MolNFT v1 · #112176 · protein
Crystal structure of yeast D3,D2-enoyl-CoA isomerase F268A mutant
4ZDE · 3,2-trans-enoyl-CoA isomerase: “Crystal structure of yeast D3,D2-enoyl-CoA isomerase F268A mutant”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.78). MolNFT v1 #112176 on GenesisL1: 3D structure, binding sites…
- PDB
- 4ZDE
- Type
- protein
- Length
- 772 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
- SO4
- Pockets
- 12 · best druggability 0.78
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 | 259 | 51% helix, 16% strand | Q05871 |
| B | 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 257 | 52% helix, 16% strand | Q05871 |
| C | 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 256 | 52% helix, 17% strand | Q05871 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.78 | 0.82 | 72 | empty |
| 2 | 91 | 0.76 | 0.97 | 19 | empty |
| 3 | 95 | 0.76 | 0.97 | 23 | empty |
| 4 | 89 | 0.75 | 0.97 | 21 | empty |
| 5 | 183 | 0.53 | 0.78 | 33 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1301 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1282 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1275 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4ZDE · Crystal structure of yeast D3,D2-enoyl-CoA isomerase F268A mutant · 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 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 4ZDE · PDBe 4ZDE · UniProt Q05871
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.