Research workbench
Crystal structure of TNF-TNFR2 complex
Analyse Crystal structure of TNF-TNFR2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ALQ
- Type
- protein
- Length
- 1,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; Tumor necrosis factor receptor superfamily member 1B
- UniProt
- P01375, P20333
- Ligands
- CO
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tumor necrosis factor | protein | 141 | 2% helix, 55% strand | P01375 |
| R, T, W | Tumor necrosis factor receptor superfamily member 1B | protein | 162 | 0% helix, 36% strand | P20333 |
| S | Tumor necrosis factor receptor superfamily member 1B | protein | 164 | 0% helix, 36% strand | P20333 |
| U, V | Tumor necrosis factor receptor superfamily member 1B | protein | 161 | 0% helix, 38% strand | P20333 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains R, S, T, U, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.78 | 0.92 | 39 | empty |
| 2 | 83 | 0.77 | 0.99 | 19 | empty |
| 3 | 206 | 0.77 | 0.92 | 38 | empty |
| 4 | 92 | 0.77 | 0.98 | 24 | empty |
| 5 | 206 | 0.77 | 0.92 | 35 | empty |
Interfaces
27 interfaces between chains.
- B–C · 1152 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1149 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1124 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1121 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide (disulfide).
Compared structures
- 3ALQ · Crystal structure of TNF-TNFR2 complex · the same entry in another collection · chain W against W, 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
- Every structure of UniProt P20333
- Elsewhere: RCSB PDB 3ALQ · PDBe 3ALQ · UniProt P01375 · UniProt P20333
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