Research workbench
Anti-P24 (HIV-1) Fab fragment CB41 complexed with a peptide
Analyse Anti-P24 (HIV-1) Fab fragment CB41 complexed with a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HH9
- 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); Pep-2
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG2A kappa antibody CB41 (light chain) | protein | 214 | 7% helix, 53% strand | — |
| B | IGG2A kappa antibody CB41 (heavy chain) | protein | 213 | 3% helix, 52% strand | — |
| C | Pep-2 | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.59 | 0.75 | 55 | empty |
| 2 | 84 | 0.38 | 0.77 | 16 | empty |
| 3 | 103 | 0.38 | 0.75 | 19 | empty |
| 4 | 66 | 0.31 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1755 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1HH9 · 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 1HH9 · PDBe 1HH9
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