Research workbench
Crystal structure of mouse cadherin-23 EC12-13 with engineered mutation S1339D
Analyse Crystal structure of mouse cadherin-23 EC12-13 with engineered mutation S1339D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VH2
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-23
- UniProt
- Q99PF4
- Ligands
- CA, NA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-23 | protein | 209 | 6% helix, 46% strand | Q99PF4 |
| B | Cadherin-23 | protein | 208 | 5% helix, 46% strand | Q99PF4 |
| C | Cadherin-23 | protein | 203 | 4% helix, 47% strand | Q99PF4 |
| D | Cadherin-23 | protein | 208 | 4% helix, 47% strand | Q99PF4 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.73 | 0.79 | 85 | empty |
| 2 | 277 | 0.54 | 0.76 | 36 | empty |
| 3 | 116 | 0.51 | 0.81 | 18 | empty |
| 4 | 111 | 0.47 | 0.80 | 18 | empty |
| 5 | 113 | 0.43 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1553 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 758 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 148 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VH2 · Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D · 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
- Elsewhere: RCSB PDB 5VH2 · PDBe 5VH2 · UniProt Q99PF4
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