MolNFT v1 · #85882 · protein
Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2 form I
4APX: “Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2 form I”. X-ray diffraction, 3 ligands (CA, K, CL), 3 pockets (best druggability 0.65). MolNFT v1 #85882 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4APX
- Type
- protein
- Length
- 446 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
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-23 | protein | 208 | 7% helix, 44% strand | Q99PF4 |
| B | Protocadherin-15 | protein | 238 | 8% helix, 39% 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
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.65 | 0.77 | 69 | empty |
| 2 | 326 | 0.58 | 0.76 | 45 | empty |
| 3 | 97 | 0.35 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4APX · Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1- 2 form I · 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 4APX · PDBe 4APX · UniProt Q99PF4 · UniProt Q99PJ1
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