Research workbench
Structure of A20 otu domain bound to ubiquitin
Analyse Structure of A20 otu domain bound to ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LRX
- Type
- protein
- Length
- 1,511 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor alpha-induced protein 3; Polyubiquitin-B
- EC
- 3.4.19.12, 6.3.2.-
- UniProt
- P21580, P0CG47
- Ligands
- AYE
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 348 | 41% helix, 20% strand | P21580 |
| B, D | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
| C | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 346 | 40% helix, 18% strand | P21580 |
| E | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 338 | 40% helix, 20% strand | P21580 |
| F | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 329 | 40% helix, 20% strand | P21580 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.76 | 0.83 | 62 | empty |
| 2 | 299 | 0.75 | 0.87 | 56 | empty |
| 3 | 144 | 0.62 | 0.85 | 29 | empty |
| 4 | 132 | 0.58 | 0.83 | 29 | empty |
| 5 | 147 | 0.50 | 0.78 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1201 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1058 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 743 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 670 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, oxidation).
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 P21580
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5LRX · PDBe 5LRX · UniProt P21580 · UniProt P0CG47
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