MolNFT v1 · #159425 · protein
Asymmetric htnf-alpha
6OOZ · Tumor necrosis factor: “Asymmetric htnf-alpha”. X-ray diffraction, 2 ligands (A6Y, CL), 4 pockets (best druggability 0.77). MolNFT v1 #159425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OOZ
- Type
- protein
- Length
- 415 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- A6Y, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 147 | 2% helix, 54% strand | P01375 |
| B | Tumor necrosis factor | protein | 142 | 2% helix, 53% strand | P01375 |
| C | Tumor necrosis factor | protein | 126 | 2% helix, 56% strand | P01375 |
Ligands and binding sites
- A6Y · (S)-{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol · ligand · chains A, B, C
- CL · Chloride ion · ion · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.77 | 0.89 | 38 | A6Y |
| 2 | 629 | 0.72 | 0.79 | 67 | empty |
| 3 | 54 | 0.56 | 0.90 | 20 | empty |
| 4 | 91 | 0.47 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1078 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6OOZ · 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 6OOZ · PDBe 6OOZ · UniProt P01375
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