MolNFT v1 · #118505 · protein
Crystal structure of harmonin NPDZ1 in complex with ANKS4B SAM-pbm
5F3X: “Crystal structure of harmonin NPDZ1 in complex with ANKS4B SAM-pbm”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.36). MolNFT v1 #118505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F3X
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Harmonin; Ankyrin repeat and SAM domain-containing protein 4B
- UniProt
- Q9Y6N9, Q8K3X6
- Ligands
- CL
- Pockets
- 4 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Harmonin | protein | 189 | 42% helix, 24% strand | Q9Y6N9 |
| B, D | Ankyrin repeat and SAM domain-containing protein 4B | protein | 75 | 63% helix, 3% strand | Q8K3X6 |
| C | Harmonin | protein | 191 | 44% helix, 24% strand | Q9Y6N9 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.36 | 0.78 | 14 | empty |
| 2 | 88 | 0.35 | 0.74 | 13 | empty |
| 3 | 69 | 0.33 | 0.75 | 13 | empty |
| 4 | 58 | 0.33 | 0.77 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1346 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1345 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5F3X · Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y6N9 · AlphaFold monomer V2.0 prediction for harmonin (Q9Y6N9) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q8K3X6 · AlphaFold monomer V2.0 prediction for ankyrin repeat and SAM domain- containing protein… · a predicted model of the same protein · chain B against A, TM-score 0.85
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 Q9Y6N9
- Every structure of UniProt Q8K3X6
- Elsewhere: RCSB PDB 5F3X · PDBe 5F3X · UniProt Q9Y6N9 · UniProt Q8K3X6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.