SMTL ID : 4wlv.1

Crystal structure of NAD bound MDH2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 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, A.143, N.144, V.146, V.171, H.202, A.249, T.250, M.253 Ligands: PO4.2, PO4.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.38, A:I.142 Hydrogen bonds: 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 Water bridges: A:G.36, A:G.39 NAD.4: 27 residues within 4Å: Chain B: 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, N.119, I.122, L.126, I.142, A.143, N.144, V.171, H.202, S.248, A.249, T.250, M.253 Ligands: PO4.5, PO4.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.35, B:G.37, B:I.38, B:I.60, B:G.103, B:V.104, B:N.119, B:N.144, B:N.144, B:V.171 NAD.7: 28 residues within 4Å: Chain C: 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, A.249, T.250, M.253 Ligands: PO4.8, PO4.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.35, C:G.37, C:I.38, C:I.60, C:G.103, C:V.104, C:N.119, C:I.142, C:N.144, C:N.144 Water bridges: C:G.36, C:G.39 NAD.10: 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, A.249, T.250, M.253 Ligands: PO4.11, PO4.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.38, D:I.142, D:M.253 Hydrogen bonds: D:G.37, D:I.38, D:I.60, D:G.103, D:G.103, D:V.104, D:N.119, D:I.142, D:N.144, D:N.144

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: P.105, R.106, R.112, L.115, N.144, V.240, S.248 Ligands: NAD.1, PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.106, A:N.144, A:S.248 Salt bridges: A:R.106 PO4.3: 10 residues within 4Å: Chain A: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: NAD.1, PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.106, A:N.144 Water bridges: A:R.112 Salt bridges: A:R.112, A:R.178, A:H.202 PO4.5: 7 residues within 4Å: Chain B: P.105, R.106, L.115, N.144, S.248 Ligands: NAD.4, PO4.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:N.144, B:S.248, B:S.248 Salt bridges: B:R.106 PO4.6: 9 residues within 4Å: Chain B: R.106, R.112, N.144, L.174, R.178, H.202, G.236 Ligands: NAD.4, PO4.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.106, B:N.144, B:G.236 Salt bridges: B:R.112, B:R.178, B:H.202 PO4.8: 9 residues within 4Å: Chain C: P.105, R.106, R.112, L.115, N.144, V.240, S.248 Ligands: NAD.7, PO4.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.106, C:N.144, C:S.248, C:S.248 Salt bridges: C:R.106 PO4.9: 9 residues within 4Å: Chain C: R.106, R.112, N.144, R.178, H.202, G.236, A.249 Ligands: NAD.7, PO4.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.106, C:N.144 Salt bridges: C:R.112, C:R.178, C:H.202 PO4.11: 10 residues within 4Å: Chain D: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: NAD.10, PO4.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.106, D:N.144 Salt bridges: D:R.112, D:R.178, D:H.202 PO4.12: 8 residues within 4Å: Chain D: P.105, R.106, R.112, L.115, N.144, S.248 Ligands: NAD.10, PO4.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.106, D:N.144, D:S.248 Salt bridges: D:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eo, Y.M. et al., Crystal structure of NAD 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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