Research workbench
Trail-R2 extracellular region complexed to a Fab fragment from human agonist antibody KMTR2
Analyse Trail-R2 extracellular region complexed to a Fab fragment from human agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X3F
- Type
- protein
- Length
- 507 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of KMTR2; Light chain of KMTR2; Tumor necrosis factor receptor superfamily…
- UniProt
- O14763
- Ligands
- NAG, CL
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of KMTR2 | protein | 222 | 11% helix, 49% strand | — |
| L | Light chain of KMTR2 | protein | 214 | 6% helix, 50% strand | — |
| A | Tumor necrosis factor receptor superfamily member 10B | protein | 71 | 0% helix, 37% strand | O14763 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- CL · Chloride ion · ion · chains H, L
- GOL · Glycerol · additive · 5 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.55 | 0.74 | 50 | GOL |
| 2 | 96 | 0.38 | 0.75 | 18 | empty |
| 3 | 107 | 0.38 | 0.75 | 23 | CL |
| 4 | 102 | 0.35 | 0.74 | 23 | empty |
| 5 | 66 | 0.32 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1930 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 420 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 405 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3X3F · TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody… · the same entry in another collection · chain L against L, TM-score 1.00
- O14763 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain A 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 O14763
- Elsewhere: RCSB PDB 3X3F · PDBe 3X3F · UniProt O14763
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