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Diels alder catalytic antibody with transition state analogue
Analyse Diels alder catalytic antibody with transition state analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A4K
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab
- UniProt
- P01834
- Ligands
- FRA, CD
- Pockets
- 13 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody Fab | protein | 217 | 6% helix, 51% strand | P01834 |
| H | Antibody Fab | protein | 217 | 9% helix, 48% strand | — |
| A | Antibody Fab | protein | 216 | 4% helix, 52% strand | P01834 |
| B | Antibody Fab | protein | 219 | 9% helix, 49% strand | — |
Ligands and binding sites
- FRA · [4-(4-acetylamino-phenyl)-3,5-dioxo-4-aza-tricyclo[5.2.2.0 2,6]undec-1-ylcarbamoyloxy]-acetic acid · ligand · 2 copies · chains L, H, A, B
- CD · Cadmium ion · metal · 4 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.51 | 0.75 | 49 | empty |
| 2 | 58 | 0.49 | 0.86 | 22 | empty |
| 3 | 152 | 0.47 | 0.77 | 21 | FRA |
| 4 | 151 | 0.47 | 0.77 | 23 | FRA |
| 5 | 180 | 0.45 | 0.74 | 30 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1704 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1684 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1A4K · Diels alder catalytic antibody with transition state analogue · the same entry in another collection · chain L against L, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain A against A, TM-score 0.48
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 P01834
- Elsewhere: RCSB PDB 1A4K · PDBe 1A4K · UniProt P01834
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