Research workbench
OX40R (TNFRSF4) bound to Fab 1A7
Analyse OX40R (TNFRSF4) bound to Fab 1A7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKN
- Type
- protein
- Length
- 1,038 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 1A7 heavy chain; Fab 1A7 light chain; Tumor necrosis factor receptor superfamily…
- UniProt
- P43489
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 1A7 heavy chain | protein | 217 | 9% helix, 50% strand | — |
| B, D | Fab 1A7 light chain | protein | 213 | 7% helix, 51% strand | — |
| C | Fab 1A7 heavy chain | protein | 220 | 7% helix, 49% strand | — |
| E | Tumor necrosis factor receptor superfamily member 4 | protein | 81 | 4% helix, 23% strand | P43489 |
| R | Tumor necrosis factor receptor superfamily member 4 | protein | 94 | 0% helix, 24% strand | P43489 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.73 | 0.77 | 99 | empty |
| 2 | 683 | 0.65 | 0.74 | 50 | empty |
| 3 | 642 | 0.64 | 0.74 | 55 | EPE |
| 4 | 93 | 0.37 | 0.75 | 18 | empty |
| 5 | 94 | 0.34 | 0.74 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1845 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1782 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 580 Ų buried · 2 hydrogen bonds · protein-protein
- A–R · 567 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 464 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (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 P43489
- Elsewhere: RCSB PDB 6OKN · PDBe 6OKN · UniProt P43489
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