: 9 residues within 4Å: Chain A: F.16, W.56, G.75, H.285, S.290, E.291, E.292, L.295 Ligands: TLA.4 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:E.266, A:E.266, A:H.285, B:K.134 Salt bridges: A:H.285, A:E.292, B:K.134 pi-Cation interactions: A:F.16 EPE.7: 9 residues within 4Å: Chain B: F.16, W.56, G.75, H.285, S.290, E.291, E.292, L.295 Ligands: TLA.10 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:H.285, B:H.285, B:E.292, A:K.134, A:K.134 Salt bridges: B:H.285, B:E.292, A:K.134 pi-Cation interactions: B:F.16

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

PEG.2: 6 residues within 4Å: Chain A: V.97, D.98, R.99, T.102, I.152, F.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.102, A:T.102 Water bridges: A:R.99 PEG.8: 6 residues within 4Å: Chain B: V.97, D.98, R.99, T.102, I.152, F.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.102 Water bridges: B:R.99

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 28 residues within 4Å: Chain A: A.77, R.95, L.101, M.105, G.149, L.150, G.151, I.152, L.153, G.154, W.171, S.172, R.173, T.174, L.202, L.203, P.204, E.208, T.209, A.235, G.236, R.237, D.261, V.262, H.285, A.288, Y.322 Ligands: TLA.4 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.77, A:L.101, A:L.153 Hydrogen bonds: A:R.95, A:L.150, A:L.150, A:I.152, A:L.153, A:G.154, A:R.173, A:T.174, A:T.174, A:T.174, A:E.208, A:D.261, A:A.287, A:A.288 Water bridges: A:D.80, A:R.95, A:G.151, A:G.151, A:S.172, A:S.172, A:R.173, A:R.173, A:R.173, A:L.205, A:Y.322, A:Y.322 Salt bridges: A:R.95 NAP.9: 28 residues within 4Å: Chain B: A.77, R.95, L.101, M.105, G.149, L.150, G.151, I.152, L.153, G.154, W.171, S.172, R.173, T.174, L.202, L.203, P.204, E.208, T.209, A.235, G.236, R.237, D.261, V.262, H.285, A.288, Y.322 Ligands: TLA.10 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.77, B:L.101, B:L.153 Hydrogen bonds: B:R.95, B:L.150, B:L.150, B:I.152, B:L.153, B:G.154, B:R.173, B:T.174, B:T.174, B:E.208, B:E.208, B:D.261, B:D.261, B:A.287, B:A.288, B:Y.322 Water bridges: B:D.80, B:R.95, B:G.151, B:G.151, B:S.172, B:S.172, B:R.173, B:R.173, B:R.173, B:L.205 Salt bridges: B:R.95

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 10 residues within 4Å: Chain A: G.76, A.77, G.78, R.237, H.285, A.288, V.289, S.290 Ligands: EPE.1, NAP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.77, A:S.290, A:S.290 Water bridges: A:G.78, A:R.237, A:H.285, A:H.285 Salt bridges: A:R.237, A:R.237, A:H.285 TLA.10: 10 residues within 4Å: Chain B: G.76, A.77, G.78, R.237, H.285, A.288, V.289, S.290 Ligands: EPE.7, NAP.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.77, B:S.290, B:S.290 Water bridges: B:G.78, B:R.237, B:H.285, B:H.285 Salt bridges: B:R.237, B:R.237, B:H.285

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

NA.5: 2 residues within 4Å: Chain A: T.244, S.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.244 NA.11: 2 residues within 4Å: Chain B: T.244, S.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.248

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

CL.6: 3 residues within 4Å: Chain A: T.244, V.247, P.273 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: T.244, V.247, P.273 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langner, K.M. et al., Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L-tartaric acid. to be published

Release Date

2015-06-17

Peptides

NADP-dependent 2-hydroxyacid dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADP-dependent 2-hydroxyacid dehydrogenase

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