Research workbench
Crystal structure of broadly neutralizing antibody C05
Analyse Crystal structure of broadly neutralizing antibody C05 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FNL
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody C05, heavy chain; Antibody C05, light chain
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody C05, heavy chain | protein | 233 | 9% helix, 52% strand | — |
| L, M | Antibody C05, light chain | protein | 213 | 6% helix, 52% strand | — |
| I | Antibody C05, heavy chain | protein | 234 | 9% helix, 52% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.62 | 0.80 | 44 | empty |
| 2 | 301 | 0.62 | 0.79 | 50 | empty |
| 3 | 214 | 0.57 | 0.80 | 31 | empty |
| 4 | 187 | 0.57 | 0.81 | 29 | empty |
| 5 | 191 | 0.50 | 0.77 | 27 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1916 Ų buried · 9 hydrogen bonds · protein-protein
- I–M · 1876 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 558 Ų buried · 3 hydrogen bonds · protein-protein
- L–M · 310 Ų buried · 8 hydrogen bonds · protein-protein
- H–M · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 4FNL · Crystal structure of broadly neutralizing antibody C05 · the same entry in another collection · chain H against H, 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 4FNL · PDBe 4FNL
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