Research workbench
CA2+-induced movement of tropomyosin on native cardiac thin filaments - "closed" state
Analyse CA2+-induced movement of tropomyosin on native cardiac thin filaments… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NOL
- Type
- protein
- Length
- 2,105 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cardiac muscle alpha actin 1; Cardiac alpha tropomyosin
- UniProt
- B6VNT8
- Ligands
- ADP, MG
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cardiac muscle alpha actin 1 | protein | 367 | 44% helix, 17% strand | B6VNT8 |
| F, G | Cardiac alpha tropomyosin | protein | 135 | 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
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.80 | 0.86 | 82 | empty |
| 2 | 220 | 0.78 | 0.92 | 46 | ADP, MG |
| 3 | 208 | 0.76 | 0.91 | 41 | ADP, MG |
| 4 | 207 | 0.76 | 0.91 | 45 | ADP, MG |
| 5 | 216 | 0.76 | 0.91 | 45 | ADP, MG |
Interfaces
10 interfaces between chains.
- F–G · 1809 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 1198 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1194 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 498 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5NOL · Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Closed" state · the same entry in another collection · chain A against A, 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 B6VNT8
- Elsewhere: RCSB PDB 5NOL · PDBe 5NOL · UniProt B6VNT8
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