SMTL ID : 5vg6.1 (4 other biounits)

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: A.100, G.101, R.118, M.128, G.172, L.173, G.174, D.175, L.176, G.177, W.194, S.195, R.196, T.197, M.226, L.227, P.228, E.232, T.233, V.254, A.255, R.256, D.280, V.281, H.304, A.306, S.307, Y.341 Ligands: MES.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.100, A:L.176 Hydrogen bonds: A:L.173, A:L.173, A:G.174, A:D.175, A:L.176, A:G.177, A:R.196, A:T.197, A:D.280, A:D.280, A:A.306, A:S.307, A:Y.341, A:Y.341, A:Y.341 Water bridges: A:V.102, A:R.118, A:R.118, A:R.118, A:S.195, A:S.195, A:K.199, A:L.229, A:T.230 Salt bridges: A:R.118, A:R.118 NDP.4: 29 residues within 4Å: Chain B: A.100, G.101, R.118, M.128, G.172, L.173, G.174, D.175, L.176, G.177, W.194, S.195, R.196, T.197, M.226, L.227, P.228, E.232, T.233, V.254, A.255, R.256, D.280, V.281, H.304, A.306, S.307, Y.341 Ligands: MES.5 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.100, B:L.176 Hydrogen bonds: B:L.173, B:L.173, B:G.174, B:D.175, B:L.176, B:G.177, B:R.196, B:T.197, B:D.280, B:A.306, B:S.307, B:Y.341, B:Y.341 Water bridges: B:A.100, B:V.102, B:R.118, B:R.118, B:R.118, B:R.118, B:S.195, B:S.195, B:L.229, B:L.229, B:T.230, B:E.232 Salt bridges: B:R.118, B:R.118, B:R.196

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 10 residues within 4Å: Chain A: V.37, D.38, W.79, L.98, G.99, A.100, G.101, R.256, H.304 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.100, A:G.101, A:G.101 Salt bridges: A:R.256, A:H.304 MES.3: 3 residues within 4Å: Chain A: R.196, T.197, L.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.210 Water bridges: A:R.196 Salt bridges: A:R.196 MES.5: 9 residues within 4Å: Chain B: V.37, D.38, W.79, G.99, A.100, G.101, R.256, H.304 Ligands: NDP.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.100, B:G.101 Salt bridges: B:D.38, B:R.256, B:H.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lipowska, J. et al., Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES. to be published

Release Date

2017-04-26

Peptides

D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
J

D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding

Related Entries With Identical Sequence