SMTL ID : 1y7t.1

Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 24 residues within 4Å: Chain A: T.10, G.11, A.13, G.14, Q.15, I.16, L.41, E.42, I.43, A.46, V.87, G.88, A.89, Q.112, V.129, G.130, N.131, L.158, S.236, S.237, A.238, A.241 Ligands: TRS.2, TRS.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.43 Hydrogen bonds: A:G.11, A:Q.15, A:Q.15, A:I.16, A:L.41, A:N.131, A:N.131, A:S.236, A:S.237 Water bridges: A:G.17, A:S.237 NDP.4: 25 residues within 4Å: Chain B: T.10, G.11, A.13, G.14, Q.15, I.16, L.41, E.42, I.43, A.46, V.87, G.88, A.89, I.108, Q.112, V.129, G.130, N.131, L.158, S.236, S.237, A.238, A.241 Ligands: TRS.5, TRS.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.43, B:I.108 Hydrogen bonds: B:G.11, B:Q.15, B:Q.15, B:I.16, B:L.41, B:N.131, B:N.131, B:S.236, B:S.237 Water bridges: B:A.13, B:G.14, B:G.17, B:S.237

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 4 residues within 4Å: Chain A: N.131, G.226, S.236 Ligands: NDP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.131 Water bridges: A:R.162, A:G.226, A:G.226, A:A.227, A:S.236, A:S.236, A:S.237 TRS.3: 6 residues within 4Å: Chain A: N.131, L.158, D.159, R.162, H.187 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.131, A:N.131, A:R.162, A:H.187, A:H.187 Water bridges: A:D.159, A:D.159, A:R.162, A:R.162, A:S.188, A:V.222, A:A.223 TRS.5: 6 residues within 4Å: Chain B: N.131, G.226, I.230, S.236 Ligands: NDP.4, TRS.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.131 Water bridges: B:R.162, B:G.226, B:A.227, B:S.236, B:S.236, B:S.237 TRS.6: 8 residues within 4Å: Chain B: N.131, L.158, D.159, R.162, H.187, M.191 Ligands: NDP.4, TRS.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.131, B:N.131, B:R.162, B:H.187 Water bridges: B:D.159, B:V.222, B:S.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomita, T. et al., Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H). Biochem.Biophys.Res.Commun. (2005)

Release Date

2005-08-02

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase

Related Entries With Identical Sequence