MolNFT v1 · #81199 · protein
Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with mn peptide
3UJI · Light chain of anti-HIV-1 V3 monoclonal antibody 2558: “Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with mn peptide”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 2 pockets (best druggability 0.68). MolNFT v1 #81199 on…
- PDB
- 3UJI
- Type
- protein
- Length
- 444 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 2558; Fab region of the heavy chain of…
- UniProt
- P05877
- Ligands
- NAG, FUC, CA
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of anti-HIV-1 V3 monoclonal antibody 2558 | protein | 208 | 9% helix, 52% strand | — |
| H | Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 2558 | protein | 218 | 9% helix, 56% strand | — |
| P | Envelope glycoprotein GP160 | protein | 18 | 17% helix, 33% strand | P05877 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, H
- FUC · alpha-L-fucopyranose · sugar · chains H
- CA · Calcium ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.68 | 0.76 | 66 | empty |
| 2 | 58 | 0.34 | 0.78 | 17 | NAG |
Interfaces
3 interfaces between chains.
- L–H · 1703 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 682 Ų buried · 15 hydrogen bonds · protein-protein
- L–P · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3UJI · Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with MN peptide · 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
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 3UJI · PDBe 3UJI · UniProt P05877
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.