Research workbench
Human A20 otu domain (wt) with acetamidylated C103
Analyse Human A20 otu domain (wt) with acetamidylated C103 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V3B
- Type
- protein
- Length
- 1,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor alpha-induced protein 3
- EC
- 3.4.19.12, 6.3.2.-
- UniProt
- P21580
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 17% 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 | 312 | 44% helix, 16% strand | P21580 |
| B | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 323 | 43% helix, 17% strand | P21580 |
| C | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 314 | 43% helix, 18% strand | P21580 |
| D | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 316 | 43% helix, 18% strand | P21580 |
| E | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 318 | 43% helix, 16% strand | P21580 |
| F | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 322 | 42% helix, 16% strand | P21580 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.60 | 0.87 | 27 | empty |
| 2 | 371 | 0.56 | 0.74 | 41 | empty |
| 3 | 74 | 0.54 | 0.86 | 24 | empty |
| 4 | 229 | 0.53 | 0.77 | 22 | empty |
| 5 | 90 | 0.53 | 0.84 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–B · 606 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 582 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 577 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 242 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (alkylation).
Compared structures
- 5V3B · Human A20 OTU domain (WT) with acetamidylated C103 · the same entry in another collection · chain B against B, TM-score 1.00
- P21580 · AlphaFold monomer V2.0 prediction for tumor necrosis factor alpha- induced protein 3… · a predicted model of the same protein · chain C 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 P21580
- Elsewhere: RCSB PDB 5V3B · PDBe 5V3B · UniProt P21580
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