Research workbench
Crystal structure of the 4-1BB/4-1BBL complex
Analyse Crystal structure of the 4-1BB/4-1BBL complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BWV
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 9; Tumor necrosis factor receptor…
- UniProt
- P41273, Q07011
- Pockets
- 7 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 9 | protein | 143 | 2% helix, 59% strand | P41273 |
| B | Tumor necrosis factor ligand superfamily member 9 | protein | 143 | 2% helix, 60% strand | P41273 |
| D, E | Tumor necrosis factor receptor superfamily member 9 | protein | 135 | 7% helix, 36% strand | Q07011 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.38 | 0.79 | 15 | empty |
| 2 | 59 | 0.34 | 0.77 | 15 | empty |
| 3 | 68 | 0.30 | 0.74 | 17 | empty |
| 4 | 68 | 0.29 | 0.74 | 14 | empty |
| 5 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–E · 873 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 859 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 666 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 145 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 138 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6BWV · Crystal Structure of the 4-1BB/4-1BBL Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P41273 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 9… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q07011 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P41273
- Every structure of UniProt Q07011
- Elsewhere: RCSB PDB 6BWV · PDBe 6BWV · UniProt P41273 · UniProt Q07011
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