Research workbench
Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 GP120
Analyse Crystal structure of broadly and potently neutralizing antibody VRC03 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SE8
- Type
- protein
- Length
- 779 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade ae strain 93TH057 GP120; Heavy chain of antibody VRC03; Light chain of…
- Ligands
- NAG, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 clade ae strain 93TH057 GP120 | protein | 344 | 19% helix, 38% strand | — |
| H | Heavy chain of antibody VRC03 | protein | 227 | 9% helix, 51% strand | — |
| L | Light chain of antibody VRC03 | protein | 208 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- SO4 · Sulfate ion · ion · 8 copies · chains G, H, L
- EDO · 1,2-ethanediol · additive · 2 copies · chains H, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.72 | 0.79 | 53 | NAG, SO4 |
| 2 | 80 | 0.58 | 0.87 | 17 | NAG |
| 3 | 351 | 0.57 | 0.75 | 39 | EDO |
| 4 | 103 | 0.50 | 0.82 | 20 | empty |
| 5 | 79 | 0.42 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1725 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1144 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 293 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3SE8 · Crystal structure of broadly and potently neutralizing antibody VRC03 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 3SE8 · PDBe 3SE8
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