SMTL ID : 1v9n.1

Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 28 residues within 4Å: Chain A: K.4, R.50, V.52, H.55, H.127, G.129, I.130, A.131, T.149, S.151, T.167, P.169, L.182, L.183, D.184, M.185, A.186, P.191, W.320, H.322, G.323, E.324, K.325, G.326 Chain B: E.238, H.243, K.244, Y.246 36 PLIP interactions: 31 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.169, A:A.186 Hydrogen bonds: A:G.129, A:G.129, A:A.131, A:D.184, A:D.184, A:D.184, A:A.186, A:G.323, A:K.325, A:K.325, A:G.326, B:E.238 Water bridges: A:K.4, A:K.4, A:R.50, A:R.50, A:R.50, A:Y.128, A:T.149, A:T.149, A:T.149, A:L.182, A:D.184, A:D.184, A:W.320, A:W.320, A:E.324, A:E.324 Salt bridges: A:K.4, A:R.50, B:H.243, B:K.244, B:K.244 pi-Cation interactions: B:H.243 NDP.3: 28 residues within 4Å: Chain A: E.238, H.243, K.244, Y.246 Chain B: K.4, R.50, V.52, H.55, H.127, G.129, I.130, A.131, T.149, S.151, T.167, P.169, L.182, L.183, D.184, M.185, A.186, P.191, W.320, H.322, G.323, E.324, K.325, G.326 34 PLIP interactions: 29 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.169, B:A.186 Hydrogen bonds: B:G.129, B:G.129, B:A.131, B:D.184, B:D.184, B:D.184, B:A.186, B:G.323, B:K.325, B:K.325, B:G.326, A:E.238 Water bridges: B:K.4, B:K.4, B:R.50, B:R.50, B:R.50, B:Y.128, B:L.182, B:D.184, B:D.184, B:D.184, B:W.320, B:W.320, B:E.324, B:E.324 Salt bridges: B:K.4, B:R.50, A:H.243, A:K.244, A:K.244 pi-Cation interactions: A:H.243

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: A.156, P.157, T.158, G.159, G.160, L.231, P.232, F.236 Chain B: H.313, F.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.159 GOL.4: 10 residues within 4Å: Chain A: H.313, F.316 Chain B: A.156, P.157, T.158, G.159, G.160, L.231, P.232, F.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lokanath, N.K. et al., Structure of Malate Dehydrogenase from Pyrococcus horikoshii OT3. To be Published

Release Date

2005-03-29

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Malate dehydrogenase