MolNFT v1 · #134291 · protein
Protocadherin gamma B7 extracellular cadherin domains 1-4 P41212 crystal form
5SZO: “Protocadherin gamma B7 extracellular cadherin domains 1-4 P41212 crystal form”. X-ray diffraction, 4 ligands (MAN, NAG, FUC), 8 pockets (best druggability 0.56). MolNFT v1 #134291 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5SZO
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin gamma B7
- UniProt
- Q91XX3
- Ligands
- MAN, NAG, FUC, CA
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin gamma B7 | protein | 412 | 6% helix, 47% strand | Q91XX3 |
| B | Protocadherin gamma B7 | protein | 414 | 7% helix, 47% strand | Q91XX3 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- CA · Calcium ion · metal · 18 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.56 | 0.76 | 44 | empty |
| 2 | 209 | 0.56 | 0.79 | 36 | empty |
| 3 | 136 | 0.54 | 0.81 | 32 | empty |
| 4 | 215 | 0.49 | 0.76 | 39 | empty |
| 5 | 209 | 0.46 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2202 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 2 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 5SZO · Protocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 crystal form · 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 Q91XX3
- Elsewhere: RCSB PDB 5SZO · PDBe 5SZO · UniProt Q91XX3
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