MolNFT v1 · #25884 · protein
Crystal structure of myosin V motor domain - nucleotide-free
1W8J · Myosin va: “Crystal structure of myosin V motor domain - nucleotide-free”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1 #25884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W8J
- Type
- protein
- Length
- 2,880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin va
- UniProt
- Q02440
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin va | protein | 722 | 44% helix, 15% strand | Q02440 |
| B | Myosin va | protein | 718 | 44% helix, 17% strand | Q02440 |
| C | Myosin va | protein | 723 | 44% helix, 17% strand | Q02440 |
| D | Myosin va | protein | 717 | 43% helix, 15% strand | Q02440 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.75 | 0.80 | 76 | empty |
| 2 | 690 | 0.73 | 0.79 | 62 | empty |
| 3 | 636 | 0.73 | 0.80 | 82 | SO4 |
| 4 | 711 | 0.73 | 0.79 | 60 | empty |
| 5 | 640 | 0.73 | 0.80 | 59 | empty |
Interfaces
1 interface between chains.
- B–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
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 Q02440
- Elsewhere: RCSB PDB 1W8J · PDBe 1W8J · UniProt Q02440
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