Research workbench
Crystal structure of antiRSVF Fab B21m
Analyse Crystal structure of antiRSVF Fab B21m in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QRG
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.699
- Source
- Homo sapiens
- Molecule
- Fab light chain; Fab heavy chain Fd fragment
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.699 · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 217 | 6% helix, 52% strand | — |
| H | Fab heavy chain Fd fragment | protein | 220 | 10% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains L, H
- GOL · Glycerol · additive · 9 copies · chains L, H
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains L, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.64 | 0.74 | 59 | GOL, BTB |
| 2 | 53 | 0.52 | 0.88 | 20 | GOL |
| 3 | 59 | 0.29 | 0.74 | 18 | empty |
| 4 | 55 | 0.28 | 0.74 | 17 | SO4 |
Interfaces
1 interface between chains.
- L–H · 1991 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 3QRG · Crystal structure of antirsvf Fab B21M · 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 3QRG · PDBe 3QRG
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.