Research workbench
Human P-cadherin EC12 with scfv TSP11 bound
Analyse Human P-cadherin EC12 with scfv TSP11 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JYM
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-3; Antibody scfv TSP11
- UniProt
- P22223
- Ligands
- CA
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cadherin-3 | protein | 213 | 3% helix, 45% strand | P22223 |
| B | Antibody scfv TSP11 | protein | 225 | 8% helix, 47% strand | — |
| D | Antibody scfv TSP11 | protein | 223 | 8% helix, 47% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.60 | 0.81 | 34 | empty |
| 2 | 94 | 0.49 | 0.81 | 17 | empty |
| 3 | 86 | 0.43 | 0.79 | 15 | empty |
| 4 | 62 | 0.37 | 0.79 | 19 | empty |
| 5 | 83 | 0.31 | 0.73 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 900 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P22223
- Elsewhere: RCSB PDB 5JYM · PDBe 5JYM · UniProt P22223
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