SMTL ID : 2dfd.1 (2 other biounits)

Crystal Structure of Human Malate Dehydrogenase Type 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MLT: D-MALATE(Non-covalent)

MLT.1: 11 residues within 4Å: Chain A: R.108, R.114, N.146, L.176, R.180, H.204, G.238, V.242, S.250, A.251 Ligands: NAD.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.114, A:N.146, A:H.204 Water bridges: A:R.180, A:G.238, A:S.250 Salt bridges: A:R.108, A:R.114, A:R.114, A:R.180, A:H.204 MLT.7: 9 residues within 4Å: Chain B: R.108, R.114, N.146, R.180, H.204, G.238, S.250, A.251 Ligands: NAD.9 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.114, B:N.146, B:H.204 Water bridges: B:R.180, B:G.238, B:S.250, B:A.251 Salt bridges: B:R.108, B:R.114, B:R.114, B:R.180, B:H.204

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.114 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: P.167, N.168, K.283 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: V.220, F.222 Ligand excluded by PLIP

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

NAD.4: 28 residues within 4Å: Chain A: G.35, S.37, G.38, G.39, I.40, Y.60, D.61, I.62, P.103, A.104, G.105, V.106, P.107, L.117, N.121, I.124, L.128, I.144, A.145, N.146, V.148, V.173, L.176, H.204, A.251, T.252, M.255 Ligands: MLT.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.40, A:I.144 Hydrogen bonds: A:G.39, A:I.40, A:I.62, A:G.105, A:V.106, A:N.121, A:I.144, A:N.146, A:N.146 Water bridges: A:G.38, A:G.41, A:S.250 NAD.9: 27 residues within 4Å: Chain B: G.35, S.37, G.38, G.39, I.40, Y.60, D.61, I.62, P.103, A.104, G.105, V.106, P.107, L.117, N.121, I.124, L.128, I.144, A.145, N.146, V.148, V.173, H.204, A.251, T.252, M.255 Ligands: MLT.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.40, B:I.144, B:M.255 Hydrogen bonds: B:S.37, B:G.39, B:I.40, B:I.62, B:G.105, B:V.106, B:N.121, B:I.144, B:N.146, B:N.146 Water bridges: B:G.38, B:S.250, B:S.250

2 x HIS: HISTIDINE(Non-covalent)

HIS.5: 8 residues within 4Å: Chain A: N.182, P.193, A.194, V.196, N.197, R.261 Chain B: E.76 Ligands: ALA.6 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:V.196, A:N.197, A:R.261, H.5, H.5 Water bridges: A:N.182, A:Y.257 HIS.10: 7 residues within 4Å: Chain A: E.76 Chain B: N.182, P.193, A.194, V.196, N.197, R.261 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:A.194, B:V.196, B:R.261, H.10 Water bridges: B:R.261

1 x ALA: ALANINE(Non-covalent)

ALA.6: 3 residues within 4Å: Chain A: R.261, S.265 Ligands: HIS.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.261, A:E.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ugochukwu, E. et al., Crystal Structure of Human Malate Dehydrogenase Type 2. To be Published

Release Date

2006-03-28

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase

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