MolNFT v1 · #156963 · protein
Crystal structure of murine 4-1BB ligand
6MKB · Tumor necrosis factor ligand superfamily member 9: “Crystal structure of murine 4-1BB ligand”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.71). MolNFT v1 #156963 on GenesisL1: 3D structure, binding…
- PDB
- 6MKB
- Type
- protein
- Length
- 650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 9
- UniProt
- P41274
- Ligands
- NAG, BMA, MAN, NA, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 9 | protein | 160 | 3% helix, 54% strand | P41274 |
| B, C | Tumor necrosis factor ligand superfamily member 9 | protein | 165 | 2% helix, 53% strand | P41274 |
| D | Tumor necrosis factor ligand superfamily member 9 | protein | 160 | 3% helix, 54% strand | P41274 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.71 | 0.78 | 68 | empty |
| 2 | 651 | 0.70 | 0.78 | 63 | empty |
| 3 | 74 | 0.29 | 0.72 | 13 | empty |
| 4 | 65 | 0.28 | 0.73 | 14 | empty |
| 5 | 70 | 0.28 | 0.72 | 14 | empty |
Interfaces
2 interfaces between chains.
- C–D · 926 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 6MKB · PDBe 6MKB · UniProt P41274
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