Research workbench
Anti-P24 (HIV-1) Fab fragment CB41 complexed with an epitope-related peptide
Analyse Anti-P24 (HIV-1) Fab fragment CB41 complexed with an epitope-related peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CFN
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (IGG2A kappa antibody CB41 (light chain)); Protein (IGG2A-kappa antibody CB41…
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (IGG2A kappa antibody CB41 (light chain)) | protein | 214 | 6% helix, 50% strand | — |
| B | Protein (IGG2A-kappa antibody CB41 (heavy chain)) | protein | 213 | 9% helix, 53% strand | — |
| C | Protein (bound peptide) | protein | 10 | 0% helix, 0% strand | — |
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 | 296 | 0.53 | 0.75 | 41 | empty |
| 2 | 116 | 0.43 | 0.77 | 17 | empty |
| 3 | 83 | 0.33 | 0.74 | 16 | empty |
| 4 | 54 | 0.30 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1784 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1CFN · Anti-P24 (HIV-1) Fab fragment CB41 complexed with an epitope-related 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 1CFN · PDBe 1CFN
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