Research workbench
Myosin VI nucleotide-free (MDINSERT2) L310G mutant crystal structure
Analyse Myosin VI nucleotide-free (MDINSERT2) L310G mutant crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9I
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-VI; Calmodulin
- UniProt
- Q29122, P62152
- Ligands
- CA, PO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-VI | protein | 791 | 49% helix, 16% strand | Q29122 |
| C | Calmodulin | protein | 145 | 57% helix, 1% strand | P62152 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C
- PO4 · Phosphate ion · ion · 4 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- TBU · Tertiary-butyl alcohol · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.79 | 0.83 | 96 | ACT |
| 2 | 984 | 0.74 | 0.77 | 74 | empty |
| 3 | 431 | 0.73 | 0.83 | 53 | TBU |
| 4 | 61 | 0.53 | 0.87 | 17 | empty |
| 5 | 224 | 0.50 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–C · 2362 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3L9I · Myosin VI nucleotide-free (mdinsert2) L310G mutant crystal structure · 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 0.85
- P62152 · AlphaFold monomer V2.0 prediction for calmodulin (P62152) · a predicted model of the same protein · chain C against A, TM-score 0.49
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 3L9I · PDBe 3L9I · UniProt Q29122 · UniProt P62152
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