MolNFT v1 · #145493 · protein
Crystal structure of 4-1BBL/4-1BB complex in C2 space group
6CPR · Tumor necrosis factor ligand superfamily member 9: “Crystal structure of 4-1BBL/4-1BB complex in C2 space group”. X-ray diffraction, 4 ligands (NAG, NA, CL), 6 pockets (best druggability 0.80). MolNFT v1 #145493 on GenesisL1: 3D…
- PDB
- 6CPR
- Type
- protein
- Length
- 848 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, NA, CL, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 9 | protein | 152 | 0% helix, 57% strand | P41273 |
| B | Tumor necrosis factor ligand superfamily member 9 | protein | 151 | 0% helix, 56% strand | P41273 |
| C | Tumor necrosis factor ligand superfamily member 9 | protein | 148 | 0% helix, 56% strand | P41273 |
| D | Tumor necrosis factor receptor superfamily member 9 | protein | 132 | 5% helix, 32% strand | Q07011 |
| F | Tumor necrosis factor receptor superfamily member 9 | protein | 132 | 5% helix, 33% strand | Q07011 |
| E | Tumor necrosis factor receptor superfamily member 9 | protein | 133 | 5% helix, 35% strand | Q07011 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, F, E
- NA · Sodium ion · metal · 2 copies · chains B, D, E
- CL · Chloride ion · ion · 7 copies · chains A, C, B, F, D, E
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, F, B, D
- GOL · Glycerol · additive · chains A, B, 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 | 661 | 0.80 | 0.85 | 59 | GOL |
| 2 | 827 | 0.73 | 0.78 | 80 | CL, SO4 |
| 3 | 878 | 0.73 | 0.78 | 86 | SO4, CL |
| 4 | 755 | 0.71 | 0.78 | 72 | SO4 |
| 5 | 159 | 0.48 | 0.77 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–F · 820 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 813 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 811 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 772 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 763 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CPR · Crystal structure of 4-1BBL/4-1BB complex in C2 space group · the same entry in another collection · chain E against E, 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 B 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 F against A, TM-score 0.96
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 6CPR · PDBe 6CPR · UniProt P41273 · UniProt Q07011
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