Research workbench
Crystal structure of human protocadherin-24 EC1-2 form II
Analyse Crystal structure of human protocadherin-24 EC1-2 form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N86
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-related family member 2
- UniProt
- Q9BYE9
- Ligands
- NAG, BMA, CA, NA, CL, IOD
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-related family member 2 | protein | 215 | 3% helix, 46% strand | Q9BYE9 |
| B | Cadherin-related family member 2 | protein | 213 | 5% helix, 44% strand | Q9BYE9 |
| C | Cadherin-related family member 2 | protein | 210 | 5% helix, 49% strand | Q9BYE9 |
| D | Cadherin-related family member 2 | protein | 210 | 3% helix, 42% strand | Q9BYE9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- IOD · Iodide ion · ion · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.80 | 0.86 | 63 | empty |
| 2 | 191 | 0.72 | 0.89 | 30 | empty |
| 3 | 191 | 0.72 | 0.89 | 26 | empty |
| 4 | 185 | 0.71 | 0.89 | 31 | empty |
| 5 | 164 | 0.70 | 0.89 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1108 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1082 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7N86 · Crystal Structure of Human Protocadherin-24 EC1-2 Form II · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BYE9 · AlphaFold monomer V2.0 prediction for cadherin-related family member 2 (Q9BYE9) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9BYE9
- Elsewhere: RCSB PDB 7N86 · PDBe 7N86 · UniProt Q9BYE9
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