SMTL ID : 4wln.1

Crystal structure of apo MDH2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: P.105, R.106, R.112, L.115, N.144, S.248 Ligands: PO4.2, PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.106, A:N.144, A:S.248, A:S.248 Salt bridges: A:R.106 PO4.2: 10 residues within 4Å: Chain A: I.38, P.101, A.102, G.103, V.104, N.119, I.142, A.143, N.144 Ligands: PO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.103, A:N.119, A:N.144, A:N.144 PO4.3: 9 residues within 4Å: Chain A: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: PO4.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.106, A:N.144 Water bridges: A:R.178, A:R.178 Salt bridges: A:R.112, A:R.178, A:H.202 PO4.4: 9 residues within 4Å: Chain B: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: PO4.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.106, B:N.144 Water bridges: B:R.112, B:S.248 Salt bridges: B:R.112, B:R.178, B:H.202 PO4.5: 11 residues within 4Å: Chain B: I.38, P.101, A.102, G.103, V.104, P.105, N.119, I.142, A.143, N.144 Ligands: PO4.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.103, B:V.104, B:I.142, B:N.144, B:N.144 PO4.6: 7 residues within 4Å: Chain B: P.105, R.106, R.112, N.144, S.248 Ligands: PO4.4, PO4.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:N.144, B:S.248 Salt bridges: B:R.106, B:R.112 PO4.7: 9 residues within 4Å: Chain C: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: PO4.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.144, C:G.236 Water bridges: C:R.112 Salt bridges: C:R.106, C:R.112, C:R.178, C:H.202 PO4.8: 8 residues within 4Å: Chain C: P.105, R.106, R.112, L.115, N.144, S.248 Ligands: PO4.7, PO4.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.106, C:N.144, C:S.248, C:S.248, C:S.248 Salt bridges: C:R.106 PO4.9: 11 residues within 4Å: Chain C: I.38, P.101, A.102, G.103, V.104, P.105, N.119, I.142, A.143, N.144 Ligands: PO4.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.119, C:N.144, C:N.144 Water bridges: C:P.101, C:G.103, C:S.248 PO4.10: 10 residues within 4Å: Chain D: I.38, P.101, A.102, G.103, V.104, N.119, I.142, A.143, N.144 Ligands: PO4.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.102, D:N.144, D:N.144, D:N.144 Water bridges: D:N.119, D:N.119, D:S.248, D:A.249 PO4.11: 7 residues within 4Å: Chain D: P.105, R.106, R.112, N.144, S.248 Ligands: PO4.10, PO4.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.106, D:N.144, D:S.248, D:S.248 Salt bridges: D:R.106 PO4.12: 9 residues within 4Å: Chain D: R.106, R.112, N.144, L.174, R.178, H.202, G.236, A.249 Ligands: PO4.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.106, D:N.144 Water bridges: D:R.112, D:R.178, D:R.178 Salt bridges: 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 apo 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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