MolNFT v1 · #112173 · protein
Yeast enoyl-CoA isomerase (SCECI2) complexed with acetoacetyl-CoA
4ZDB · 3,2-trans-enoyl-CoA isomerase: “Yeast enoyl-CoA isomerase (SCECI2) complexed with acetoacetyl-CoA”. X-ray diffraction, 2 ligands (CAA, SO4), 11 pockets (best druggability 0.79). MolNFT v1 #112173 on GenesisL1: 3D structure, binding…
- PDB
- 4ZDB
- Type
- protein
- Length
- 791 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,2-trans-enoyl-CoA isomerase
- EC
- 5.3.3.8
- UniProt
- Q05871
- Ligands
- CAA, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 267 | 52% helix, 15% strand | Q05871 |
| B | 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 261 | 53% helix, 16% strand | Q05871 |
| C | 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 263 | 52% helix, 16% strand | Q05871 |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B
- GOL · Glycerol · additive · 7 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 | 808 | 0.79 | 0.82 | 83 | empty |
| 2 | 94 | 0.76 | 0.97 | 21 | GOL |
| 3 | 91 | 0.75 | 0.96 | 20 | GOL |
| 4 | 91 | 0.74 | 0.96 | 21 | GOL |
| 5 | 242 | 0.59 | 0.80 | 44 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1270 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1262 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1255 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (artifact).
Compared structures
- 4ZDB · Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA · the same entry in another collection · chain B against B, 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 B 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 4ZDB · PDBe 4ZDB · UniProt Q05871
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