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Crystal structure of myosin-2 dictyostelium discoideum motor domain S456Y mutant in complex with ADP-orthovanadate
Analyse Crystal structure of myosin-2 dictyostelium discoideum motor domain S456Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKD
- Type
- protein
- Length
- 692 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-2 heavy chain
- EC
- 3.6.4.1
- UniProt
- P08799
- Ligands
- ADP, MG, VO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-2 heavy chain (EC 3.6.4.1) | protein | 692 | 45% helix, 17% strand | P08799 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- VO4 · Vanadate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.78 | 0.80 | 84 | empty |
| 2 | 522 | 0.70 | 0.79 | 63 | MG, VO4, ADP |
| 3 | 177 | 0.50 | 0.77 | 21 | empty |
| 4 | 61 | 0.34 | 0.77 | 13 | empty |
| 5 | 63 | 0.33 | 0.76 | 15 | empty |
Compared structures
- 3MKD · Crystal structure of myosin-2 dictyostelium discoideum motor domain S456Y mutant in… · the same entry in another collection · chain A against A, TM-score 1.00
- P08799 · AlphaFold monomer V2.0 prediction for myosin-2 heavy chain (P08799) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P08799
- Elsewhere: RCSB PDB 3MKD · PDBe 3MKD · UniProt P08799
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