MolNFT v1 · #87037 · protein
Structure of OTUD1 otu domain
4BOP · Otu domain-containing protein 1: “Structure of OTUD1 otu domain”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.57). MolNFT v1 #87037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BOP
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Otu domain-containing protein 1
- EC
- 3.4.19.12
- UniProt
- Q5VV17
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Otu domain-containing protein 1 (EC 3.4.19.12) | protein | 149 | 48% helix, 23% strand | Q5VV17 |
| B | Otu domain-containing protein 1 (EC 3.4.19.12) | protein | 150 | 48% helix, 23% strand | Q5VV17 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.57 | 0.79 | 23 | empty |
| 2 | 93 | 0.40 | 0.77 | 32 | empty |
| 3 | 66 | 0.36 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1249 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 Q5VV17
- Elsewhere: RCSB PDB 4BOP · PDBe 4BOP · UniProt Q5VV17
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