Research workbench
Protocadherin GAMMAC4 EC1-4 crystal structure disrupted trans interface
Analyse Protocadherin GAMMAC4 EC1-4 crystal structure disrupted trans interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RGF
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin gamma C4
- UniProt
- Q91XX0
- Ligands
- NAG, MAN, BMA, FUC, GAL, CA, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protocadherin gamma C4 | protein | 418 | 9% helix, 46% strand | Q91XX0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar
- CA · Calcium ion · metal · 18 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.76 | 0.79 | 109 | empty |
| 2 | 470 | 0.68 | 0.79 | 48 | empty |
| 3 | 92 | 0.42 | 0.78 | 23 | empty |
| 4 | 142 | 0.41 | 0.75 | 22 | empty |
| 5 | 51 | 0.36 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1620 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, O-glycosylation, disulfide).
Compared structures
- 7RGF · Protocadherin gammaC4 EC1-4 crystal structure disrupted trans interface · 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 Q91XX0
- Elsewhere: RCSB PDB 7RGF · PDBe 7RGF · UniProt Q91XX0
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