Research workbench
Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with con a peptide
Analyse Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with con a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UJJ
- Type
- protein
- Length
- 460 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of anti-HIV-1 V3 monoclonal antibody 4025; Fab region of the heavy chain of…
- UniProt
- Q9YXJ8
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of anti-HIV-1 V3 monoclonal antibody 4025 | protein | 213 | 7% helix, 50% strand | — |
| H | Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025 | protein | 230 | 8% helix, 48% strand | — |
| P | GP120 | protein | 17 | 0% helix, 29% strand | Q9YXJ8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains L, H, P
- GOL · Glycerol · additive · 19 copies · chains L, H
- ACT · Acetate ion · additive · 7 copies · chains L, H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.55 | 0.75 | 47 | GOL |
| 2 | 183 | 0.43 | 0.74 | 37 | GOL, SO4 |
| 3 | 115 | 0.41 | 0.76 | 20 | GOL |
| 4 | 54 | 0.31 | 0.76 | 9 | empty |
| 5 | 72 | 0.30 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1760 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 518 Ų buried · 13 hydrogen bonds · protein-protein
- L–P · 429 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3UJJ · Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A peptide · 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 Q9YXJ8
- Elsewhere: RCSB PDB 3UJJ · PDBe 3UJJ · UniProt Q9YXJ8
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