MolNFT v1 · #112589 · protein
Crystal structure of protocadherin gamma C5 EC1-3
4ZPQ · MCG133388, isoform CRA_F: “Crystal structure of protocadherin gamma C5 EC1-3”. X-ray diffraction, 4 ligands (MAN, NAG, FUC), 5 pockets (best druggability 0.68). MolNFT v1 #112589 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4ZPQ
- Type
- protein
- Length
- 938 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MCG133388, isoform CRA_F
- UniProt
- Q91XW9
- Ligands
- MAN, NAG, FUC, CA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MCG133388, isoform CRA_F | protein | 315 | 9% helix, 43% strand | Q91XW9 |
| B | MCG133388, isoform CRA_F | protein | 312 | 10% helix, 43% strand | Q91XW9 |
| C | MCG133388, isoform CRA_F | protein | 311 | 10% helix, 44% strand | Q91XW9 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 18 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.68 | 0.75 | 72 | MAN |
| 2 | 232 | 0.56 | 0.78 | 31 | empty |
| 3 | 161 | 0.45 | 0.76 | 26 | empty |
| 4 | 81 | 0.36 | 0.76 | 13 | empty |
| 5 | 55 | 0.26 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 831 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 613 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 3 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 4ZPQ · Crystal Structure of Protocadherin Gamma C5 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 Q91XW9
- Elsewhere: RCSB PDB 4ZPQ · PDBe 4ZPQ · UniProt Q91XW9
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