Research workbench
Asymmetric htnf-alpha
Analyse Asymmetric htnf-alpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OOY
- Type
- protein
- Length
- 414 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- A7M
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 140 | 0% helix, 56% strand | P01375 |
| B | Tumor necrosis factor | protein | 140 | 2% helix, 55% strand | P01375 |
| C | Tumor necrosis factor | protein | 134 | 0% helix, 55% strand | P01375 |
Ligands and binding sites
- A7M · {1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol · ligand · chains A, B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.81 | 0.90 | 45 | MRD, A7M |
| 2 | 342 | 0.66 | 0.80 | 41 | empty |
| 3 | 53 | 0.50 | 0.87 | 17 | empty |
| 4 | 88 | 0.45 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1058 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 955 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6OOY · 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 6OOY · PDBe 6OOY · UniProt P01375
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