Research workbench
Crystal structure of myosin V motor with essential light chain + ADP-befx - near rigor
Analyse Crystal structure of myosin V motor with essential light chain + ADP-befx… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7J
- Type
- protein
- Length
- 883 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin va; Myosin light chain 1
- UniProt
- Q02440, P14649
- Ligands
- ADP, BEF, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin va | protein | 752 | 48% helix, 15% strand | Q02440 |
| B | Myosin light chain 1 | protein | 131 | 51% helix, 9% strand | P14649 |
Ligands and binding sites
- ADP · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.76 | 0.78 | 115 | MG, ADP, BEF |
| 2 | 902 | 0.74 | 0.78 | 91 | empty |
| 3 | 147 | 0.46 | 0.77 | 23 | empty |
| 4 | 59 | 0.35 | 0.78 | 14 | empty |
| 5 | 58 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1535 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1W7J · Crystal Structure Of Myosin V Motor With Essential Light Chain + ADP-BeFx - Near Rigor · the same entry in another collection · chain A against A, TM-score 1.00
- Q02440 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q02440) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P14649 · AlphaFold monomer V2.0 prediction for myosin light chain 6B (P14649) · a predicted model of the same protein · chain B 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 Q02440
- Every structure of UniProt P14649
- Elsewhere: RCSB PDB 1W7J · PDBe 1W7J · UniProt Q02440 · UniProt P14649
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