Research workbench
Crystal structure of rabbit mab R56 Fab in complex with V3 crown of HIV-1 jr-fl GP120
Analyse Crystal structure of rabbit mab R56 Fab in complex with V3 crown of HIV-1 jr-fl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JO1
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-HIV-1 GP120 V3 antibody R56 light chain; Monoclonal anti-HIV-1 GP120 V3…
- UniProt
- Q9YX36
- Ligands
- CA
- Pockets
- 12 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Monoclonal anti-HIV-1 GP120 V3 antibody R56 light chain | protein | 216 | 8% helix, 53% strand | — |
| H, I | Monoclonal anti-HIV-1 GP120 V3 antibody R56 heavy chain | protein | 213 | 4% helix, 53% strand | — |
| P, Q | GP120 | protein | 10 | 0% helix, 0% strand | Q9YX36 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.58 | 0.74 | 50 | empty |
| 2 | 365 | 0.55 | 0.74 | 50 | empty |
| 3 | 335 | 0.53 | 0.74 | 45 | empty |
| 4 | 84 | 0.50 | 0.83 | 26 | empty |
| 5 | 117 | 0.44 | 0.77 | 24 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1528 Ų buried · 13 hydrogen bonds · protein-protein
- M–I · 1520 Ų buried · 11 hydrogen bonds · protein-protein
- M–Q · 399 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 399 Ų buried · 6 hydrogen bonds · protein-protein
- I–Q · 362 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4JO1 · Crystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 JR-FL gp120 · 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
- Every structure of UniProt Q9YX36
- Elsewhere: RCSB PDB 4JO1 · PDBe 4JO1 · UniProt Q9YX36
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