SMTL ID : 4ros.1

Crystal structure of Methylobacterium extorquens malate dehydrogenase complexed with oxaloacetate and adenosine-5-diphosphoribose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: E.287 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.287, H2O.5, H2O.5, H2O.5, H2O.5 CA.2: 2 residues within 4Å: Chain A: E.166 Chain C: G.55 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.166, H2O.1, H2O.4, H2O.17 CA.5: 1 residues within 4Å: Chain B: E.287 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.287, H2O.10, H2O.10, H2O.10, H2O.10 CA.6: 2 residues within 4Å: Chain B: E.166 Chain D: G.55 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.166, H2O.6, H2O.9, H2O.13 CA.9: 1 residues within 4Å: Chain C: E.287 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.287, H2O.15, H2O.15, H2O.15, H2O.15 CA.10: 2 residues within 4Å: Chain A: G.55 Chain C: E.166 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.166, H2O.8, H2O.11, H2O.14 CA.13: 1 residues within 4Å: Chain D: E.287 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.287, H2O.20, H2O.20, H2O.20, H2O.20 CA.14: 2 residues within 4Å: Chain B: G.55 Chain D: E.166 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.166, H2O.3, H2O.16, H2O.19

4 x OAA: OXALOACETATE ION(Non-covalent)

OAA.3: 10 residues within 4Å: Chain A: R.83, R.89, N.121, L.148, R.152, H.176, G.219, S.230, A.231 Ligands: APR.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.121, A:S.230, A:S.230 Water bridges: A:A.231 Salt bridges: A:R.83, A:R.89, A:R.89, A:R.152, A:H.176 OAA.7: 10 residues within 4Å: Chain B: R.83, R.89, N.121, L.148, R.152, H.176, G.219, S.230, A.231 Ligands: APR.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.121, B:S.230, B:S.230 Water bridges: B:A.231 Salt bridges: B:R.83, B:R.89, B:R.89, B:R.152, B:H.176 OAA.11: 10 residues within 4Å: Chain C: R.83, R.89, N.121, L.148, R.152, H.176, G.219, S.230, A.231 Ligands: APR.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.121, C:S.230, C:S.230 Water bridges: C:A.231 Salt bridges: C:R.83, C:R.89, C:R.89, C:R.152, C:H.176 OAA.15: 10 residues within 4Å: Chain D: R.83, R.89, N.121, L.148, R.152, H.176, G.219, S.230, A.231 Ligands: APR.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.121, D:S.230, D:S.230 Water bridges: D:A.231 Salt bridges: D:R.83, D:R.89, D:R.89, D:R.152, D:H.176

4 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.4: 19 residues within 4Å: Chain A: G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.81, P.82, L.92, N.96, V.99, I.119, T.120, N.121 Ligands: OAA.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.12, A:Q.13, A:I.14, A:I.35, A:G.80, A:V.81, A:N.96, A:N.121, A:N.121 Water bridges: A:G.15, A:I.119, A:N.121 APR.8: 19 residues within 4Å: Chain B: G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.81, P.82, L.92, N.96, V.99, I.119, T.120, N.121 Ligands: OAA.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.12, B:Q.13, B:I.14, B:I.35, B:G.80, B:V.81, B:N.96, B:N.121, B:N.121 Water bridges: B:G.15, B:I.119, B:N.121 APR.12: 19 residues within 4Å: Chain C: G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.81, P.82, L.92, N.96, V.99, I.119, T.120, N.121 Ligands: OAA.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.12, C:Q.13, C:I.14, C:I.35, C:G.80, C:V.81, C:N.96, C:N.121, C:N.121 Water bridges: C:G.15, C:I.119, C:N.121 APR.16: 19 residues within 4Å: Chain D: G.12, Q.13, I.14, F.33, D.34, I.35, V.36, T.78, A.79, G.80, V.81, P.82, L.92, N.96, V.99, I.119, T.120, N.121 Ligands: OAA.15 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.12, D:Q.13, D:I.14, D:I.35, D:G.80, D:V.81, D:N.96, D:N.121, D:N.121 Water bridges: D:G.15, D:I.119, D:N.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez, J.M. et al., Crystal structure of Methylobacterium extorquens malate dehydrogenase complexed with oxaloacetate and adenosine-5-diphosphoribose. To be Published

Release Date

2014-12-17

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Malate dehydrogenase

Related Entries With Identical Sequence