Research workbench
Protocadherin gamma B2 extracellular cadherin domains 1-5
Analyse Protocadherin gamma B2 extracellular cadherin domains 1-5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T9T
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin gamma B2-alpha C
- UniProt
- Q8K486
- Ligands
- MAN, NAG, BMA, FUC, CA
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin gamma B2-alpha C | protein | 526 | 7% helix, 46% strand | Q8K486 |
| B | Protocadherin gamma B2-alpha C | protein | 526 | 6% helix, 45% strand | Q8K486 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- CA · Calcium ion · metal · 26 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 | 286 | 0.58 | 0.78 | 36 | empty |
| 2 | 132 | 0.54 | 0.82 | 25 | empty |
| 3 | 116 | 0.52 | 0.81 | 23 | empty |
| 4 | 187 | 0.51 | 0.77 | 34 | empty |
| 5 | 132 | 0.42 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2148 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 2 disulfide (O-glycosylation, N-glycosylation, disulfide).
Compared structures
- 5T9T · Protocadherin Gamma B2 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 Q8K486
- Elsewhere: RCSB PDB 5T9T · PDBe 5T9T · UniProt Q8K486
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