MolNFT v1 · #180101 · protein
Asymmetric htnf-alpha
7KP9 · Tumor necrosis factor: “Asymmetric htnf-alpha”. X-ray diffraction, 1 ligand (A7G), 6 pockets (best druggability 0.79). MolNFT v1 #180101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KP9
- Type
- protein
- Length
- 418 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- A7G
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 148 | 2% helix, 53% strand | P01375 |
| B | Tumor necrosis factor | protein | 139 | 2% helix, 55% strand | P01375 |
| C | Tumor necrosis factor | protein | 131 | 2% helix, 57% strand | P01375 |
Ligands and binding sites
- A7G · 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.79 | 0.87 | 44 | A7G |
| 2 | 471 | 0.71 | 0.81 | 58 | empty |
| 3 | 106 | 0.49 | 0.80 | 21 | empty |
| 4 | 64 | 0.48 | 0.84 | 17 | empty |
| 5 | 91 | 0.39 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1022 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7KP9 · asymmetric hTNF-alpha · 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 7KP9 · PDBe 7KP9 · UniProt P01375
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