SMTL ID : 4l9z.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-hexamer

Ligands

6 x COA: COENZYME A(Non-covalent)

COA.1: 15 residues within 4Å: Chain A: F.40, G.41, P.42, R.45, L.48, K.51, M.52, S.67, R.97, I.272, H.273, P.274 Chain C: L.318, D.320 Ligands: OXL.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.40, A:R.45, A:S.67, A:I.272 Water bridges: A:K.51, A:K.51 Salt bridges: A:K.51, A:H.273 COA.4: 18 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, W.270, I.272, H.273, P.274 Ligands: OXL.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.40, B:R.45, B:S.67, B:I.272 Salt bridges: B:R.45, B:K.51, B:H.273 COA.7: 18 residues within 4Å: Chain B: V.313, L.318, D.320 Chain C: F.40, G.41, P.42, R.45, L.48, K.51, M.52, D.63, S.67, R.97, W.270, I.272, H.273, P.274 Ligands: OXL.8 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.318 Hydrogen bonds: C:F.40, C:S.67, C:I.272 Water bridges: C:R.45, C:K.51, C:K.51 Salt bridges: C:R.45, C:K.51, C:H.273 COA.10: 19 residues within 4Å: Chain D: F.40, G.41, P.42, R.45, L.48, K.51, M.52, D.63, S.67, R.97, F.248, W.270, I.272, H.273, P.274 Chain F: V.313, L.318, D.320 Ligands: OXL.11 11 PLIP interactions: 1 interactions with chain F, 10 interactions with chain D Hydrophobic interactions: F:L.318, D:F.248 Hydrogen bonds: D:F.40, D:R.45, D:K.51, D:S.67, D:I.272 Water bridges: D:R.45 Salt bridges: D:R.45, D:K.51, D:H.273 COA.13: 18 residues within 4Å: Chain D: V.313, L.318, D.320 Chain E: F.40, G.41, P.42, R.45, L.48, K.51, M.52, D.63, S.67, R.97, W.270, I.272, H.273, P.274 Ligands: OXL.14 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:F.40, E:K.51, E:S.67, E:I.272 Salt bridges: E:R.45, E:K.51, E:H.273 Hydrophobic interactions: D:L.318 COA.16: 18 residues within 4Å: Chain E: V.313, L.318, D.320 Chain F: F.40, G.41, P.42, R.45, L.48, K.51, M.52, D.63, S.67, R.97, W.270, I.272, H.273, P.274 Ligands: OXL.17 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:F.40, F:R.45, F:S.67, F:I.272 Salt bridges: F:H.273

6 x OXL: OXALATE ION(Non-covalent)

OXL.2: 10 residues within 4Å: Chain A: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.1, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.188, A:D.189 Water bridges: A:R.97, A:R.97 Salt bridges: A:R.97 OXL.5: 12 residues within 4Å: Chain A: A.322 Chain B: R.97, I.160, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.4, MG.6 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Water bridges: A:D.320, B:D.66, B:R.97, B:R.97 Hydrogen bonds: B:E.162, B:A.188, B:D.189 Salt bridges: B:R.97 OXL.8: 11 residues within 4Å: Chain B: A.322 Chain C: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.7, MG.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.188, C:D.189 Water bridges: C:R.97, B:D.320 Salt bridges: C:R.97 OXL.11: 10 residues within 4Å: Chain D: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.10, MG.12 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.188, D:D.189 Water bridges: D:R.97, D:R.97, D:E.162 Salt bridges: D:R.97 OXL.14: 12 residues within 4Å: Chain D: A.322 Chain E: R.97, I.160, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.13, MG.15 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.188, E:D.189, E:D.189, E:D.189 Water bridges: E:R.97, E:R.97, E:E.162, E:D.189 Salt bridges: E:R.97 OXL.17: 11 residues within 4Å: Chain E: A.322 Chain F: R.97, E.162, G.186, A.187, A.188, D.189, P.244, W.270 Ligands: COA.16, MG.18 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:A.188, F:D.189, F:D.189, F:D.189 Water bridges: F:R.97, F:R.97, F:E.162, F:D.189 Salt bridges: F:R.97

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.66, E.162, D.189 Ligands: OXL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.162, A:D.189, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.66, E.162, D.189 Ligands: OXL.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.162, B:D.189, H2O.18, H2O.18 MG.9: 4 residues within 4Å: Chain C: D.66, E.162, D.189 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.162, C:D.189, H2O.34, H2O.50 MG.12: 4 residues within 4Å: Chain D: D.66, E.162, D.189 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.162, D:D.189, H2O.51, H2O.51 MG.15: 5 residues within 4Å: Chain E: D.66, R.97, E.162, D.189 Ligands: OXL.14 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.162, E:D.189, H2O.66, H2O.66 MG.18: 5 residues within 4Å: Chain F: D.66, R.97, E.162, D.189 Ligands: OXL.17 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.162, F:D.189, H2O.82, H2O.82

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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