MolNFT v1 · #159426 · protein
Asymmetric htnf-alpha
6OP0 · Tumor necrosis factor: “Asymmetric htnf-alpha”. X-ray diffraction, 1 ligand (A7A), 4 pockets (best druggability 0.81). MolNFT v1 #159426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OP0
- Type
- protein
- Length
- 407 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- A7A
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 55% 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 | 141 | 2% helix, 53% strand | P01375 |
| C | Tumor necrosis factor | protein | 119 | 0% helix, 59% strand | P01375 |
Ligands and binding sites
- A7A · (R)-{1-[(2,5-dimethylphenyl)methyl]-6-(1-methyl-1H-pyrazol-4-yl)-1H-benzimidazol-2-yl}(pyridin-4-yl) methanol · ligand · chains A, 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 | 323 | 0.81 | 0.91 | 39 | A7A |
| 2 | 445 | 0.72 | 0.82 | 49 | empty |
| 3 | 59 | 0.56 | 0.89 | 21 | empty |
| 4 | 105 | 0.48 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1036 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 898 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6OP0 · 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 6OP0 · PDBe 6OP0 · UniProt P01375
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