SMTL ID : 1xx4.1 (1 other biounit)

Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: L.31, R.75, H.79, E.82 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.75 Salt bridges: A:H.79 PO4.2: 6 residues within 4Å: Chain A: D.189, H.192, R.196 Ligands: PO4.3, ZN.5, ZN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.189, A:D.189, A:R.196 PO4.3: 5 residues within 4Å: Chain A: H.192, R.196 Ligands: PO4.2, ZN.5, ZN.6 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.20, A:H.192, A:R.196 PO4.10: 5 residues within 4Å: Chain B: L.31, R.75, H.79, E.82 Ligands: ZN.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.75 Salt bridges: B:H.79 PO4.11: 6 residues within 4Å: Chain B: D.189, H.192, R.196 Ligands: PO4.12, ZN.14, ZN.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.189, B:D.189, B:R.196 PO4.12: 5 residues within 4Å: Chain B: H.192, R.196 Ligands: PO4.11, ZN.14, ZN.15 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.20, B:H.192, B:R.196 PO4.19: 5 residues within 4Å: Chain C: L.31, R.75, H.79, E.82 Ligands: ZN.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.75 Salt bridges: C:H.79 PO4.20: 6 residues within 4Å: Chain C: D.189, H.192, R.196 Ligands: PO4.21, ZN.23, ZN.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.189, C:D.189, C:R.196 PO4.21: 5 residues within 4Å: Chain C: H.192, R.196 Ligands: PO4.20, ZN.23, ZN.24 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.20, C:H.192, C:R.196

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 3 residues within 4Å: Chain A: H.79, E.82 Ligands: PO4.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.79, A:E.82 ZN.5: 4 residues within 4Å: Chain A: H.192 Ligands: PO4.2, PO4.3, ZN.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.192 ZN.6: 3 residues within 4Å: Ligands: PO4.2, PO4.3, ZN.5 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Chain B: H.79, E.82 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.79, B:E.82 ZN.14: 4 residues within 4Å: Chain B: H.192 Ligands: PO4.11, PO4.12, ZN.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.192 ZN.15: 3 residues within 4Å: Ligands: PO4.11, PO4.12, ZN.14 No protein-ligand interaction detected (PLIP) ZN.22: 3 residues within 4Å: Chain C: H.79, E.82 Ligands: PO4.19 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.79, C:E.82 ZN.23: 4 residues within 4Å: Chain C: H.192 Ligands: PO4.20, PO4.21, ZN.24 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.192 ZN.24: 3 residues within 4Å: Ligands: PO4.20, PO4.21, ZN.23 No protein-ligand interaction detected (PLIP)

9 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.7: 6 residues within 4Å: Chain A: W.84, V.143, F.236, F.239 Ligands: BEN.8, BEN.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:V.143, A:F.236, A:F.239 BEN.8: 8 residues within 4Å: Chain A: W.84, V.143, P.145, D.232, N.235, F.239 Ligands: BEN.7, BEN.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.84, A:V.143, A:P.145, A:F.239, A:F.239 Hydrogen bonds: A:D.232 Water bridges: A:F.146, A:N.235 BEN.9: 7 residues within 4Å: Chain A: W.84, I.142, V.143, F.236, F.239 Ligands: BEN.7, BEN.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.84, A:V.143, A:F.236, A:F.236, A:F.239, A:F.239 BEN.16: 6 residues within 4Å: Chain B: W.84, V.143, F.236, F.239 Ligands: BEN.17, BEN.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.84, B:W.84, B:V.143, B:F.236, B:F.239 BEN.17: 8 residues within 4Å: Chain B: W.84, V.143, P.145, D.232, N.235, F.239 Ligands: BEN.16, BEN.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.84, B:V.143, B:P.145, B:F.239, B:F.239 Hydrogen bonds: B:D.232 Water bridges: B:F.146, B:N.235 BEN.18: 7 residues within 4Å: Chain B: W.84, I.142, V.143, F.236, F.239 Ligands: BEN.16, BEN.17 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.84, B:V.143, B:F.236, B:F.236, B:F.239, B:F.239 BEN.25: 6 residues within 4Å: Chain C: W.84, V.143, F.236, F.239 Ligands: BEN.26, BEN.27 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.84, C:W.84, C:V.143, C:F.236, C:F.239 BEN.26: 8 residues within 4Å: Chain C: W.84, V.143, P.145, D.232, N.235, F.239 Ligands: BEN.25, BEN.27 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.84, C:V.143, C:P.145, C:F.239, C:F.239 Hydrogen bonds: C:D.232 Water bridges: C:F.146, C:N.235 BEN.27: 7 residues within 4Å: Chain C: W.84, I.142, V.143, F.236, F.239 Ligands: BEN.25, BEN.26 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.84, C:V.143, C:F.236, C:F.236, C:F.239, C:F.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hubbard, P.A. et al., Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase. Protein Sci. (2005)

Release Date

2004-11-23

Peptides

3,2-trans-enoyl-CoA isomerase, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

3,2-trans-enoyl-CoA isomerase, mitochondrial

Related Entries With Identical Sequence