Research workbench
Crystal structure of protocadherin gamma C5 EC1-3
Analyse Crystal structure of protocadherin gamma C5 EC1-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZPP
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MCG133388, isoform CRA_F
- UniProt
- Q91XW9
- Ligands
- NAG, MAN, CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MCG133388, isoform CRA_F | protein | 311 | 10% helix, 42% strand | Q91XW9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.69 | 0.80 | 55 | empty |
| 2 | 147 | 0.55 | 0.81 | 32 | empty |
| 3 | 253 | 0.54 | 0.77 | 30 | empty |
| 4 | 187 | 0.52 | 0.78 | 33 | MAN |
| 5 | 51 | 0.47 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 730 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 4ZPP · Crystal Structure of Protocadherin Gamma C5 EC1-3 · 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 Q91XW9
- Elsewhere: RCSB PDB 4ZPP · PDBe 4ZPP · UniProt Q91XW9
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