Research workbench
Crystal structure of Fab PCT64_LMCA (sar), the least mutated common ancestor of the HIV-1 broadly neutralizing antibody lineage PCT64
Analyse Crystal structure of Fab PCT64_LMCA (sar), the least mutated common ancestor of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CA9
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PCT64_LMCA Fab light chain; PCT64_LMCA Fab heavy chain
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | PCT64_LMCA Fab light chain | protein | 212 | 7% helix, 50% strand | — |
| B | PCT64_LMCA Fab heavy chain | protein | 231 | 6% helix, 46% strand | — |
| D | PCT64_LMCA Fab heavy chain | protein | 231 | 6% helix, 46% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.56 | 0.75 | 48 | empty |
| 2 | 232 | 0.52 | 0.76 | 32 | empty |
| 3 | 254 | 0.50 | 0.75 | 39 | PEG |
| 4 | 84 | 0.41 | 0.79 | 20 | empty |
| 5 | 83 | 0.40 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1856 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, sulfation).
Compared structures
- 6CA9 · Crystal structure of Fab PCT64_LMCA (SAR), the least mutated common ancestor of the HIV-1… · 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 6CA9 · PDBe 6CA9
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