Research workbench
Crystal structure of MYO7B C-terminal MYTH4-ferm in complex with USH1C PDZ3
Analyse Crystal structure of MYO7B C-terminal MYTH4-ferm in complex with USH1C PDZ3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XBF
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-viib; Harmonin
- UniProt
- Q6PIF6, Q9Y6N9
- Ligands
- MLT
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-viib | protein | 467 | 48% helix, 17% strand | Q6PIF6 |
| B | Harmonin | protein | 119 | 21% helix, 29% strand | Q9Y6N9 |
Ligands and binding sites
- MLT · D-malate · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.56 | 0.81 | 32 | empty |
| 2 | 146 | 0.47 | 0.77 | 24 | empty |
| 3 | 124 | 0.46 | 0.77 | 16 | GOL |
| 4 | 93 | 0.45 | 0.79 | 16 | empty |
| 5 | 131 | 0.43 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1221 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5XBF · Crystal Structure of Myo7b C-terminal MyTH4-FERM in complex with USH1C PDZ3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PIF6 · AlphaFold monomer V2.0 prediction for unconventional myosin-viib (Q6PIF6) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9Y6N9 · AlphaFold monomer V2.0 prediction for harmonin (Q9Y6N9) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q6PIF6
- Every structure of UniProt Q9Y6N9
- Elsewhere: RCSB PDB 5XBF · PDBe 5XBF · UniProt Q6PIF6 · UniProt Q9Y6N9
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