MolNFT v1 · #112585 · protein
Crystal structure of protocadherin alpha C2 EC1-3
4ZPM · Protein PCDHAC2: “Crystal structure of protocadherin alpha C2 EC1-3”. X-ray diffraction, 3 ligands (MAN, NAG, CA), 8 pockets (best druggability 0.39). MolNFT v1 #112585 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZPM
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein PCDHAC2
- UniProt
- Q91Y09
- Ligands
- MAN, NAG, CA
- Pockets
- 8 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein PCDHAC2 | protein | 317 | 8% helix, 45% strand | Q91Y09 |
| B | Protein PCDHAC2 | protein | 314 | 8% helix, 45% strand | Q91Y09 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- 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
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.39 | 0.74 | 19 | empty |
| 2 | 116 | 0.38 | 0.74 | 20 | MAN |
| 3 | 119 | 0.37 | 0.73 | 17 | empty |
| 4 | 70 | 0.35 | 0.76 | 17 | empty |
| 5 | 57 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 4ZPM · Crystal Structure of Protocadherin Alpha C2 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 Q91Y09
- Elsewhere: RCSB PDB 4ZPM · PDBe 4ZPM · UniProt Q91Y09
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