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Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2, form I 2.2A.
Analyse Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1-2, form I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AXW
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-23; Protocadherin-15
- UniProt
- Q99PF4, H3BKS0
- Ligands
- CA, K, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-23 | protein | 208 | 7% helix, 43% strand | Q99PF4 |
| B | Protocadherin-15 | protein | 236 | 8% helix, 38% strand | H3BKS0 |
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
- PG4 · Tetraethylene glycol · 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
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 | 546 | 0.66 | 0.77 | 63 | empty |
| 2 | 338 | 0.58 | 0.77 | 42 | empty |
| 3 | 52 | 0.43 | 0.83 | 18 | GOL |
| 4 | 95 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 980 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4AXW · Crystal structure of mouse cadherin-23 EC1-2 and protocadherin-15 EC1- 2, form I 2.2A. · the same entry in another collection · chain A against A, TM-score 1.00
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 H3BKS0
- Elsewhere: RCSB PDB 4AXW · PDBe 4AXW · UniProt Q99PF4 · UniProt H3BKS0
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