Research workbench
Protocadherin gamma A1 extracellular cadherin domains 1-4
Analyse Protocadherin gamma A1 extracellular cadherin domains 1-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SZL
- Type
- protein
- Length
- 1,659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin gamma A1 extracellular cadherin domains 1-4, protein PCDHGA1
- UniProt
- A0A0A6YW27
- Ligands
- NAG, MAN, BMA, FUC, CA
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin gamma A1 extracellular cadherin domains 1-4, protein PCDHGA1 | protein | 413 | 8% helix, 43% strand | A0A0A6YW27 |
| B | Protocadherin gamma A1 extracellular cadherin domains 1-4, protein PCDHGA1 | protein | 412 | 8% helix, 43% strand | A0A0A6YW27 |
| C | Protocadherin gamma A1 extracellular cadherin domains 1-4, protein PCDHGA1 | protein | 418 | 8% helix, 45% strand | A0A0A6YW27 |
| D | Protocadherin gamma A1 extracellular cadherin domains 1-4, protein PCDHGA1 | protein | 416 | 8% helix, 45% strand | A0A0A6YW27 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, D, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains D
- CA · Calcium ion · metal · 36 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.76 | 0.80 | 76 | empty |
| 2 | 547 | 0.75 | 0.83 | 56 | empty |
| 3 | 210 | 0.72 | 0.88 | 44 | empty |
| 4 | 127 | 0.71 | 0.91 | 36 | empty |
| 5 | 1031 | 0.70 | 0.74 | 105 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1656 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1340 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 578 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 259 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 4 disulfide (N-glycosylation, O-glycosylation, disulfide).
Compared structures
- 5SZL · Protocadherin gamma A1 extracellular cadherin domains 1-4 · 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 A0A0A6YW27
- Elsewhere: RCSB PDB 5SZL · PDBe 5SZL · UniProt A0A0A6YW27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.