MolNFT v1 · #84111 · protein
Fab fragment from anti trail-R2 human agonist antibody KMTR2
3X3G · Heavy chain of KMTR2: “Fab fragment from anti trail-R2 human agonist antibody KMTR2”. X-ray diffraction, 3 ligands (NAG, CL, SO4), 4 pockets (best druggability 0.58). MolNFT v1 #84111 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3X3G
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of KMTR2; Light chain of KMTR2
- Ligands
- NAG, CL, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of KMTR2 | protein | 224 | 8% helix, 51% strand | — |
| L | Light chain of KMTR2 | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- CL · Chloride ion · ion · 3 copies · chains H, L
- SO4 · Sulfate ion · ion · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.58 | 0.75 | 60 | empty |
| 2 | 130 | 0.43 | 0.76 | 19 | empty |
| 3 | 115 | 0.40 | 0.75 | 22 | empty |
| 4 | 64 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 1926 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3X3G · Fab fragment from anti TRAIL-R2 Human Agonist Antibody KMTR2 · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3X3G · PDBe 3X3G
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