MolNFT v1 · #84821 · protein
Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed with 3S-hydroxy-decanoyl-CoA
3ZWC · Peroxisomal bifunctional enzyme: “Crystal structure of rat peroxisomal multifunctional enzyme type 1 (RPMFE1) complexed with…”. X-ray diffraction, 3 ligands (NAD, HSC, SO4), 17 pockets (best druggability 0.79). MolNFT v1 #84821 on…
- PDB
- 3ZWC
- Type
- protein
- Length
- 1,444 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
- NAD, HSC, SO4
- Pockets
- 17 · best druggability 0.79
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 | 50% helix, 12% strand | P07896 |
| B | Peroxisomal bifunctional enzyme (EC 4.2.1.17, 5.3.3.8, 1.1.1.35) | protein | 719 | 50% helix, 13% strand | P07896 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- HSC · (S)-3-hydroxydecanoyl-coa · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.79 | 0.80 | 84 | NAD |
| 2 | 463 | 0.71 | 0.81 | 64 | NAD |
| 3 | 384 | 0.70 | 0.82 | 37 | GOL |
| 4 | 411 | 0.67 | 0.79 | 67 | HSC |
| 5 | 264 | 0.65 | 0.82 | 49 | HSC |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZWC · 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 0.97
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 3ZWC · PDBe 3ZWC · UniProt P07896
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