Research workbench
Crystal structure of the HIV-2 neutralizing Fab fragment 7C8
Analyse Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NZ8
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse anti V3 antibody 7C8 Fab, heavy chain; Mouse anti V3 antibody 7C8 Fab, light chain
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Mouse anti V3 antibody 7C8 Fab, heavy chain | protein | 217 | 7% helix, 53% strand | — |
| B | Mouse anti V3 antibody 7C8 Fab, light chain | protein | 217 | 6% helix, 53% strand | — |
| L | Mouse anti V3 antibody 7C8 Fab, light chain | protein | 218 | 7% helix, 53% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.70 | 0.77 | 46 | empty |
| 2 | 717 | 0.66 | 0.75 | 65 | empty |
| 3 | 262 | 0.50 | 0.74 | 33 | empty |
| 4 | 72 | 0.46 | 0.83 | 23 | empty |
| 5 | 173 | 0.42 | 0.73 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1969 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1964 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 177 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 71 Ų buried · 1 hydrogen bond · protein-protein
- B–H · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3NZ8 · Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 · 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 3NZ8 · PDBe 3NZ8
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