MolNFT v1 · #110411 · protein
Crystal structure of HIV-1 donor 45 D45-01DG5 coree GP120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)
4XVS · VRC07_1995 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O…: “Crystal structure of HIV-1 donor 45 D45-01DG5 coree GP120 with antibody…”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.77). MolNFT v1 #110411 on…
- PDB
- 4XVS
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC07_1995 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O- 110653 heavy chain…
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC07_1995 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O- 110653 heavy chain | protein | 228 | 8% helix, 50% strand | — |
| L | 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 light chain | protein | 210 | 6% helix, 50% strand | — |
| G | Donor 45 01DG5 coree GP120 | protein | 342 | 17% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G, H
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 | 137 | 0.77 | 0.95 | 23 | empty |
| 2 | 283 | 0.71 | 0.85 | 44 | empty |
| 3 | 275 | 0.61 | 0.80 | 41 | empty |
| 4 | 130 | 0.50 | 0.80 | 29 | empty |
| 5 | 89 | 0.50 | 0.82 | 17 | NAG |
Interfaces
3 interfaces between chains.
- H–L · 1831 Ų buried · 21 hydrogen bonds · protein-protein
- H–G · 972 Ų buried · 20 hydrogen bonds · protein-protein
- L–G · 258 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 4XVS · Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody… · 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
- Elsewhere: RCSB PDB 4XVS · PDBe 4XVS
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.