Research workbench
Cryo-EM structure of the ADP state wild type myosin-15-F-actin complex
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
- 7RB8
- Type
- protein
- Length
- 1,786 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle, intermediate form; Isoform 3 of unconventional myosin-xv
- UniProt
- P68139, Q9QZZ4
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Actin, alpha skeletal muscle, intermediate form | protein | 373 | 42% helix, 20% strand | P68139 |
| D | Isoform 3 of unconventional myosin-xv | protein | 667 | 47% helix, 13% strand | Q9QZZ4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
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 | 982 | 0.81 | 0.82 | 76 | empty |
| 2 | 751 | 0.80 | 0.84 | 91 | empty |
| 3 | 469 | 0.78 | 0.86 | 66 | ADP, MG |
| 4 | 256 | 0.76 | 0.89 | 40 | ADP, MG |
| 5 | 340 | 0.75 | 0.86 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1268 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 1227 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
- A–D · 457 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 7RB8 · cryo-EM structure of the ADP state wild type myosin-15-F-actin complex · the same entry in another collection · chain A against A, TM-score 1.00
- P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain C 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 7RB8 · PDBe 7RB8 · UniProt P68139 · UniProt Q9QZZ4
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