MolNFT v1 · #96473 · protein
Restricting HIV-1 pathways for escape using rationally-designed anti- HIV-1 antibodies
4JKP · GP120: “Restricting HIV-1 pathways for escape using rationally-designed anti- HIV-1 antibodies”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 12 pockets (best druggability 0.73). MolNFT v1 #96473 on GenesisL1: 3D structure, binding…
- PDB
- 4JKP
- Type
- protein
- Length
- 769 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120; Heavy chain of antibody 45-46M2; Light chain of antibody 45-46M2
- Ligands
- NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | GP120 | protein | 340 | 18% helix, 36% strand | — |
| H | Heavy chain of antibody 45-46M2 | protein | 222 | 5% helix, 50% strand | — |
| L | Light chain of antibody 45-46M2 | protein | 207 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains L, G
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains L, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.73 | 0.88 | 40 | empty |
| 2 | 81 | 0.55 | 0.86 | 19 | NAG |
| 3 | 158 | 0.55 | 0.81 | 21 | empty |
| 4 | 53 | 0.52 | 0.88 | 18 | empty |
| 5 | 222 | 0.50 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1730 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1228 Ų buried · 24 hydrogen bonds · protein-protein
- G–L · 226 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4JKP · Restricting HIV-1 Pathways for Escape using Rationally-Designed Anti-HIV-1 Antibodies · the same entry in another collection · chain G against G, 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 4JKP · PDBe 4JKP
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