Research workbench
Crystal structure of murine 4-1BB/4-1BBL complex
Analyse Crystal structure of murine 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
- 6MKZ
- Type
- protein
- Length
- 528 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
- P41274, P20334
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 9 | protein | 164 | 4% helix, 53% strand | P41274 |
| B | Tumor necrosis factor receptor superfamily member 9 | protein | 120 | 0% helix, 28% strand | P20334 |
| C | Tumor necrosis factor ligand superfamily member 9 | protein | 159 | 5% helix, 56% strand | P41274 |
| D | Tumor necrosis factor receptor superfamily member 9 | protein | 85 | 0% helix, 31% strand | P20334 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.72 | 0.91 | 22 | empty |
| 2 | 215 | 0.66 | 0.84 | 43 | empty |
| 3 | 355 | 0.57 | 0.75 | 37 | empty |
| 4 | 347 | 0.55 | 0.74 | 40 | empty |
| 5 | 52 | 0.35 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1082 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1048 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 933 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MKZ · Crystal structure of murine 4-1BB/4-1BBL complex · the same entry in another collection · chain D against D, TM-score 1.00
- P41274 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 9… · a predicted model of the same protein · chain C against A, TM-score 0.98
- P20334 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P41274
- Every structure of UniProt P20334
- Elsewhere: RCSB PDB 6MKZ · PDBe 6MKZ · UniProt P41274 · UniProt P20334
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