MolNFT v1 · #186234 · protein
Crystal structure of llama vhh antibody in complex with HIV-1 HXBC2 GP120 core
7R74 · Glycoprotein 120: “Crystal structure of llama vhh antibody in complex with HIV-1 HXBC2 GP120 core”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.66). MolNFT v1 #186234 on GenesisL1: 3D structure, binding sites…
- PDB
- 7R74
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 120; Antibody C8 vhh domain
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein 120 | protein | 296 | 17% helix, 38% strand | — |
| B, D | Antibody C8 vhh domain | protein | 118 | 8% helix, 54% strand | — |
| C | Glycoprotein 120 | protein | 297 | 20% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.66 | 0.78 | 47 | empty |
| 2 | 429 | 0.63 | 0.77 | 42 | empty |
| 3 | 229 | 0.62 | 0.81 | 32 | NAG |
| 4 | 181 | 0.59 | 0.82 | 24 | empty |
| 5 | 103 | 0.54 | 0.83 | 21 | NAG |
Interfaces
3 interfaces between chains.
- A–D · 1362 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1339 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R74 · Crystal structure of llama VHH antibody in complex with HIV-1 HXBC2 gp120 core · 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
- Elsewhere: RCSB PDB 7R74 · PDBe 7R74
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