MolNFT v1 · #120582 · protein
The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 ångström.
5H53 · Skeletal muscle myosin heavy chain myhc-EO/IIL: “The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 ångström.”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #120582 on…
- 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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