SMTL ID : 4cl3.2 (1 other biounit)

1.70 A resolution structure of the malate dehydrogenase from Chloroflexus aurantiacus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

11 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.1: 1 residues within 4Å: Chain A: E.165 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.165, H2O.11, H2O.12, H2O.12, H2O.18 CD.2: 2 residues within 4Å: Chain A: D.33 Ligands: ACT.8 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.33, H2O.3, H2O.18, ACT.8 CD.3: 1 residues within 4Å: Chain A: D.90 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.90, H2O.7, H2O.18 CD.4: 2 residues within 4Å: Chain A: E.159, R.201 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.159, A:E.159, H2O.11, H2O.11 CD.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CD.12: 1 residues within 4Å: Chain B: E.165 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.165, B:E.165, H2O.15, H2O.15, H2O.36 CD.13: 3 residues within 4Å: Chain B: D.33 Ligands: ACT.20, PEG.21 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.33 CD.14: 2 residues within 4Å: Chain B: E.89, D.90 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.89, B:D.90, H2O.26 CD.15: 1 residues within 4Å: Chain B: D.200 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.200, B:D.200, H2O.32 CD.16: 1 residues within 4Å: Chain B: E.36 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.36, B:E.36 CD.17: 1 residues within 4Å: Chain B: D.177 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.177, B:D.177

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

CL.6: 1 residues within 4Å: Chain A: R.208 Ligand excluded by PLIP

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: P.121, L.122, D.123, A.124, E.178, T.302 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.121, A:T.302 Hydrogen bonds: A:D.123, A:D.123, A:A.124, A:E.178 Water bridges: A:E.178 ACT.8: 9 residues within 4Å: Chain A: I.8, G.9, L.32, D.33, I.34, Y.65, S.78, C.102 Ligands: CD.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.8, A:L.32, A:I.34 Hydrogen bonds: A:I.34 ACT.18: 4 residues within 4Å: Chain B: E.159, I.197, A.198, R.201 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.159, B:R.201 Hydrogen bonds: B:A.198 Water bridges: B:R.201 ACT.19: 6 residues within 4Å: Chain B: W.20, K.24, L.26, A.234, Q.235, E.238 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.235 Salt bridges: B:K.24 ACT.20: 8 residues within 4Å: Chain B: I.8, G.9, L.32, D.33, I.34, Y.65, S.78 Ligands: CD.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.8, B:L.32, B:I.34 Hydrogen bonds: B:I.34, B:S.78 Water bridges: B:S.78

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 6 residues within 4Å: Chain B: F.12, L.220, T.222, G.223, S.224, Y.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.224, B:S.224 Water bridges: B:Y.226 PEG.10: 3 residues within 4Å: Chain A: R.100, E.131, V.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.100, A:R.100, A:V.132 Water bridges: A:R.100 PEG.11: 4 residues within 4Å: Chain A: R.82, G.214, V.217, N.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.214 PEG.21: 6 residues within 4Å: Chain B: A.10, G.11, D.33, V.38, K.42 Ligands: CD.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.42 Water bridges: B:G.11, B:D.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Talon, R. et al., An Experimental Point of View on Hydration/Solvation in Halophilic Proteins. Front.Microbiol. (2014)

Release Date

2014-02-05

Peptides

MALATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

MALATE DEHYDROGENASE

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