SMTL ID : 4zde.1

Crystal structure of yeast D3,D2-enoyl-CoA isomerase F268A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: G.89, A.90, F.117, R.120, G.145, L.146, L.173, L.175, E.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.90, A:R.120, A:L.146, A:E.178 GOL.7: 12 residues within 4Å: Chain B: G.89, A.90, F.92, F.117, R.120, G.145, L.146, F.170, L.173, L.175, E.178, W.279 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.90, B:R.120, B:L.146, B:E.178 Water bridges: B:S.88 GOL.12: 10 residues within 4Å: Chain C: G.89, A.90, F.92, F.117, R.120, G.145, L.146, F.170, L.175, E.178 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.90, C:R.120, C:L.146, C:E.178 Water bridges: C:S.88, C:A.90 GOL.18: 9 residues within 4Å: Chain D: G.89, A.90, F.117, R.120, G.145, L.146, L.173, L.175, E.178 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.90, D:R.120, D:L.146, D:E.178 GOL.24: 12 residues within 4Å: Chain E: G.89, A.90, F.92, F.117, R.120, G.145, L.146, F.170, L.173, L.175, E.178, W.279 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:A.90, E:R.120, E:L.146, E:E.178 Water bridges: E:S.88 GOL.29: 10 residues within 4Å: Chain F: G.89, A.90, F.92, F.117, R.120, G.145, L.146, F.170, L.175, E.178 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:A.90, F:R.120, F:L.146, F:E.178 Water bridges: F:S.88, F:A.90

28 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: Y.245, P.247 Chain B: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: K.277, Y.278, D.281 Chain C: Y.245 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: E.29, I.45, N.46 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: S.82, G.83, A.226, E.227 Ligands: SO4.10 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: I.45, P.47 Ligands: SO4.9 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: E.29, K.30, I.45, N.46 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain C: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain C: S.32, H.43, I.45 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: Y.245, P.247 Chain C: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: E.29, K.30, I.45, N.46 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain D: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain D: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain D: Y.245, P.247 Chain E: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain D: K.277, Y.278, D.281 Chain F: Y.245 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: E.29, I.45, N.46 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain E: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain E: S.82, G.83, A.226, E.227 Ligands: SO4.27 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain E: I.45, P.47 Ligands: SO4.26 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain E: E.29, K.30, I.45, N.46 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain F: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain F: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain F: S.32, H.43, I.45 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain E: Y.245, P.247 Chain F: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain F: E.29, K.30, I.45, N.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Onwukwe, G.U. et al., Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-11-11

Peptides

3,2-trans-enoyl-CoA isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

3,2-trans-enoyl-CoA isomerase