Research workbench
In situ structure of actomyosin complex in skeletal sarcomere
Analyse In situ structure of actomyosin complex in skeletal sarcomere in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QIN
- Type
- protein
- Length
- 3,939 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Nebulin (mouse); Tropomyosin, alpha-1 (mouse); Myosin-4
- UniProt
- P68134, Q5SX39
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 371 | 43% helix, 18% strand | P68134 |
| F | Nebulin (mouse) | protein | 105 | 74% helix, 0% strand | — |
| G | Nebulin (mouse) | protein | 70 | 74% helix, 0% strand | — |
| H | Tropomyosin, alpha-1 (mouse) | protein | 117 | 98% helix, 0% strand | — |
| I | Tropomyosin, alpha-1 (mouse) | protein | 118 | 98% helix, 0% strand | — |
| J, K | Tropomyosin, alpha-1 (mouse) | protein | 88 | 98% helix, 0% strand | — |
| L, M | Myosin-4 | protein | 749 | 46% helix, 14% strand | Q5SX39 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.88 | 0.89 | 137 | empty |
| 2 | 706 | 0.87 | 0.91 | 103 | ADP, MG |
| 3 | 996 | 0.86 | 0.87 | 126 | empty |
| 4 | 600 | 0.85 | 0.90 | 88 | ADP, MG |
| 5 | 391 | 0.85 | 0.93 | 69 | ADP, MG |
Interfaces
32 interfaces between chains.
- A–C · 1186 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 1182 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1174 Ų buried · 7 hydrogen bonds · protein-protein
- E–L · 1052 Ų buried · 12 hydrogen bonds · protein-protein
- C–M · 1014 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 7QIN · In situ structure of actomyosin complex in skeletal sarcomere · the same entry in another collection · chain M against M, TM-score 1.00
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 P68134
- Every structure of UniProt Q5SX39
- Elsewhere: RCSB PDB 7QIN · PDBe 7QIN · UniProt P68134 · UniProt Q5SX39
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