Research workbench
Crystal structure of zebrafish protocadherin-19 EC3-4
Analyse Crystal structure of zebrafish protocadherin-19 EC3-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CO1
- Type
- protein
- Length
- 831 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-19 isoform 1
- UniProt
- C4P340
- Ligands
- CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin-19 isoform 1 | protein | 206 | 3% helix, 48% strand | C4P340 |
| B | Protocadherin-19 isoform 1 | protein | 205 | 4% helix, 50% strand | C4P340 |
| C, D | Protocadherin-19 isoform 1 | protein | 210 | 5% helix, 47% strand | C4P340 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.73 | 0.78 | 87 | empty |
| 2 | 352 | 0.64 | 0.79 | 34 | empty |
| 3 | 229 | 0.50 | 0.75 | 35 | empty |
| 4 | 177 | 0.46 | 0.75 | 23 | empty |
| 5 | 189 | 0.46 | 0.75 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–C · 566 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 545 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 506 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5CO1 · Crystal Structure of Zebrafish Protocadherin-19 EC3-4 · 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 C4P340
- Elsewhere: RCSB PDB 5CO1 · PDBe 5CO1 · UniProt C4P340
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