MolNFT v1 · #156834 · protein
Structure of human 4-1BB / 4-1BBL complex
6MGP · Tumor necrosis factor ligand superfamily member 9: “Structure of human 4-1BB / 4-1BBL complex”. X-ray diffraction, 2 ligands (NAG, FUC), 5 pockets (best druggability 0.77). MolNFT v1 #156834 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MGP
- Type
- protein
- Length
- 885 residues
- Chains
- 6
- 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
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 9 | protein | 150 | 2% helix, 59% strand | P41273 |
| B | Tumor necrosis factor ligand superfamily member 9 | protein | 152 | 5% helix, 57% strand | P41273 |
| C | Tumor necrosis factor ligand superfamily member 9 | protein | 152 | 2% helix, 55% strand | P41273 |
| X, Z | Tumor necrosis factor receptor superfamily member 9 | protein | 144 | 5% helix, 33% strand | Q07011 |
| Y | Tumor necrosis factor receptor superfamily member 9 | protein | 143 | 3% helix, 33% strand | Q07011 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains X, Y, Z
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains Y, Z
- ACT · Acetate ion · additive · 5 copies · chains A, X, C, Z, B, Y
- GOL · Glycerol · additive · 4 copies · chains A, B, C, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.77 | 0.84 | 46 | GOL |
| 2 | 672 | 0.75 | 0.81 | 67 | ACT |
| 3 | 838 | 0.74 | 0.78 | 89 | empty |
| 4 | 452 | 0.73 | 0.83 | 54 | ACT |
| 5 | 137 | 0.48 | 0.78 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–Z · 897 Ų buried · 10 hydrogen bonds · protein-protein
- B–Y · 876 Ų buried · 10 hydrogen bonds · protein-protein
- A–X · 860 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MGP · Structure of human 4-1BB / 4-1BBL complex · the same entry in another collection · chain Z against Z, 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 0.98
- Q07011 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain X against A, TM-score 0.93
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 6MGP · PDBe 6MGP · UniProt P41273 · UniProt Q07011
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