Research workbench
Crystal structure of human protocadherin-15 EC1-3 G16D N369D Q370N and mouse cadherin-23 EC1-2 T15E
Analyse Crystal structure of human protocadherin-15 EC1-3 G16D N369D Q370N and mouse… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N2E
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-15; Cadherin-23
- UniProt
- A0A087X1T6, Q99PF4
- Ligands
- CA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin-15 | protein | 352 | 7% helix, 40% strand | A0A087X1T6 |
| B | Protocadherin-15 | protein | 365 | 6% helix, 39% strand | A0A087X1T6 |
| C | Cadherin-23 | protein | 193 | 7% helix, 37% strand | Q99PF4 |
| D | Cadherin-23 | protein | 189 | 7% helix, 35% strand | Q99PF4 |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.80 | 0.82 | 90 | empty |
| 2 | 444 | 0.70 | 0.81 | 61 | empty |
| 3 | 357 | 0.63 | 0.78 | 33 | empty |
| 4 | 130 | 0.58 | 0.84 | 26 | empty |
| 5 | 159 | 0.52 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1296 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1220 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 393 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6N2E · Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23… · 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 A0A087X1T6
- Every structure of UniProt Q99PF4
- Elsewhere: RCSB PDB 6N2E · PDBe 6N2E · UniProt A0A087X1T6 · UniProt Q99PF4
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