Research workbench
The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 ångström.
Analyse The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H53
- Type
- protein
- Length
- 1,894 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Skeletal muscle myosin heavy chain myhc-EO/IIL; Myosin regulatory light chain 2, skeletal…
- UniProt
- Q9GJP9, P24732, P02602, P68135
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Skeletal muscle myosin heavy chain myhc-EO/IIL | protein | 845 | 49% helix, 11% strand | Q9GJP9 |
| B | Myosin regulatory light chain 2, skeletal muscle isoform type 1 | protein | 146 | 50% helix, 0% strand | P24732 |
| C | Myosin light chain 1/3, skeletal muscle isoform | protein | 153 | 56% helix, 0% strand | P02602 |
| D, E | Actin, alpha skeletal muscle | protein | 375 | 43% helix, 16% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.86 | 0.92 | 93 | empty |
| 2 | 632 | 0.85 | 0.90 | 93 | empty |
| 3 | 225 | 0.80 | 0.93 | 51 | empty |
| 4 | 601 | 0.78 | 0.84 | 73 | empty |
| 5 | 453 | 0.78 | 0.87 | 58 | ADP |
Interfaces
6 interfaces between chains.
- A–C · 1611 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1421 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1232 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 746 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 205 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5H53 · The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 angstrom. · the same entry in another collection · chain E against E, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain E against A, TM-score 0.93
- P02602 · AlphaFold monomer V2.0 prediction for myosin light chain 1/3, skeletal muscle isoform… · a predicted model of the same protein · chain C against A, TM-score 0.83
- P24732 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain 2, skeletal muscle… · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9GJP9
- Every structure of UniProt P24732
- Every structure of UniProt P02602
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 5H53 · PDBe 5H53 · UniProt Q9GJP9 · UniProt P24732 · UniProt P02602 · UniProt P68135
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