MolNFT v1 · #104010 · protein
Crystal structure of human DCAF1 WD40 repeats (Q1250L)
4PXW · Protein vprbp: “Crystal structure of human DCAF1 WD40 repeats (Q1250L)”. X-ray diffraction, 1 ligand (UNX), 6 pockets (best druggability 0.80). MolNFT v1 #104010 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PXW
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein vprbp
- EC
- 2.7.11.1
- UniProt
- Q9Y4B6
- Ligands
- UNX
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein vprbp (EC 2.7.11.1) | protein | 292 | 1% helix, 52% strand | Q9Y4B6 |
| B | Protein vprbp (EC 2.7.11.1) | protein | 293 | 1% helix, 51% strand | Q9Y4B6 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 45 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.80 | 0.82 | 68 | UNX |
| 2 | 808 | 0.79 | 0.82 | 68 | UNX |
| 3 | 134 | 0.50 | 0.79 | 22 | UNX |
| 4 | 76 | 0.39 | 0.78 | 17 | empty |
| 5 | 77 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 526 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4PXW · Crystal structure of human DCAF1 WD40 repeats (Q1250L) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y4B6
- Elsewhere: RCSB PDB 4PXW · PDBe 4PXW · UniProt Q9Y4B6
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