MolNFT v1 · #134290 · protein
Protocadherin gamma A9 extracellular cadherin domains 1-5
5SZN: “Protocadherin gamma A9 extracellular cadherin domains 1-5”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.62). MolNFT v1 #134290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5SZN
- Type
- protein
- Length
- 523 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin gamma A9
- UniProt
- Q91XX9
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin gamma A9 | protein | 523 | 6% helix, 44% strand | Q91XX9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 15 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.62 | 0.84 | 36 | empty |
| 2 | 77 | 0.61 | 0.89 | 18 | empty |
Modifications
Observed in the structure: 5 glycan, 1 disulfide (O-glycosylation, N-glycosylation, disulfide).
Compared structures
- 5SZN · Protocadherin gamma A9 extracellular cadherin domains 1-5 · 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 Q91XX9
- Elsewhere: RCSB PDB 5SZN · PDBe 5SZN · UniProt Q91XX9
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