Research workbench
1.4 a resolution structure of mouse tumor necrosis factor, towards modulation of its selectivity and trimerisation
Analyse 1.4 a resolution structure of mouse tumor necrosis factor, towards modulation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2TNF
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (tumor necrosis factor alpha)
- UniProt
- P06804
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (tumor necrosis factor alpha) | protein | 148 | 2% helix, 51% strand | P06804 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
- IPA · Isopropyl alcohol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.78 | 0.83 | 56 | empty |
| 2 | 63 | 0.73 | 0.98 | 20 | TRS |
| 3 | 88 | 0.59 | 0.87 | 22 | empty |
| 4 | 60 | 0.55 | 0.88 | 19 | empty |
| 5 | 99 | 0.48 | 0.81 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1018 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 992 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 989 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2TNF · 1.4 a resolution structure of mouse tumor necrosis factor, towards modulation of its… · the same entry in another collection · chain A against A, TM-score 1.00
- P06804 · AlphaFold monomer V2.0 prediction for tumor necrosis factor (P06804) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06804
- Elsewhere: RCSB PDB 2TNF · PDBe 2TNF · UniProt P06804
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