Research workbench
Dictyostelium discoideum myosin II motor domain S456E with bound mgadp-befx
Analyse Dictyostelium discoideum myosin II motor domain S456E with bound mgadp-befx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W9K
- Type
- protein
- Length
- 719 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin II heavy chain
- EC
- 3.6.4.1
- UniProt
- P08799
- Ligands
- ADP, BEF, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin II heavy chain (EC 3.6.4.1) | protein | 719 | 47% helix, 16% strand | P08799 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.86 | 114 | MG, ADP, BEF, EDO |
| 2 | 51 | 0.61 | 0.92 | 15 | EDO |
| 3 | 291 | 0.56 | 0.76 | 32 | EDO |
| 4 | 92 | 0.44 | 0.79 | 18 | empty |
| 5 | 64 | 0.30 | 0.74 | 13 | empty |
Compared structures
- 1W9K · Dictyostelium discoideum Myosin II motor domain S456E with bound MgADP-BeFx · 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 0.92
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 1W9K · PDBe 1W9K · UniProt P08799
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