MolNFT v1 · #167275 · protein
Crystal structure of human protocadherin 19 EC1-EC4
6VFU · Protocadherin-19: “Crystal structure of human protocadherin 19 EC1-EC4”. X-ray diffraction, 6 ligands (NAG, FUC, BMA), 14 pockets (best druggability 0.65). MolNFT v1 #167275 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VFU
- Type
- protein
- Length
- 1,267 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-19
- UniProt
- Q8TAB3
- Ligands
- NAG, FUC, BMA, CA, NI, CL
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Protocadherin-19 | protein | 428 | 6% helix, 46% strand | Q8TAB3 |
| B | Protocadherin-19 | protein | 411 | 7% helix, 47% strand | Q8TAB3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 27 copies · chains C, A, B
- NI · Nickel (II) ion · metal · 2 copies · chains C, A
- CL · Chloride ion · ion · 4 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.65 | 0.78 | 52 | empty |
| 2 | 549 | 0.65 | 0.76 | 52 | empty |
| 3 | 141 | 0.56 | 0.82 | 19 | empty |
| 4 | 279 | 0.55 | 0.76 | 25 | empty |
| 5 | 135 | 0.47 | 0.78 | 26 | empty |
Interfaces
2 interfaces between chains.
- C–A · 2129 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 482 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q8TAB3
- Elsewhere: RCSB PDB 6VFU · PDBe 6VFU · UniProt Q8TAB3
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