MolNFT v1 · #137587 · protein
Crystal structure of mouse cadherin-23 EC24-25
5VT8: “Crystal structure of mouse cadherin-23 EC24-25”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.69). MolNFT v1 #137587 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VT8
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-23
- UniProt
- Q99PF4
- Ligands
- CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cadherin-23 | protein | 207 | 5% helix, 48% strand | Q99PF4 |
| A | Cadherin-23 | protein | 208 | 5% helix, 45% strand | Q99PF4 |
| C | Cadherin-23 | protein | 211 | 7% helix, 44% strand | Q99PF4 |
| D | Cadherin-23 | protein | 195 | 5% helix, 44% strand | Q99PF4 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.69 | 0.76 | 72 | empty |
| 2 | 413 | 0.60 | 0.76 | 44 | empty |
| 3 | 483 | 0.59 | 0.74 | 41 | empty |
| 4 | 52 | 0.38 | 0.81 | 15 | empty |
| 5 | 80 | 0.30 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 782 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 726 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 436 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VT8 · Crystal Structure of Mouse Cadherin-23 EC24-25 · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 5VT8 · PDBe 5VT8 · UniProt Q99PF4
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