SMTL ID : 4wlo.1

Crystal structure of oxaloacetate and NADH bound MDH2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 27 residues within 4Å: Chain A: G.33, S.35, G.36, G.37, I.38, Y.58, D.59, I.60, P.101, A.102, G.103, V.104, P.105, L.115, N.119, I.122, L.126, I.142, N.144, V.146, V.171, L.174, H.202, A.249, T.250, M.253 Ligands: OAA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.142 Hydrogen bonds: A:S.35, A:G.37, A:I.38, A:I.60, A:G.103, A:V.104, A:N.119, A:I.142, A:N.144, A:N.144 NAI.3: 25 residues within 4Å: Chain B: S.35, G.36, G.37, I.38, Y.58, D.59, I.60, P.101, A.102, G.103, V.104, P.105, L.115, N.119, I.122, L.126, I.142, N.144, V.146, V.171, H.202, A.249, T.250, M.253 Ligands: OAA.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.38, B:I.142 Hydrogen bonds: B:G.33, B:S.35, B:G.37, B:I.38, B:G.103, B:V.104, B:N.119, B:I.142, B:N.144, B:N.144 Water bridges: B:G.36, B:G.39, B:Y.58 NAI.5: 26 residues within 4Å: Chain C: S.35, G.36, G.37, I.38, Y.58, D.59, I.60, P.101, A.102, G.103, V.104, P.105, L.115, N.119, I.122, L.126, I.142, N.144, V.146, V.171, H.202, S.248, A.249, T.250, M.253 Ligands: OAA.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.38, C:M.253 Hydrogen bonds: C:S.35, C:S.35, C:G.37, C:I.38, C:G.103, C:V.104, C:V.104, C:N.119, C:I.142, C:N.144, C:N.144 NAI.7: 28 residues within 4Å: Chain D: G.33, S.35, G.36, G.37, I.38, Y.58, D.59, I.60, P.101, A.102, G.103, V.104, P.105, L.115, N.119, I.122, L.126, I.142, A.143, N.144, V.146, V.171, H.202, S.248, A.249, T.250, M.253 Ligands: OAA.8 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.38 Hydrogen bonds: D:S.35, D:G.37, D:I.38, D:I.60, D:G.103, D:V.104, D:N.119, D:I.142, D:N.144, D:N.144

4 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 9 residues within 4Å: Chain A: R.106, R.112, N.144, R.178, H.202, G.236, S.248, A.249 Ligands: NAI.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.112, A:N.144, A:S.248 Salt bridges: A:R.106, A:R.112, A:R.112, A:R.178, A:H.202 OAA.4: 9 residues within 4Å: Chain B: R.106, R.112, N.144, R.178, H.202, G.236, S.248, A.249 Ligands: NAI.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.112, B:N.144, B:S.248 Salt bridges: B:R.106, B:R.112, B:R.112, B:R.178, B:H.202 OAA.6: 9 residues within 4Å: Chain C: R.106, R.112, N.144, R.178, H.202, G.236, S.248, A.249 Ligands: NAI.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.106, C:R.112, C:N.144, C:S.248 Salt bridges: C:R.106, C:R.112, C:R.112, C:R.178, C:H.202 OAA.8: 10 residues within 4Å: Chain D: R.106, R.112, N.144, L.174, R.178, H.202, G.236, S.248, A.249 Ligands: NAI.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.112, D:N.144 Salt bridges: D:R.106, D:R.112, D:R.112, D:R.178, D:H.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eo, Y.M. et al., Crystal structure of oxaloacetate and NADH bound MDH2. To Be Published

Release Date

2015-11-25

Peptides

Malate dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Malate dehydrogenase, mitochondrial

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