Research workbench
Cryo-EM structure of the ADP state wild type myosin-15-F-actin complex (symmetry expansion and re-centering)
Analyse Cryo-EM structure of the ADP state wild type myosin-15-F-actin complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UDU
- Type
- protein
- Length
- 1,966 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Unconventional myosin-xv; Regulatory light chain
- UniProt
- P68139, Q9QZZ4
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Actin, alpha skeletal muscle | protein | 373 | 42% helix, 20% strand | P68139 |
| D | Unconventional myosin-xv | protein | 701 | 50% helix, 12% strand | Q9QZZ4 |
| E | Regulatory light chain | protein | 146 | 49% helix, 3% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.82 | 0.83 | 85 | empty |
| 2 | 331 | 0.78 | 0.89 | 50 | ADP, MG |
| 3 | 321 | 0.77 | 0.88 | 48 | ADP, MG |
| 4 | 94 | 0.75 | 0.96 | 26 | empty |
| 5 | 1000 | 0.75 | 0.78 | 78 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1480 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1265 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1220 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 7UDU · cryo-EM structure of the ADP state wild type myosin-15-F-actin complex (symmetry… · the same entry in another collection · chain E against E, TM-score 1.00
- P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P68139
- Every structure of UniProt Q9QZZ4
- Elsewhere: RCSB PDB 7UDU · PDBe 7UDU · UniProt P68139 · UniProt Q9QZZ4
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