MolNFT v1 · #136780 · protein
Human A20 otu domain (I325N) with acetamidylated C103
5V3P · Tumor necrosis factor alpha-induced protein 3: “Human A20 otu domain (I325N) with acetamidylated C103”. X-ray diffraction, 20 pockets (best druggability 0.54). MolNFT v1 #136780 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V3P
- Type
- protein
- Length
- 1,777 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 0.54
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 15% 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 | 316 | 42% helix, 16% strand | P21580 |
| B | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 300 | 45% helix, 15% strand | P21580 |
| C | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 305 | 44% helix, 15% strand | P21580 |
| D | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 308 | 43% helix, 15% strand | P21580 |
| E | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 286 | 46% helix, 13% strand | P21580 |
| F | Tumor necrosis factor alpha-induced protein 3 (EC 3.4.19.12, 6.3.2.-) | protein | 262 | 40% helix, 14% strand | P21580 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.54 | 0.79 | 28 | empty |
| 2 | 60 | 0.51 | 0.87 | 23 | empty |
| 3 | 117 | 0.51 | 0.81 | 16 | empty |
| 4 | 130 | 0.51 | 0.80 | 35 | empty |
| 5 | 260 | 0.46 | 0.72 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–D · 793 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 783 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 773 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 153 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (alkylation).
Compared structures
- 5V3P · Human A20 OTU domain (I325N) with acetamidylated C103 · the same entry in another collection · chain F against F, 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 B 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 P21580
- Elsewhere: RCSB PDB 5V3P · PDBe 5V3P · UniProt P21580
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