Research workbench
The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 fv fragment
Analyse The crystal structure of anti-carcinoembryonic antigen monoclonal antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J05
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-cea mab T84.66, light chain; Anti-cea mab T84.66, heavy chain
- UniProt
- P01660, Q9JL85
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Anti-cea mab T84.66, light chain | protein | 111 | 3% helix, 51% strand | P01660 |
| H, B | Anti-cea mab T84.66, heavy chain | protein | 121 | 10% helix, 51% strand | Q9JL85 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains H, B
- GOL · Glycerol · additive · 2 copies · chains L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.49 | 0.76 | 29 | empty |
| 2 | 93 | 0.34 | 0.73 | 19 | empty |
| 3 | 81 | 0.32 | 0.74 | 16 | empty |
| 4 | 63 | 0.31 | 0.75 | 18 | empty |
| 5 | 65 | 0.27 | 0.72 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 822 Ų buried · 8 hydrogen bonds · protein-protein
- L–H · 799 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 524 Ų buried · 8 hydrogen bonds · protein-protein
- L–B · 126 Ų buried · 0 hydrogen bonds · protein-protein
- H–A · 99 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1J05 · The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv… · the same entry in another collection · chain L against L, TM-score 1.00
- P01660 · AlphaFold monomer V2.0 prediction for ig kappa chain V-III region pc 3741/TEPC 111… · a predicted model of the same protein · chain L against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01660
- Every structure of UniProt Q9JL85
- Elsewhere: RCSB PDB 1J05 · PDBe 1J05 · UniProt P01660 · UniProt Q9JL85
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