Research workbench
Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed with 2TRANS-hexenoyl-CoA
Analyse Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZWB
- Type
- protein
- Length
- 1,446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal bifunctional enzyme
- EC
- 4.2.1.17, 5.3.3.8, 1.1.1.35
- UniProt
- P07896
- Ligands
- TC6, SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal bifunctional enzyme (EC 4.2.1.17, 5.3.3.8, 1.1.1.35) | protein | 725 | 51% helix, 13% strand | P07896 |
| B | Peroxisomal bifunctional enzyme (EC 4.2.1.17, 5.3.3.8, 1.1.1.35) | protein | 721 | 50% helix, 13% strand | P07896 |
Ligands and binding sites
- TC6 · (2E)-Hexenoyl-CoA · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.81 | 0.82 | 98 | GOL |
| 2 | 438 | 0.74 | 0.84 | 66 | empty |
| 3 | 311 | 0.72 | 0.84 | 42 | SO4 |
| 4 | 273 | 0.66 | 0.82 | 47 | TC6 |
| 5 | 412 | 0.66 | 0.79 | 59 | SO4, TC6 |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZWB · Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P07896 · AlphaFold monomer V2.0 prediction for peroxisomal bifunctional enzyme (P07896) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P07896
- Elsewhere: RCSB PDB 3ZWB · PDBe 3ZWB · UniProt P07896
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.