Research workbench
Crystal structure of broadly and potently neutralizing antibody VRC23 in complex with HIV-1 GP120
Analyse Crystal structure of broadly and potently neutralizing antibody VRC23 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J6R
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Heavy chain of antibody VRC23; Light chain of antibody VRC23
- Ligands
- NAG, CA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 343 | 18% helix, 38% strand | — |
| H | Heavy chain of antibody VRC23 | protein | 222 | 8% helix, 53% strand | — |
| L | Light chain of antibody VRC23 | protein | 210 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G, L
- CA · Calcium ion · metal · 2 copies · chains G, L
- EDO · 1,2-ethanediol · additive · 15 copies · chains G, H, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains H, L
- BU3 · (R,R)-2,3-butanediol · additive · chains L
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 | 355 | 0.80 | 0.90 | 44 | empty |
| 2 | 80 | 0.68 | 0.93 | 28 | empty |
| 3 | 50 | 0.65 | 0.96 | 22 | EDO |
| 4 | 268 | 0.61 | 0.80 | 35 | empty |
| 5 | 378 | 0.55 | 0.74 | 58 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1814 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 960 Ų buried · 13 hydrogen bonds · protein-protein
- G–L · 372 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 9 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4J6R · Crystal structure of broadly and potently neutralizing antibody VRC23 in complex with… · 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 4J6R · PDBe 4J6R
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.