MolNFT v1 · #136856 · protein
Protocadherin GAMMAB7 EC3-6 cis-dimer structure
5V5X · MCG133388, isoform CRA_Y: “Protocadherin GAMMAB7 EC3-6 cis-dimer structure”. X-ray diffraction, 5 ligands (MAN, NAG, FUC), 19 pockets (best druggability 0.65). MolNFT v1 #136856 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V5X
- Type
- protein
- Length
- 1,682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MCG133388, isoform CRA_Y
- UniProt
- Q91XX3
- Ligands
- MAN, NAG, FUC, BMA, CA
- Pockets
- 19 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MCG133388, isoform CRA_Y | protein | 425 | 4% helix, 47% strand | Q91XX3 |
| B, C | MCG133388, isoform CRA_Y | protein | 415 | 4% helix, 48% strand | Q91XX3 |
| D | MCG133388, isoform CRA_Y | protein | 427 | 4% helix, 47% strand | Q91XX3 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains B, A, C, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- 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
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.65 | 0.82 | 36 | empty |
| 2 | 288 | 0.65 | 0.81 | 24 | empty |
| 3 | 243 | 0.64 | 0.82 | 29 | empty |
| 4 | 216 | 0.62 | 0.82 | 35 | empty |
| 5 | 57 | 0.60 | 0.92 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1067 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1038 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 869 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan (O-glycosylation, N-glycosylation).
Compared structures
- 5V5X · Protocadherin gammaB7 EC3-6 cis-dimer structure · 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 5V5X · PDBe 5V5X · UniProt Q91XX3
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