SMTL ID : 5ujk.1

Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: G.10, A.11, G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.99, I.119, T.120, N.121, L.123, M.144, A.145, L.148, H.176, A.231, P.235 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.14, A:I.119, A:L.148, A:P.235 Hydrogen bonds: A:A.11, A:G.12, A:Q.13, A:I.14, A:I.35, A:G.80, A:I.119, A:N.121 Water bridges: A:G.15, A:A.79, A:N.96 NAD.5: 23 residues within 4Å: Chain B: G.10, A.11, G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.99, I.119, T.120, N.121, L.123, M.144, A.145, L.148, H.176, A.231, P.235 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.14, B:I.119, B:L.148, B:P.235 Hydrogen bonds: B:A.11, B:G.12, B:Q.13, B:I.14, B:I.35, B:G.80, B:I.119, B:N.121 Water bridges: B:G.15, B:A.79, B:N.96 NAD.9: 23 residues within 4Å: Chain C: G.10, A.11, G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.99, I.119, T.120, N.121, L.123, M.144, A.145, L.148, H.176, A.231, P.235 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.14, C:I.119, C:L.148, C:P.235 Hydrogen bonds: C:A.11, C:G.12, C:Q.13, C:I.14, C:I.35, C:G.80, C:I.119, C:N.121 Water bridges: C:G.15, C:A.79, C:N.96 NAD.13: 23 residues within 4Å: Chain D: G.10, A.11, G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.99, I.119, T.120, N.121, L.123, M.144, A.145, L.148, H.176, A.231, P.235 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.14, D:I.119, D:L.148, D:P.235 Hydrogen bonds: D:A.11, D:G.12, D:Q.13, D:I.14, D:I.35, D:G.80, D:I.119, D:N.121 Water bridges: D:G.15, D:A.79, D:N.96

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: E.287 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.287, A:E.287, H2O.8, H2O.9 CA.3: 1 residues within 4Å: Chain A: E.166 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.7, H2O.20, H2O.23, H2O.27, H2O.40 CA.6: 1 residues within 4Å: Chain B: E.287 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.287, B:E.287, H2O.20, H2O.20 CA.7: 1 residues within 4Å: Chain B: E.166 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.9, H2O.18, H2O.29, H2O.35, H2O.38 CA.10: 1 residues within 4Å: Chain C: E.287 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.287, C:E.287, H2O.31, H2O.31 CA.11: 1 residues within 4Å: Chain C: E.166 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.5, H2O.17, H2O.29, H2O.43 CA.14: 1 residues within 4Å: Chain D: E.287 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.287, D:E.287, H2O.42, H2O.42 CA.15: 1 residues within 4Å: Chain D: E.166 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.6, H2O.12, H2O.16, H2O.32, H2O.40

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

CL.4: 2 residues within 4Å: Chain A: R.154, R.252 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.154, R.252 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: R.154, R.252 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: R.154, R.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez, J.M. et al., Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2017-02-08

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Malate dehydrogenase

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