MolNFT v1 · #9006 · protein
Anti-P24 (HIV-1) Fab fragment CB41 complexed with a peptide
1HI6 · IGG2A kappa antibody CB41 (light chain): “Anti-P24 (HIV-1) Fab fragment CB41 complexed with a peptide”. X-ray diffraction, 1 ligand (NH2), 6 pockets (best druggability 0.61). MolNFT v1 #9006 on GenesisL1: 3D structure, binding sites…
- PDB
- 1HI6
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A kappa antibody CB41 (light chain); IGG2A kappa antibody CB41 (heavy chain); Peptide…
- Ligands
- NH2
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG2A kappa antibody CB41 (light chain) | protein | 214 | 6% helix, 51% strand | — |
| B | IGG2A kappa antibody CB41 (heavy chain) | protein | 213 | 8% helix, 53% strand | — |
| C | Peptide 5 | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.61 | 0.75 | 63 | empty |
| 2 | 96 | 0.36 | 0.75 | 16 | empty |
| 3 | 54 | 0.30 | 0.75 | 14 | empty |
| 4 | 62 | 0.30 | 0.74 | 19 | empty |
| 5 | 68 | 0.29 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1760 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 359 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1HI6 · Anti-P24 (HIV-1) Fab fragment CB41 complexed with a peptide · 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 1HI6 · PDBe 1HI6
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