Research workbench
Selection of a novel highly specific tnfalpha antagonist: insight from the crystal structure of the antagonist-tnfalpha complex
Analyse Selection of a novel highly specific tnfalpha antagonist: insight from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9J
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tnfalpha; Tumor necrosis factor, soluble form
- UniProt
- P01375
- Ligands
- MG
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tnfalpha | protein | 130 | 22% helix, 32% strand | — |
| T | Tumor necrosis factor, soluble form | protein | 149 | 2% helix, 51% strand | P01375 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.48 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- C–T · 901 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3L9J · Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal… · the same entry in another collection · chain C against C, 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 3L9J · PDBe 3L9J · UniProt P01375
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