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Crystal structure of broadly and potently neutralizing antibody VRC08C in complex with HIV-1 clade a strain Q842.D12 GP120
Analyse Crystal structure of broadly and potently neutralizing antibody VRC08C in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XNY
- Type
- protein
- Length
- 779 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160, envelope glycoprotein GP160…
- UniProt
- Q8JDI3
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160, envelope glycoprotein GP160 | protein | 334 | 16% helix, 38% strand | Q8JDI3 |
| H | Heavy chain of antibody VRC08C | protein | 234 | 8% helix, 47% strand | — |
| L | Light chain of antibody VRC08C | protein | 211 | 8% helix, 50% 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.80 | 0.89 | 68 | empty |
| 2 | 508 | 0.61 | 0.75 | 45 | empty |
| 3 | 79 | 0.51 | 0.84 | 20 | NAG |
| 4 | 166 | 0.51 | 0.78 | 24 | empty |
| 5 | 64 | 0.49 | 0.85 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1990 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1190 Ų buried · 25 hydrogen bonds · protein-protein
- G–L · 379 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4XNY · Crystal structure of broadly and potently neutralizing antibody VRC08C 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
- Every structure of UniProt Q8JDI3
- Elsewhere: RCSB PDB 4XNY · PDBe 4XNY · UniProt Q8JDI3
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