MolNFT v1 · #52118 · protein
Crystal structure of human peroxisomal DELTA3,5,DELTA2,4-dienoyl CoA isomerase
2VRE · DELTA(3,5)-DELTA(2,4)-dienoyl-CoA isomerase: “Crystal structure of human peroxisomal DELTA3,5,DELTA2,4-dienoyl CoA isomerase”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.85). MolNFT v1 #52118 on GenesisL1: 3D…
- PDB
- 2VRE
- Type
- protein
- Length
- 793 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DELTA(3,5)-DELTA(2,4)-dienoyl-CoA isomerase
- EC
- 5.3.3.-
- UniProt
- Q13011
- Ligands
- CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DELTA(3,5)-DELTA(2,4)-dienoyl-CoA isomerase (EC 5.3.3.-) | protein | 272 | 52% helix, 15% strand | Q13011 |
| B | DELTA(3,5)-DELTA(2,4)-dienoyl-CoA isomerase (EC 5.3.3.-) | protein | 260 | 52% helix, 16% strand | Q13011 |
| C | DELTA(3,5)-DELTA(2,4)-dienoyl-CoA isomerase (EC 5.3.3.-) | protein | 261 | 51% helix, 17% strand | Q13011 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.85 | 0.91 | 78 | empty |
| 2 | 276 | 0.75 | 0.88 | 43 | CL |
| 3 | 293 | 0.74 | 0.86 | 39 | empty |
| 4 | 235 | 0.70 | 0.86 | 29 | empty |
| 5 | 227 | 0.54 | 0.78 | 36 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1833 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1721 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1670 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2VRE · crystal structure of human peroxisomal delta3,5,delta2,4-dienoyl coa isomerase · the same entry in another collection · chain A against A, TM-score 1.00
- Q13011 · AlphaFold monomer V2.0 prediction for DELTA(3,5)-DELTA(2,4)-dienoyl- CoA isomerase… · 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 Q13011
- Elsewhere: RCSB PDB 2VRE · PDBe 2VRE · UniProt Q13011
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