SMTL ID : 4l9y.1

Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and propionyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.65, D.66, E.162, D.189 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.162, A:D.189, H2O.1, H2O.1, H2O.2, H2O.4 MG.5: 5 residues within 4Å: Chain B: D.66, E.162, D.189 Ligands: 1VU.3, GLV.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.162, B:D.189, H2O.9, H2O.17 MG.6: 4 residues within 4Å: Chain C: E.65, D.66, E.162, D.189 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.162, C:D.189, H2O.18, H2O.18, H2O.18, H2O.28 MG.9: 5 residues within 4Å: Chain D: D.66, K.128, E.162, D.189 Ligands: GLV.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.162, D:D.189, H2O.30, H2O.39 MG.10: 5 residues within 4Å: Chain E: E.65, D.66, R.97, E.162, D.189 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.162, E:D.189, H2O.40, H2O.40, H2O.48, H2O.50 MG.12: 4 residues within 4Å: Chain F: E.65, D.66, E.162, D.189 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.162, F:D.189, H2O.50, H2O.50, H2O.51, H2O.59

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

CL.2: 5 residues within 4Å: Chain A: G.186, A.187, A.188, D.189, P.244 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: G.186, A.187, A.188, D.189, P.244 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain E: G.186, A.187, A.188, D.189, P.244 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain F: G.186, A.187, A.188, D.189, P.244 Ligand excluded by PLIP

1 x 1VU: propionyl Coenzyme A(Non-covalent)

1VU.3: 22 residues within 4Å: Chain A: V.313, L.318, D.320 Chain B: F.40, G.41, P.42, R.45, L.48, K.51, M.52, D.63, S.67, R.97, A.188, I.201, P.244, W.270, I.272, H.273, P.274 Ligands: GLV.4, MG.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.188, B:I.201, B:P.244, A:L.318 Hydrogen bonds: B:F.40, B:K.51, B:S.67, B:R.97, B:R.97, B:I.272 Salt bridges: B:R.45, B:K.51, B:H.273

2 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.4: 10 residues within 4Å: Chain B: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: 1VU.3, MG.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.97, B:E.162, B:A.188, B:D.189 GLV.8: 9 residues within 4Å: Chain D: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: MG.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.97, D:A.188, D:D.189, D:D.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarzycki, J. et al., The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases. Bmc Struct.Biol. (2013)

Release Date

2013-12-04

Peptides

Malyl-CoA lyase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Malyl-CoA lyase

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