MolNFT v1 · #31123 · protein
Structure of the nucleotide-free myosin II motor domain from dictyostelium discoideum fused to the GTPase domain of dynamin 1 from rattus norvegicus
2AKA · Myosin II heavy chain: “Structure of the nucleotide-free myosin II motor domain from dictyostelium discoideum fused to the GTPase…”. X-ray diffraction, 10 pockets (best druggability 0.79). MolNFT v1 #31123 on GenesisL1: 3D…
- PDB
- 2AKA
- Type
- protein
- Length
- 1,069 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin II heavy chain; Linker; Dynamin-1
- EC
- 3.6.5.5
- UniProt
- P08799, P21575
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin II heavy chain | protein | 764 | 45% helix, 16% strand | P08799 |
| L | Linker | protein | 6 | 0% helix, 0% strand | — |
| B | Dynamin-1 (EC 3.6.5.5) | protein | 299 | 39% helix, 17% strand | P21575 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.79 | 0.92 | 26 | empty |
| 2 | 1052 | 0.78 | 0.80 | 86 | empty |
| 3 | 525 | 0.77 | 0.85 | 85 | empty |
| 4 | 949 | 0.74 | 0.78 | 78 | empty |
| 5 | 50 | 0.51 | 0.88 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 672 Ų buried · 8 hydrogen bonds · protein-protein
- L–B · 399 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 191 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2AKA · Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum… · the same entry in another collection · chain A against A, TM-score 1.00
- P21575 · AlphaFold monomer V2.0 prediction for dynamin-1 (P21575) · a predicted model of the same protein · chain B against A, TM-score 0.94
- 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 0.86
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
- Every structure of UniProt P21575
- Elsewhere: RCSB PDB 2AKA · PDBe 2AKA · UniProt P08799 · UniProt P21575
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