Research workbench
Crystal structure of antibody PC282 in complex with PS1 peptide
Analyse Crystal structure of antibody PC282 in complex with PS1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KCS
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PC282 immunoglobulin; PS1 peptide
- UniProt
- P01837, P18532
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PC282 immunoglobulin | protein | 214 | 6% helix, 50% strand | P01837 |
| H | PC282 immunoglobulin | protein | 217 | 6% helix, 51% strand | P18532 |
| P | PS1 peptide | protein | 7 | 43% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.53 | 0.74 | 48 | empty |
| 2 | 64 | 0.36 | 0.78 | 16 | empty |
| 3 | 56 | 0.34 | 0.78 | 18 | empty |
| 4 | 53 | 0.33 | 0.78 | 15 | empty |
| 5 | 56 | 0.30 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1674 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 281 Ų buried · 5 hydrogen bonds · protein-protein
- L–P · 215 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1KCS · Crystal structure of antibody PC282 in complex with PS1 peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain L against A, TM-score 0.50
- P18532 · AlphaFold monomer V2.0 prediction for ig heavy chain V region 1B43 (P18532) · a predicted model of the same protein · chain H against A, TM-score 0.45
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 P01837
- Every structure of UniProt P18532
- Elsewhere: RCSB PDB 1KCS · PDBe 1KCS · UniProt P01837 · UniProt P18532
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