Research workbench
Structure of harmonin NPDZ1 in complex with the SAM-pbm of sans
Analyse Structure of harmonin NPDZ1 in complex with the SAM-pbm of sans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K1R
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Harmonin; Usher syndrome type-1G protein
- UniProt
- Q9Y6N9, Q495M9
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Harmonin | protein | 192 | 44% helix, 23% strand | Q9Y6N9 |
| B | Usher syndrome type-1G protein | protein | 74 | 61% helix, 3% strand | Q495M9 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.34 | 0.74 | 15 | empty |
| 2 | 68 | 0.32 | 0.75 | 23 | empty |
| 3 | 65 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1372 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3K1R · Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6N9 · AlphaFold monomer V2.0 prediction for harmonin (Q9Y6N9) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q495M9 · AlphaFold monomer V2.0 prediction for usher syndrome type-1G protein (Q495M9) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q495M9
- Elsewhere: RCSB PDB 3K1R · PDBe 3K1R · UniProt Q9Y6N9 · UniProt Q495M9
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