Research workbench
Myosin VI (md-INSERT2-cam, delta-INSERT1) post-rigor state
Analyse Myosin VI (md-INSERT2-cam, delta-INSERT1) post-rigor state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VAS
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin VI; Calmodulin
- UniProt
- Q29122, P62152
- Ligands
- ADP, BEF, CA, MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin VI | protein | 732 | 50% helix, 15% strand | Q29122 |
| B | Calmodulin | protein | 141 | 58% helix, 3% strand | P62152 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.80 | 0.82 | 113 | ADP, BEF, MG |
| 2 | 629 | 0.72 | 0.79 | 52 | empty |
| 3 | 197 | 0.60 | 0.82 | 41 | empty |
| 4 | 150 | 0.47 | 0.77 | 26 | empty |
| 5 | 53 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2374 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2VAS · Myosin VI (MD-insert2-CaM, Delta-Insert1) Post-rigor state · the same entry in another collection · chain A against A, TM-score 1.00
- Q29122 · AlphaFold monomer V2.0 prediction for unconventional myosin-VI (Q29122) · a predicted model of the same protein · chain A against A, TM-score 0.82
- P62152 · AlphaFold monomer V2.0 prediction for calmodulin (P62152) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 Q29122
- Every structure of UniProt P62152
- Elsewhere: RCSB PDB 2VAS · PDBe 2VAS · UniProt Q29122 · UniProt P62152
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