Research workbench
Crystal structure of human protocadherin-15 EC2-3
Analyse Crystal structure of human protocadherin-15 EC2-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ULY
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-15
- UniProt
- Q96QU1
- Ligands
- CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin-15 | protein | 224 | 6% helix, 40% strand | Q96QU1 |
| B | Protocadherin-15 | protein | 215 | 7% helix, 41% strand | Q96QU1 |
| C | Protocadherin-15 | protein | 221 | 6% helix, 40% strand | Q96QU1 |
| D | Protocadherin-15 | protein | 233 | 6% helix, 40% strand | Q96QU1 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.82 | 0.86 | 70 | empty |
| 2 | 656 | 0.81 | 0.86 | 68 | empty |
| 3 | 229 | 0.72 | 0.88 | 37 | empty |
| 4 | 401 | 0.65 | 0.79 | 41 | empty |
| 5 | 161 | 0.49 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1107 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1085 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 656 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 164 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 Q96QU1
- Elsewhere: RCSB PDB 5ULY · PDBe 5ULY · UniProt Q96QU1
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