SMTL ID : 1xx4.2 (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-dimer

Ligands

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

PO4.1: 11 residues within 4Å: Chain A: L.31, R.75, H.79, E.82 Chain B: R.75, N.76, H.79, E.82 Ligands: ZN.4, PO4.10, ZN.13 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.75, B:N.76, A:R.75 Water bridges: B:N.76, B:N.76 Salt bridges: B:H.79, 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: 11 residues within 4Å: Chain A: R.75, N.76, H.79, E.82 Chain B: L.31, R.75, H.79, E.82 Ligands: PO4.1, ZN.4, ZN.13 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.75, A:R.75, A:N.76 Salt bridges: B:H.79, A:H.79 Water bridges: A:N.76, A:N.76 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

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

ZN.4: 4 residues within 4Å: Chain A: H.79, E.82 Ligands: PO4.1, PO4.10 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: 4 residues within 4Å: Chain B: H.79, E.82 Ligands: PO4.1, 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)

6 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

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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