Research workbench
Crystal structure of antibody VRC07-G54R in complex with clade A/E 93TH057 HIV-1 GP120 core
Analyse Crystal structure of antibody VRC07-G54R in complex with clade A/E 93TH057… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OLY
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Antigen binding fragment of heavy chain: antibody VRC01…
- UniProt
- Q0ED31
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 342 | 16% helix, 38% strand | Q0ED31 |
| H | Antigen binding fragment of heavy chain: antibody VRC01 | protein | 228 | 8% helix, 49% strand | — |
| L | Antigen binding fragment of light chain: antibody VRC01 | protein | 208 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.83 | 0.89 | 78 | empty |
| 2 | 80 | 0.58 | 0.88 | 16 | NAG |
| 3 | 262 | 0.56 | 0.77 | 33 | empty |
| 4 | 72 | 0.47 | 0.83 | 26 | empty |
| 5 | 132 | 0.41 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1847 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1019 Ų buried · 17 hydrogen bonds · protein-protein
- G–L · 219 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4OLY · Crystal structure of antibody VRC07-G54R in complex with clade A/E 93TH057 HIV-1 gp120… · 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 Q0ED31
- Elsewhere: RCSB PDB 4OLY · PDBe 4OLY · UniProt Q0ED31
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