MolNFT v2 · #222625 · protein
The structure of the native cardiac thin filament troponin core in Ca2+-bound fully activated state 1 from the lower strand
8V01 · Actin, alpha cardiac muscle 1: “The structure of the native cardiac thin filament troponin core in Ca2+-bound fully activated state 1 from…”. Electron microscopy at 5.5, 3 ligands (ADP, CA, MG), 14 pockets (best druggability 0.82).…
- PDB
- 8V01
- Type
- protein
- Length
- 1,274 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.5
- Source
- Sus scrofa
- Molecule
- Actin, alpha cardiac muscle 1; Troponin C, slow skeletal and cardiac muscles; Troponin I…
- UniProt
- B6VNT8, P63317, A0A4X1V710, A0A5G2Q8N0, P42639
- Ligands
- ADP, CA, MG
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · resolution 5.5 · 5 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha cardiac muscle 1 | protein | 375 | 39% helix, 18% strand | B6VNT8 |
| C | Troponin C, slow skeletal and cardiac muscles | protein | 160 | 58% helix, 0% strand | P63317 |
| D | Troponin I, cardiac muscle | protein | 126 | 72% helix, 0% strand | A0A4X1V710 |
| E | Troponin T2, cardiac type | protein | 74 | 82% helix, 0% strand | A0A5G2Q8N0 |
| F, G | Tropomyosin alpha-1 chain | protein | 82 | 98% helix, 0% strand | P42639 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.82 | 0.84 | 107 | empty |
| 2 | 621 | 0.79 | 0.84 | 90 | ADP, MG |
| 3 | 974 | 0.77 | 0.79 | 97 | ADP, MG |
| 4 | 711 | 0.68 | 0.76 | 56 | empty |
| 5 | 254 | 0.64 | 0.81 | 31 | empty |
Interfaces
15 interfaces between chains.
- D–E · 2165 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 2004 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1832 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 392 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- P63317 · AlphaFold monomer V2.0 prediction for troponin C, slow skeletal and cardiac muscles… · a predicted model of the same protein · chain C against A, TM-score 0.42
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
- Every structure of UniProt P63317
- Every structure of UniProt A0A4X1V710
- Every structure of UniProt A0A5G2Q8N0
- Every structure of UniProt P42639
- Elsewhere: RCSB PDB 8V01 · PDBe 8V01 · UniProt B6VNT8 · UniProt P63317 · UniProt A0A4X1V710 · UniProt A0A5G2Q8N0 · UniProt P42639
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