MolNFT v1 · #188059 · protein
Trimer-to-monomer disruption of tumor necrosis factor-alpha (TNF- alpha) by alpha-peptide-3
7TA3: “Trimer-to-monomer disruption of tumor necrosis factor-alpha (TNF- alpha) by alpha-peptide-3”. X-ray diffraction, 1 ligand (NH2), 4 pockets (best druggability 0.40). MolNFT v1 #188059 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TA3
- Type
- protein
- Length
- 353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-peptide-3; Tumor necrosis factor
- UniProt
- P01375
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-peptide-3 | protein | 31 | 74% helix, 0% strand | — |
| B | Tumor necrosis factor | protein | 142 | 4% helix, 51% strand | P01375 |
| D | Tumor necrosis factor | protein | 149 | 4% helix, 51% strand | P01375 |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.40 | 0.74 | 21 | empty |
| 2 | 65 | 0.32 | 0.75 | 15 | empty |
| 3 | 55 | 0.30 | 0.76 | 15 | empty |
| 4 | 75 | 0.30 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 928 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 853 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 507 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7TA3 · Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by alpha-peptide-3 · 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 P01375
- Elsewhere: RCSB PDB 7TA3 · PDBe 7TA3 · UniProt P01375
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