Research workbench
Dictyostelium myosin S1DC (motor domain fragment) complexed with O- nitrophenyl aminoethyldiphosphate beryllium fluoride.
Analyse Dictyostelium myosin S1DC (motor domain fragment) complexed with O- nitrophenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D0Y
- Type
- protein
- Length
- 741 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin S1DC motor domain
- UniProt
- P08799
- Ligands
- ONP, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin S1DC motor domain | protein | 741 | 47% helix, 15% strand | P08799 |
Ligands and binding sites
- ONP · O-nitrophenyl aminoethyldiphosphate beryllium trifluoride · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.85 | 0.86 | 112 | MG, ONP |
| 2 | 947 | 0.72 | 0.76 | 80 | empty |
| 3 | 129 | 0.51 | 0.80 | 26 | empty |
| 4 | 93 | 0.49 | 0.82 | 19 | empty |
| 5 | 64 | 0.30 | 0.74 | 13 | empty |
Compared structures
- 1D0Y · Dictyostelium myosin S1DC (motor domain fragment) complexed with O-nitrophenyl… · 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 1D0Y · PDBe 1D0Y · UniProt P08799
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