MolNFT v1 · #129515 · protein
Crystal structure of rat peroxisomal multifunctional enzyme type-1 (RPMFE1) complexed with with 3S-hydroxy-decanoyl-CoA and 3-keto- decanoyl-CoA
5OMO · Peroxisomal bifunctional enzyme: “Crystal structure of rat peroxisomal multifunctional enzyme type-1 (RPMFE1) complexed with with…”. X-ray diffraction, 3 ligands (HSC, ZOZ, SO4), 12 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5OMO
- Type
- protein
- Length
- 1,443 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
- HSC, ZOZ, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 718 | 52% helix, 13% strand | P07896 |
Ligands and binding sites
- HSC · (S)-3-hydroxydecanoyl-coa · ligand · 2 copies · chains A, B
- ZOZ · 3-keto-decanoyl-coa · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 912 | 0.82 | 0.83 | 76 | ZOZ |
| 2 | 922 | 0.80 | 0.82 | 97 | SO4 |
| 3 | 656 | 0.70 | 0.78 | 84 | HSC |
| 4 | 394 | 0.66 | 0.80 | 64 | HSC |
| 5 | 206 | 0.63 | 0.83 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 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 5OMO · PDBe 5OMO · UniProt P07896
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