SMTL ID : 2dfd.3 (2 other biounits)

Crystal Structure of Human Malate Dehydrogenase Type 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 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 MLT.11: 10 residues within 4Å: Chain C: R.108, R.114, N.146, R.180, H.204, G.238, V.242, S.250, A.251 Ligands: NAD.14 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.114, C:N.146, C:H.204 Water bridges: C:R.180, C:G.238, C:S.250 Salt bridges: C:R.108, C:R.114, C:R.114, C:R.180, C:H.204 MLT.16: 9 residues within 4Å: Chain D: R.108, R.114, N.146, R.180, H.204, G.238, S.250, A.251 Ligands: NAD.19 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.114, D:N.146, D:H.204 Water bridges: D:R.180, D:G.238, D:S.250, D:S.250, D:A.251 Salt bridges: D:R.108, D:R.114, D:R.114, D:R.180, D:H.204

7 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 CL.12: 2 residues within 4Å: Chain C: R.114, A.205 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: K.283, S.284, Q.285 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain D: R.114 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain D: V.220, F.222 Ligand excluded by PLIP

4 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 NAD.14: 28 residues within 4Å: Chain C: 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.11 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.40, C:I.144, C:M.255 Hydrogen bonds: C:S.37, C:G.39, C:I.40, C:I.62, C:G.105, C:V.106, C:N.121, C:I.144, C:N.146, C:N.146 Water bridges: C:G.38, C:Y.60, C:S.250, C:S.250 NAD.19: 27 residues within 4Å: Chain D: 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.16 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.40, D:I.144, D:M.255 Hydrogen bonds: D:S.37, D:G.39, D:I.40, D:I.62, D:G.105, D:V.106, D:N.121, D:I.144, D:N.146, D:N.146 Water bridges: D:G.38, D:G.41, D:S.250, D:S.250, D:S.250, D:S.250, A:K.109

3 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 HIS.15: 8 residues within 4Å: Chain C: N.182, P.193, A.194, V.196, N.197, Y.257, R.261 Chain D: E.76 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: H.15, H.15, C:N.197 Water bridges: C:N.182

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Malate dehydrogenase

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