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The crystal structure of human peroxisomal DELTA3, DELTA2 enoyl CoA isomerase (peci)
Analyse The crystal structure of human peroxisomal DELTA3, DELTA2 enoyl CoA isomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F6Q
- Type
- protein
- Length
- 740 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal 3,2-trans-enoyl-CoA isomerase
- EC
- 5.3.3.8
- UniProt
- O75521
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 247 | 50% helix, 18% strand | O75521 |
| B | Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 252 | 54% helix, 17% strand | O75521 |
| C | Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) | protein | 241 | 53% helix, 17% strand | O75521 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.86 | 0.90 | 67 | empty |
| 2 | 397 | 0.71 | 0.82 | 51 | empty |
| 3 | 394 | 0.67 | 0.79 | 36 | empty |
| 4 | 240 | 0.63 | 0.82 | 39 | TRS |
| 5 | 228 | 0.60 | 0.80 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1172 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1105 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2F6Q · The crystal structure of human peroxisomal delta3, delta2 enoyl CoA isomerase (PECI) · the same entry in another collection · chain A against A, TM-score 1.00
- O75521 · AlphaFold monomer V2.0 prediction for enoyl-CoA delta isomerase 2 (O75521) · 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 O75521
- Elsewhere: RCSB PDB 2F6Q · PDBe 2F6Q · UniProt O75521
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