Research workbench
Crystal structure of rabbit mab R20 Fab
Analyse Crystal structure of rabbit mab R20 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JO4
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-HIV-1 GP120 V3 antibody R20 light chain; Monoclonal anti-HIV-1 GP120 V3…
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Monoclonal anti-HIV-1 GP120 V3 antibody R20 light chain | protein | 214 | 7% helix, 52% strand | — |
| H, I | Monoclonal anti-HIV-1 GP120 V3 antibody R20 heavy chain | protein | 227 | 4% helix, 55% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, I
- 1PE · Pentaethylene glycol · additive · 3 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.76 | 0.81 | 73 | empty |
| 2 | 858 | 0.67 | 0.74 | 82 | empty |
| 3 | 477 | 0.61 | 0.75 | 52 | empty |
| 4 | 110 | 0.41 | 0.76 | 19 | empty |
| 5 | 77 | 0.35 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1986 Ų buried · 14 hydrogen bonds · protein-protein
- M–I · 1971 Ų buried · 17 hydrogen bonds · protein-protein
- H–M · 460 Ų buried · 14 hydrogen bonds · protein-protein
- L–I · 249 Ų buried · 2 hydrogen bonds · protein-protein
- H–I · 224 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4JO4 · Crystal structure of rabbit mAb R20 Fab · 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 4JO4 · PDBe 4JO4
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