MolNFT v1 · #81451 · protein
Crystal structure of human wd repeat domain 5 with compound
3UR4 · Wd repeat-containing protein 5: “Crystal structure of human wd repeat domain 5 with compound”. X-ray diffraction, 4 ligands (0BW, UNX, CL), 5 pockets (best druggability 0.73). MolNFT v1 #81451 on GenesisL1: 3D structure, binding…
- PDB
- 3UR4
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 0BW, UNX, CL, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 301 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- 0BW · methyl 3-[(3-methoxybenzoyl)amino]-4-(4-methylpiperazin-1-yl)benzoate · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 29 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.73 | 0.82 | 37 | SO4 |
| 2 | 441 | 0.71 | 0.81 | 35 | CL, SO4 |
| 3 | 257 | 0.63 | 0.81 | 36 | 0BW, UNX |
| 4 | 246 | 0.62 | 0.81 | 34 | 0BW, CL, UNX |
| 5 | 54 | 0.36 | 0.79 | 14 | empty |
Compared structures
- 3UR4 · Crystal structure of human WD repeat domain 5 with compound · the same entry in another collection · chain A against A, TM-score 1.00
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 P61964
- Elsewhere: RCSB PDB 3UR4 · PDBe 3UR4 · UniProt P61964
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