Research workbench
X-ray crystal structure of the mg (dot) 2'(3')-O-(N- methylanthraniloyl) nucleotide bound to dictyostelium discoideum myosin motor domain
Analyse X-ray crystal structure of the mg (dot) 2'(3')-O-(N- methylanthraniloyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LVK
- Type
- protein
- Length
- 743 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin
- UniProt
- P08799
- Ligands
- MNT, 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 | protein | 743 | 47% helix, 16% strand | P08799 |
Ligands and binding sites
- MNT · 2'(3')-O-N-methylanthraniloyl-adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · 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 | 1062 | 0.85 | 0.86 | 118 | MG, MNT, BEF |
| 2 | 861 | 0.71 | 0.77 | 71 | empty |
| 3 | 98 | 0.49 | 0.81 | 19 | empty |
| 4 | 76 | 0.40 | 0.79 | 15 | empty |
| 5 | 69 | 0.32 | 0.76 | 14 | empty |
Compared structures
- 1LVK · X-ray crystal structure of the mg (dot) 2'(3')-O-(N-methylanthraniloyl) nucleotide bound… · 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 0.89
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 1LVK · PDBe 1LVK · UniProt P08799
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