SMTL ID : 4zdc.1

Yeast enoyl-CoA isomerase complexed with octanoyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: Y.245, P.247 Chain B: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain B: S.82, G.83, S.224, N.225, A.226, E.227 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: 3 residues within 4Å: Chain B: R.84, K.163, S.223 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain C: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: K.277, Y.278, D.281 Chain C: Y.245, P.247 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain C: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: Y.245, P.247 Chain C: K.277, Y.278 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain D: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain D: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: Y.245, P.247 Chain E: K.277, Y.278, D.281 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain E: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain E: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain E: R.84, K.163, S.223 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain F: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain D: K.277, Y.278, D.281 Chain F: Y.245, P.247 Ligand excluded by PLIP SO4.37: 6 residues within 4Å: Chain F: S.82, G.83, S.224, N.225, A.226, E.227 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: Y.245, P.247 Chain F: K.277, Y.278 Ligand excluded by PLIP

6 x CO8: OCTANOYL-COENZYME A(Non-covalent)

CO8.4: 24 residues within 4Å: Chain A: D.48, N.49, L.50, A.52, F.85, S.88, G.89, A.90, D.91, F.92, K.93, N.116, F.117, R.120, N.121, I.144, G.145, L.146, Y.165, P.169, L.173, E.178, F.288 Ligands: GOL.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.85, A:F.117, A:F.117, A:R.120, A:L.146 Hydrogen bonds: A:S.88, A:S.88, A:A.90, A:A.90, A:F.92, A:K.93, A:L.146 CO8.10: 11 residues within 4Å: Chain B: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.85, B:I.144 Hydrogen bonds: B:S.88, B:S.88, B:A.90, B:F.92, B:K.93 CO8.18: 22 residues within 4Å: Chain C: D.48, N.49, L.50, A.52, F.85, S.88, G.89, A.90, D.91, F.92, K.93, N.116, F.117, R.120, N.121, I.144, G.145, L.146, L.173, E.178, F.288 Ligands: GOL.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.85, C:A.90, C:F.117, C:R.120 Hydrogen bonds: C:S.88, C:S.88, C:A.90, C:A.90, C:F.92, C:K.93, C:L.146 CO8.25: 24 residues within 4Å: Chain D: D.48, N.49, L.50, A.52, F.85, S.88, G.89, A.90, D.91, F.92, K.93, N.116, F.117, R.120, N.121, I.144, G.145, L.146, Y.165, P.169, L.173, E.178, F.288 Ligands: GOL.26 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.85, D:F.117, D:F.117, D:R.120, D:L.146 Hydrogen bonds: D:S.88, D:S.88, D:A.90, D:A.90, D:F.92, D:K.93, D:L.146 CO8.31: 11 residues within 4Å: Chain E: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.85, E:I.144 Hydrogen bonds: E:S.88, E:S.88, E:A.90, E:F.92, E:K.93 CO8.39: 22 residues within 4Å: Chain F: D.48, N.49, L.50, A.52, F.85, S.88, G.89, A.90, D.91, F.92, K.93, N.116, F.117, R.120, N.121, I.144, G.145, L.146, L.173, E.178, F.288 Ligands: GOL.41 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.85, F:A.90, F:F.117, F:R.120 Hydrogen bonds: F:S.88, F:S.88, F:A.90, F:A.90, F:F.92, F:K.93, F:L.146

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: G.89, A.90, G.145, L.146, F.170, L.175, E.178, W.279 Ligands: CO8.4 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: I.129, L.153, C.154, K.188, K.257, F.264 Ligand excluded by PLIP GOL.11: 10 residues within 4Å: Chain B: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.173, L.175, E.178 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: I.129, L.153, D.155, K.253, K.257, F.264 Chain C: Y.195 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: H.260 Chain B: H.260 Chain C: H.260 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain C: R.34, E.36, L.234, R.238 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain C: G.89, A.90, F.117, G.145, L.146, F.170, L.175, E.178 Ligands: CO8.18 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain A: Y.195 Chain C: I.129, L.153, D.155, K.253, K.257, F.264 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain D: G.89, A.90, G.145, L.146, F.170, L.175, E.178, W.279 Ligands: CO8.25 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain D: I.129, L.153, C.154, K.188, K.257, F.264 Ligand excluded by PLIP GOL.32: 10 residues within 4Å: Chain E: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.173, L.175, E.178 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain E: I.129, L.153, D.155, K.253, K.257, F.264 Chain F: Y.195 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain D: H.260 Chain E: H.260 Chain F: H.260 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain F: R.34, E.36, L.234, R.238 Ligand excluded by PLIP GOL.41: 9 residues within 4Å: Chain F: G.89, A.90, F.117, G.145, L.146, F.170, L.175, E.178 Ligands: CO8.39 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain D: Y.195 Chain F: I.129, L.153, D.155, K.253, K.257, F.264 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

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