Research workbench
Myosin VI motor domain in the pi release state (with pi) space group P21
Analyse Myosin VI motor domain in the pi release state (with pi) space group P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PFP
- Type
- protein
- Length
- 1,526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-VI
- UniProt
- F1RQI7
- Ligands
- ADP, MG, PO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-VI | protein | 760 | 47% helix, 16% strand | F1RQI7 |
| C | Unconventional myosin-VI | protein | 766 | 47% helix, 16% strand | F1RQI7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
- PGO · S-1,2-propanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.86 | 0.87 | 131 | MG, ADP, PGO, PO4 |
| 2 | 911 | 0.74 | 0.78 | 86 | empty |
| 3 | 533 | 0.71 | 0.80 | 54 | ADP, PO4, MG |
| 4 | 654 | 0.70 | 0.78 | 62 | empty |
| 5 | 465 | 0.70 | 0.81 | 46 | empty |
Interfaces
1 interface between chains.
- A–C · 282 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PFP · Myosin VI motor domain in the Pi release state (with Pi) space group P21 · 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 F1RQI7
- Elsewhere: RCSB PDB 4PFP · PDBe 4PFP · UniProt F1RQI7
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