Research workbench
Crystal structure of human wd repeat domain 5 with compound
Analyse Crystal structure of human wd repeat domain 5 with compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SMR
- Type
- protein
- Length
- 1,211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- NP7, UNX
- Pockets
- 14 · best druggability 0.85
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 | 302 | 0% helix, 51% strand | P61964 |
| B, C, D | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 52% strand | P61964 |
Ligands and binding sites
- NP7 · 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide · ligand · 4 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 32 copies · chains A, C, D, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.85 | 0.86 | 71 | NP7, EDO, UNX |
| 2 | 1124 | 0.82 | 0.83 | 116 | NP7, UNX |
| 3 | 704 | 0.81 | 0.85 | 55 | EDO |
| 4 | 705 | 0.75 | 0.81 | 65 | NP7, UNX |
| 5 | 925 | 0.73 | 0.77 | 67 | EDO, UNX |
Interfaces
5 interfaces between chains.
- A–D · 455 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 378 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 223 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SMR · 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 3SMR · PDBe 3SMR · UniProt P61964
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.