MolNFT v1 · #117162 · protein
Protocadherin beta 8 extracellular cadherin domains 1-4
5DZY · PCDHB8 protein: “Protocadherin beta 8 extracellular cadherin domains 1-4”. X-ray diffraction, 6 ligands (MAN, NAG, FUC), 20 pockets (best druggability 0.73). MolNFT v1 #117162 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DZY
- Type
- protein
- Length
- 2,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PCDHB8 protein
- UniProt
- A8E4K6
- Ligands
- MAN, NAG, FUC, BMA, GAL, CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PCDHB8 protein | protein | 414 | 5% helix, 46% strand | A8E4K6 |
| B, F | PCDHB8 protein | protein | 415 | 6% helix, 47% strand | A8E4K6 |
| C | PCDHB8 protein | protein | 415 | 7% helix, 47% strand | A8E4K6 |
| D | PCDHB8 protein | protein | 412 | 5% helix, 46% strand | A8E4K6 |
| E | PCDHB8 protein | protein | 413 | 6% helix, 48% strand | A8E4K6 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 21 copies · chains A, D, B, C, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains F
- GAL · beta-D-galactopyranose · sugar
- CA · Calcium ion · metal · 54 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.73 | 0.79 | 82 | empty |
| 2 | 75 | 0.73 | 0.96 | 19 | empty |
| 3 | 69 | 0.71 | 0.96 | 20 | empty |
| 4 | 61 | 0.70 | 0.97 | 18 | empty |
| 5 | 483 | 0.65 | 0.77 | 54 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2670 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2497 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2475 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 705 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 559 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 6 disulfide (O-glycosylation, N-glycosylation, disulfide).
Compared structures
- 5DZY · Protocadherin beta 8 extracellular cadherin domains 1-4 · the same entry in another collection · chain D against D, 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 A8E4K6
- Elsewhere: RCSB PDB 5DZY · PDBe 5DZY · UniProt A8E4K6
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