Research workbench
Myosin VI (md-INSERT2-cam, delta-INSERT1) post-rigor state - long soaking with PO4
Analyse Myosin VI (md-INSERT2-cam, delta-INSERT1) post-rigor state - long soaking with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJJ
- Type
- protein
- Length
- 889 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-VI; Calmodulin
- UniProt
- F1RQI7, P62152
- Ligands
- ADP, CA, MG, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-VI | protein | 743 | 50% helix, 15% strand | F1RQI7 |
| B | Calmodulin | protein | 146 | 58% helix, 4% strand | P62152 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.81 | 0.82 | 116 | ADP, MG, PO4, GOL |
| 2 | 1085 | 0.75 | 0.78 | 95 | empty |
| 3 | 61 | 0.71 | 0.97 | 25 | empty |
| 4 | 114 | 0.41 | 0.76 | 19 | empty |
| 5 | 75 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2459 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4PJJ · MYOSIN VI (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state - long soaking with PO4 · the same entry in another collection · chain A against A, TM-score 1.00
- P62152 · AlphaFold monomer V2.0 prediction for calmodulin (P62152) · a predicted model of the same protein · chain B against A, TM-score 0.48
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
- Every structure of UniProt P62152
- Elsewhere: RCSB PDB 4PJJ · PDBe 4PJJ · UniProt F1RQI7 · UniProt P62152
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