MolNFT v1 · #186566 · protein
Crystal structure of anti-HIV llama vhh antibody A12 in complex with HIV-1 C1086 GP120
7RI2 · Glycoprotein 120: “Crystal structure of anti-HIV llama vhh antibody A12 in complex with HIV-1 C1086 GP120”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.59). MolNFT v1 #186566 on GenesisL1: 3D structure, binding…
- PDB
- 7RI2
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 120; Anti-HIV llama vhh antibody A12
- UniProt
- R4GRV3
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein 120 | protein | 293 | 19% helix, 36% strand | R4GRV3 |
| B | Anti-HIV llama vhh antibody A12 | protein | 127 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.59 | 0.86 | 23 | NAG |
| 2 | 302 | 0.54 | 0.75 | 40 | empty |
| 3 | 73 | 0.36 | 0.77 | 18 | empty |
| 4 | 54 | 0.36 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RI2 · Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120 · the same entry in another collection · chain A against A, 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 R4GRV3
- Elsewhere: RCSB PDB 7RI2 · PDBe 7RI2 · UniProt R4GRV3
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