Research workbench
High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing
Analyse High-resolution cryo-EM structures of actin-bound myosin states reveal the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C1D
- Type
- protein
- Length
- 2,759 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Unconventional myosin-ib; Calmodulin; Phalloidin
- UniProt
- P68135, Q05096
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 375 | 40% helix, 17% strand | P68135 |
| P | Unconventional myosin-ib | protein | 729 | 45% helix, 12% strand | Q05096 |
| R | Calmodulin | protein | 148 | 55% helix, 5% strand | — |
| F | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, P
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, P
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 | 1125 | 0.84 | 0.85 | 97 | empty |
| 2 | 663 | 0.77 | 0.82 | 64 | empty |
| 3 | 521 | 0.75 | 0.83 | 54 | empty |
| 4 | 994 | 0.75 | 0.78 | 99 | empty |
| 5 | 236 | 0.72 | 0.87 | 39 | ADP, MG |
Interfaces
13 interfaces between chains.
- B–P · 1279 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1238 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1225 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1223 Ų buried · 14 hydrogen bonds · protein-protein
- D–P · 562 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 d-amino (nonstandard, D-amino acid, hydroxylation).
Compared structures
- 6C1D · High-Resolution Cryo-EM Structures of Actin-bound Myosin States Reveal the Mechanism of… · the same entry in another collection · chain F against F, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P68135
- Every structure of UniProt Q05096
- Elsewhere: RCSB PDB 6C1D · PDBe 6C1D · UniProt P68135 · UniProt Q05096
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