MolNFT v1 · #180666 · protein
Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01
7L79 · Heavy chain of VRC40.01: “Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.60). MolNFT v1 #180666 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L79
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of VRC40.01; Light chain of VRC40.01
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Heavy chain of VRC40.01 | protein | 229 | 7% helix, 50% strand | — |
| L, B | Light chain of VRC40.01 | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains H, L, B, A
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 | 494 | 0.60 | 0.74 | 54 | empty |
| 2 | 459 | 0.60 | 0.74 | 44 | empty |
| 3 | 203 | 0.55 | 0.79 | 25 | empty |
| 4 | 149 | 0.43 | 0.75 | 24 | empty |
| 5 | 115 | 0.37 | 0.74 | 22 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1933 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1803 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7L79 · Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01 · the same entry in another collection · chain H against H, 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 7L79 · PDBe 7L79
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