Research workbench
Ternary complex of OX40R (TNFRSF4) bound to FAB1 and FAB2
Analyse Ternary complex of OX40R (TNFRSF4) bound to FAB1 and FAB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OGX
- Type
- protein
- Length
- 987 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 1 heavy chain; FAB1 light chain; Tumor necrosis factor receptor superfamily member 4…
- UniProt
- P43489
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fab 1 heavy chain | protein | 218 | 9% helix, 52% strand | — |
| D | FAB1 light chain | protein | 213 | 6% helix, 51% strand | — |
| G | Tumor necrosis factor receptor superfamily member 4 | protein | 140 | 4% helix, 35% strand | P43489 |
| H | FAB2 heavy chain | protein | 206 | 7% helix, 50% strand | — |
| L | FAB2 light chain | protein | 210 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.67 | 0.77 | 70 | empty |
| 2 | 525 | 0.60 | 0.74 | 59 | empty |
| 3 | 401 | 0.55 | 0.73 | 48 | empty |
| 4 | 73 | 0.52 | 0.85 | 20 | empty |
| 5 | 70 | 0.49 | 0.85 | 21 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1890 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1657 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 589 Ų buried · 5 hydrogen bonds · protein-protein
- G–L · 528 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 516 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6OGX · Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2 · the same entry in another collection · chain C against C, TM-score 1.00
- P43489 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 4… · a predicted model of the same protein · chain G 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 P43489
- Elsewhere: RCSB PDB 6OGX · PDBe 6OGX · UniProt P43489
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