SMTL ID : 4wlu.1

Crystal structure of L-malate and NAD bound MDH2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

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

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

NAD.2: 26 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, H.202, A.249, T.250, M.253 Ligands: LMR.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.38, A:I.142, A:M.253 Hydrogen bonds: A:S.35, A:G.37, A:I.38, A:I.60, A:G.103, A:V.104, A:N.119, A:N.144, A:N.144, A:V.171 Water bridges: A:G.36, A:G.39, A:Y.58 NAD.4: 26 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, 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: LMR.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.38, B:I.142, B:M.253 Hydrogen bonds: B:S.35, B:G.37, B:I.38, B:I.60, B:G.103, B:V.104, B:V.104, B:N.119, B:N.144, B:N.144, B:V.171 Water bridges: B:G.36, B:G.39 NAD.6: 25 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, I.142, N.144, V.146, V.171, H.202, A.249, T.250, M.253 Ligands: LMR.5 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.38, C:I.142, C:M.253 Hydrogen bonds: C:S.35, C:G.37, C:I.38, C:I.60, C:G.103, C:V.104, C:V.104, C:N.119, C:N.144, C:N.144, C:V.171 Water bridges: C:S.248 NAD.8: 25 residues within 4Å: Chain D: 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, I.142, N.144, V.146, V.171, H.202, S.248, A.249, T.250, M.253 Ligands: LMR.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.38, D:I.142, D:M.253 Hydrogen bonds: D:S.35, D:G.37, D:I.38, D:G.103, D:V.104, D:N.119, D:N.144, D:N.144, D:V.171 Water bridges: D:G.36, D:G.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eo, Y.M. et al., Crystal structure of L-malate and 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

Related Entries With Identical Sequence