MolNFT v1 · #76655 · protein
Crystal structure of antirsvf Fab B21M
3QRG · Fab light chain: “Crystal structure of antirsvf Fab B21M”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.64). MolNFT v1 #76655 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3QRG
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain fd fragment
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 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 L against L, 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
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