Research workbench
Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade a strain Q842.D12 GP120
Analyse Crystal structure of broadly and potently neutralizing antibody VRC08 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XMP
- Type
- protein
- Length
- 780 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
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160, envelope glycoprotein GP160 | protein | 337 | 16% helix, 37% strand | Q8JDI3 |
| H | Heavy chain of antibody VRC08 | protein | 232 | 10% helix, 47% strand | — |
| L | Light chain of antibody VRC08 | protein | 211 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- BU3 · (R,R)-2,3-butanediol · additive · 2 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.80 | 0.89 | 73 | BU3 |
| 2 | 349 | 0.55 | 0.74 | 46 | empty |
| 3 | 208 | 0.52 | 0.77 | 35 | empty |
| 4 | 54 | 0.51 | 0.88 | 19 | empty |
| 5 | 72 | 0.38 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1796 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1175 Ų buried · 31 hydrogen bonds · protein-protein
- G–L · 311 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 11 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4XMP · Crystal structure of broadly and potently neutralizing antibody VRC08 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 4XMP · PDBe 4XMP · UniProt Q8JDI3
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