SMTL ID : 4zdb.1

Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-hexamer

Ligands

16 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: 5 residues within 4Å: Chain A: K.277, Y.278, D.281 Chain C: Y.245, P.247 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: S.82, G.83, A.226, E.227 Ligands: SO4.4 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: I.45, P.47 Ligands: SO4.3 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain B: S.82, G.83, S.224, N.225, A.226, E.227 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 C: S.82, G.83, N.225, A.226, E.227 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: 5 residues within 4Å: Chain D: K.277, Y.278, D.281 Chain F: Y.245, P.247 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain D: S.82, G.83, A.226, E.227 Ligands: SO4.22 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain D: I.45, P.47 Ligands: SO4.21 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain E: R.84, K.163, P.222, S.223, S.224 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 SO4.32: 5 residues within 4Å: Chain F: R.84, K.163, P.222, S.223, S.224 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain F: S.82, G.83, N.225, A.226, E.227 Ligand excluded by PLIP

6 x CAA: ACETOACETYL-COENZYME A(Non-covalent)

CAA.5: 15 residues within 4Å: Chain A: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144, L.167, P.169, N.172, N.201 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.85, A:I.144, A:I.144 Hydrogen bonds: A:S.88, A:A.90, A:F.92, A:K.93, A:N.201 Salt bridges: A:K.93 pi-Stacking: A:F.92 CAA.11: 15 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, L.167, P.169, N.172, N.201 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.85, B:I.144 Hydrogen bonds: B:N.49, B:S.88, B:A.90, B:F.92, B:K.93, B:N.201 Salt bridges: B:K.93 pi-Stacking: B:F.92 CAA.16: 15 residues within 4Å: Chain C: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144, L.167, P.169, N.172, N.201 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.167 Hydrogen bonds: C:N.49, C:S.88, C:A.90, C:F.92, C:K.93, C:N.201 pi-Stacking: C:F.92 CAA.23: 15 residues within 4Å: Chain D: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144, L.167, P.169, N.172, N.201 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.85, D:I.144, D:I.144 Hydrogen bonds: D:S.88, D:A.90, D:F.92, D:K.93, D:N.201 Salt bridges: D:K.93 pi-Stacking: D:F.92 CAA.29: 15 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, L.167, P.169, N.172, N.201 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.85, E:I.144 Hydrogen bonds: E:N.49, E:S.88, E:A.90, E:F.92, E:K.93, E:N.201 Salt bridges: E:K.93 pi-Stacking: E:F.92 CAA.34: 15 residues within 4Å: Chain F: D.48, N.49, L.50, A.52, F.85, S.88, A.90, D.91, F.92, K.93, I.144, L.167, P.169, N.172, N.201 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:L.167 Hydrogen bonds: F:N.49, F:S.88, F:A.90, F:F.92, F:K.93, F:N.201 pi-Stacking: F:F.92

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.175, E.178, W.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.90, A:R.120, A:I.144, A:L.146 GOL.7: 7 residues within 4Å: Chain A: I.129, L.153, D.155, K.253, K.257, F.264 Chain B: Y.195 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.155, A:K.257, A:K.257, B:Y.195 Water bridges: A:K.253, A:K.253 GOL.8: 4 residues within 4Å: Chain A: E.29, K.30, I.45, N.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.29, A:E.29 GOL.12: 11 residues within 4Å: Chain B: G.89, A.90, F.117, R.120, I.144, G.145, L.146, F.170, L.175, E.178, W.279 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.90, B:R.120, B:I.144, B:L.146 GOL.13: 7 residues within 4Å: Chain B: I.129, L.153, D.155, K.253, K.257, F.264 Chain C: Y.195 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.155, B:K.257, B:K.257, C:Y.195 Water bridges: B:K.253, B:K.253 GOL.17: 9 residues within 4Å: Chain C: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.175, E.178 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.90, C:R.120, C:L.146 GOL.18: 7 residues within 4Å: Chain A: Y.195 Chain C: I.129, L.153, D.155, K.253, K.257, F.264 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.155, C:K.257, A:Y.195 Water bridges: C:K.253, C:K.253 GOL.24: 10 residues within 4Å: Chain D: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.175, E.178, W.279 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.90, D:R.120, D:I.144, D:L.146 GOL.25: 7 residues within 4Å: Chain D: I.129, L.153, D.155, K.253, K.257, F.264 Chain E: Y.195 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.155, D:K.257, D:K.257 Water bridges: D:K.253, D:K.253 GOL.26: 4 residues within 4Å: Chain D: E.29, K.30, I.45, N.46 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.29, D:E.29 GOL.30: 11 residues within 4Å: Chain E: G.89, A.90, F.117, R.120, I.144, G.145, L.146, F.170, L.175, E.178, W.279 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:A.90, E:R.120, E:I.144, E:L.146 GOL.31: 7 residues within 4Å: Chain E: I.129, L.153, D.155, K.253, K.257, F.264 Chain F: Y.195 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.155, E:K.257, E:K.257 Water bridges: E:K.253, E:K.253 GOL.35: 9 residues within 4Å: Chain F: G.89, A.90, F.117, R.120, G.145, L.146, F.170, L.175, E.178 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:A.90, F:R.120, F:L.146 GOL.36: 7 residues within 4Å: Chain D: Y.195 Chain F: I.129, L.153, D.155, K.253, K.257, F.264 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.155, F:K.257 Water bridges: F:K.253, F:K.253

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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