MolNFT v1 · #110412 · protein
Crystal structure of HIV-1 93TH057 coree GP120 with antibody 45- VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)
4XVT · Envelope glycoprotein GP120 of HIV-1 clade A/E: “Crystal structure of HIV-1 93TH057 coree GP120 with antibody 45…”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.79). MolNFT v1 #110412 on GenesisL1: 3D structure…
- PDB
- 4XVT
- Type
- protein
- Length
- 777 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120 of HIV-1 clade A/E; Donor 45…
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 of HIV-1 clade A/E | protein | 341 | 19% helix, 37% strand | — |
| H | Donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) heavy chain | protein | 228 | 11% helix, 50% strand | — |
| L | 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) light chain | protein | 208 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.79 | 0.89 | 51 | empty |
| 2 | 174 | 0.58 | 0.81 | 32 | empty |
| 3 | 64 | 0.45 | 0.83 | 17 | NAG |
| 4 | 97 | 0.42 | 0.78 | 18 | empty |
| 5 | 80 | 0.42 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1883 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 912 Ų buried · 13 hydrogen bonds · protein-protein
- G–L · 275 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4XVT · Crystal structure of HIV-1 93TH057 coreE gp120 with antibody… · 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 4XVT · PDBe 4XVT
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.