Research workbench
The structure of yeast DELTA3-DELTA2-enoyl-CoA isomerase complexed with octanoyl-CoA
Analyse The structure of yeast DELTA3-DELTA2-enoyl-CoA isomerase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K39
- Type
- protein
- Length
- 806 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D3,D2-enoyl CoA isomerase ECI1
- EC
- 5.3.3.8
- UniProt
- Q05871
- Ligands
- CO8, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D3,D2-enoyl CoA isomerase ECI1 (EC 5.3.3.8) | protein | 269 | 50% helix, 15% strand | Q05871 |
| B | D3,D2-enoyl CoA isomerase ECI1 (EC 5.3.3.8) | protein | 271 | 51% helix, 16% strand | Q05871 |
| C | D3,D2-enoyl CoA isomerase ECI1 (EC 5.3.3.8) | protein | 266 | 53% helix, 16% strand | Q05871 |
Ligands and binding sites
- CO8 · Octanoyl-coenzyme A · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.78 | 0.82 | 75 | empty |
| 2 | 100 | 0.76 | 0.97 | 18 | empty |
| 3 | 98 | 0.76 | 0.96 | 19 | empty |
| 4 | 88 | 0.74 | 0.97 | 18 | empty |
| 5 | 312 | 0.68 | 0.82 | 40 | CO8 |
Interfaces
3 interfaces between chains.
- B–C · 1277 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1267 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1265 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1K39 · The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA · the same entry in another collection · chain A against A, TM-score 1.00
- Q05871 · AlphaFold monomer V2.0 prediction for 3,2-trans-enoyl-CoA isomerase (Q05871) · a predicted model of the same protein · chain C against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q05871
- Elsewhere: RCSB PDB 1K39 · PDBe 1K39 · UniProt Q05871
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