SMTL ID : 5ugr.1

Malyl-CoA lyase from Methylobacterium extorquens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.45, A:E.140, A:D.167, H2O.2, H2O.5, H2O.7 MG.4: 4 residues within 4Å: Chain B: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.45, B:E.140, B:D.167, H2O.17, H2O.20, H2O.22 MG.7: 4 residues within 4Å: Chain C: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.45, C:E.140, C:D.167, H2O.32, H2O.35, H2O.37 MG.10: 4 residues within 4Å: Chain D: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.45, D:E.140, D:D.167, H2O.47, H2O.50, H2O.52 MG.13: 4 residues within 4Å: Chain E: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.45, E:E.140, E:D.167, H2O.62, H2O.65, H2O.67 MG.16: 4 residues within 4Å: Chain F: E.44, D.45, E.140, D.167 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.45, F:E.140, F:D.167, H2O.77, H2O.80, H2O.82

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

CL.2: 5 residues within 4Å: Chain A: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain D: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain E: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain F: G.164, V.165, A.166, D.167, P.228 Ligand excluded by PLIP

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 3 residues within 4Å: Chain A: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.127, A:K.127 1PE.6: 3 residues within 4Å: Chain B: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.127, B:K.127 1PE.9: 3 residues within 4Å: Chain C: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.127, C:K.127 1PE.12: 3 residues within 4Å: Chain D: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.127, D:K.127 1PE.15: 3 residues within 4Å: Chain E: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.127, E:K.127 1PE.18: 3 residues within 4Å: Chain F: E.94, A.126, K.127 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.127, F:K.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez, J.M. et al., Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift. Acta Crystallogr F Struct Biol Commun (2017)

Release Date

2017-02-08

Peptides

Malyl-CoA lyase/beta-methylmalyl-CoA lyase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Malyl-CoA lyase/beta-methylmalyl-CoA lyase