MolNFT v1 · #84819 · protein
Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed with 3S-hydroxy-hexanoyl-CoA
3ZWA · Peroxisomal bifunctional enzyme: “Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed with…”. X-ray diffraction, 2 ligands (3H9, SO4), 16 pockets (best druggability 0.80). MolNFT v1 #84819 on…
- PDB
- 3ZWA
- Type
- protein
- Length
- 1,448 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
- 3H9, SO4
- Pockets
- 16 · best druggability 0.80
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 | 727 | 50% 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
- 3H9 · (S)-3-Hydroxyhexanoyl-CoA · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.80 | 0.82 | 122 | empty |
| 2 | 809 | 0.80 | 0.83 | 69 | SO4 |
| 3 | 249 | 0.64 | 0.82 | 44 | 3H9 |
| 4 | 312 | 0.63 | 0.80 | 51 | 3H9 |
| 5 | 159 | 0.49 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3ZWA · 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 3ZWA · PDBe 3ZWA · UniProt P07896
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