SMTL ID : 5kka.1

E. coli malate dehydrogenase with the inhibitor 6DHNAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 6V0: [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

6V0.1: 29 residues within 4Å: Chain A: L.6, G.7, A.9, G.10, G.11, I.12, G.13, Y.33, D.34, I.35, A.36, S.76, A.77, G.78, N.94, I.97, N.100, L.101, I.117, T.118, N.119, V.121, V.146, L.149, H.177, S.222, A.223, T.224, M.227 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.12, A:L.149 Hydrogen bonds: A:G.7, A:G.11, A:I.12, A:D.34, A:D.34, A:I.35, A:G.78, A:N.94, A:N.100, A:I.117, A:N.119, A:N.119, A:H.177 Water bridges: A:G.10, A:G.13, A:S.222, A:S.222, A:S.222 6V0.2: 30 residues within 4Å: Chain B: L.6, G.7, A.9, G.10, G.11, I.12, G.13, Y.33, D.34, I.35, A.36, S.76, A.77, G.78, V.79, N.94, I.97, N.100, L.101, I.117, T.118, N.119, V.121, V.146, L.149, H.177, S.222, A.223, T.224, M.227 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.12 Hydrogen bonds: B:G.7, B:G.11, B:I.12, B:D.34, B:D.34, B:I.35, B:G.78, B:N.100, B:I.117, B:N.119, B:N.119, B:H.177 Water bridges: B:G.10, B:G.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaupre, B.A. et al., Ligand binding phenomena that pertain to the metabolic function of renalase. Arch.Biochem.Biophys. (2016)

Release Date

2016-11-02

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase

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