Research workbench
Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2 form II
Analyse Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2 form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AQ8
- Type
- protein
- Length
- 889 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-23; Protocadherin-15
- UniProt
- Q99PF4, Q99PJ1
- Ligands
- CA
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cadherin-23 | protein | 208 | 7% helix, 43% strand | Q99PF4 |
| C | Protocadherin-15 | protein | 237 | 8% helix, 38% strand | Q99PJ1 |
| D | Protocadherin-15 | protein | 236 | 7% helix, 39% strand | Q99PJ1 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.69 | 0.84 | 41 | empty |
| 2 | 391 | 0.66 | 0.79 | 57 | empty |
| 3 | 151 | 0.50 | 0.79 | 24 | empty |
| 4 | 144 | 0.49 | 0.79 | 24 | empty |
| 5 | 167 | 0.40 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1228 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1135 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4AQ8 · Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1- 2 form II · the same entry in another collection · chain A against A, TM-score 1.00
- Q99PJ1 · AlphaFold monomer V2.0 prediction for protocadherin-15 (Q99PJ1) · a predicted model of the same protein · chain D against A, TM-score 0.82
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 Q99PF4
- Every structure of UniProt Q99PJ1
- Elsewhere: RCSB PDB 4AQ8 · PDBe 4AQ8 · UniProt Q99PF4 · UniProt Q99PJ1
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