Research workbench
CA2+-induced movement of tropomyosin on native cardiac thin filaments - "open" state
Analyse CA2+-induced movement of tropomyosin on native cardiac thin filaments - "open"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NOJ
- Type
- protein
- Length
- 2,107 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Cardiac alpha tropomyosin
- UniProt
- P68137
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 367 | 42% helix, 18% strand | P68137 |
| F, H | Cardiac alpha tropomyosin | protein | 136 | 99% helix, 0% strand | — |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.81 | 0.86 | 83 | empty |
| 2 | 237 | 0.76 | 0.90 | 42 | ADP, MG |
| 3 | 348 | 0.75 | 0.86 | 47 | empty |
| 4 | 233 | 0.75 | 0.90 | 41 | ADP, MG |
| 5 | 252 | 0.74 | 0.88 | 42 | ADP, MG |
Interfaces
13 interfaces between chains.
- F–H · 1897 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 1127 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1122 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1119 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 515 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 5NOJ · Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "OPEN" state · the same entry in another collection · chain H against H, TM-score 1.00
- P68137 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68137) · a predicted model of the same protein · chain D 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 P68137
- Elsewhere: RCSB PDB 5NOJ · PDBe 5NOJ · UniProt P68137
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