Research workbench
Plasmodium falciparum myosin a full-length, pre-powerstroke state
Analyse Plasmodium falciparum myosin a full-length, pre-powerstroke state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YCX
- Type
- protein
- Length
- 2,155 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-a; Myosin a tail domain interacting protein; Uncharacterized protein
- UniProt
- Q8IDR3, W7K1J7, A0A2I0BQX1
- Ligands
- ADP, MG, VO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-a | protein | 814 | 47% helix, 14% strand | Q8IDR3 |
| B | Myosin-a | protein | 817 | 47% helix, 14% strand | Q8IDR3 |
| D, H | Myosin a tail domain interacting protein | protein | 133 | 59% helix, 8% strand | W7K1J7 |
| F | Uncharacterized protein | protein | 133 | 54% helix, 5% strand | A0A2I0BQX1 |
| G | Uncharacterized protein | protein | 125 | 48% helix, 6% strand | A0A2I0BQX1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.86 | 0.86 | 92 | empty |
| 2 | 490 | 0.82 | 0.88 | 54 | empty |
| 3 | 157 | 0.77 | 0.94 | 31 | empty |
| 4 | 398 | 0.76 | 0.86 | 37 | empty |
| 5 | 779 | 0.75 | 0.80 | 89 | empty |
Interfaces
7 interfaces between chains.
- A–F · 1925 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 1733 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1294 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 1283 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 998 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
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 Q8IDR3
- Every structure of UniProt W7K1J7
- Every structure of UniProt A0A2I0BQX1
- Elsewhere: RCSB PDB 6YCX · PDBe 6YCX · UniProt Q8IDR3 · UniProt W7K1J7 · UniProt A0A2I0BQX1
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