MolNFT v1 · #85895 · protein
Crystal structure of deafness associated mutant mouse cadherin-23 EC1-2D124G and protocadherin-15 EC1-2 form I
4AQA: “Crystal structure of deafness associated mutant mouse cadherin-23 EC1-2D124G and protocadherin-15 EC1-2 form I”. X-ray diffraction, 3 ligands (CA, K, CL), 4 pockets (best druggability 0.63). MolNFT v1 #85895 on GenesisL1: 3D…
- PDB
- 4AQA
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-23; Protocadherin-15
- UniProt
- Q99PF4, Q99PJ1
- Ligands
- CA, K, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-23 | protein | 206 | 7% helix, 43% strand | Q99PF4 |
| B | Protocadherin-15 | protein | 237 | 8% helix, 38% strand | Q99PJ1 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B
- K · Potassium ion · metal · chains B
- CL · Chloride ion · ion · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.63 | 0.77 | 54 | empty |
| 2 | 351 | 0.58 | 0.76 | 46 | CL |
| 3 | 102 | 0.36 | 0.74 | 14 | empty |
| 4 | 90 | 0.34 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4AQA · Crystal structure of deafness associated mutant mouse cadherin-23 EC1- 2D124G and… · 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 B against A, TM-score 0.79
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 4AQA · PDBe 4AQA · UniProt Q99PF4 · UniProt Q99PJ1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.