Research workbench
Core domain of human cardiac troponin
Analyse Core domain of human cardiac troponin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y99
- Type
- protein
- Length
- 355 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Troponin C, slow skeletal and cardiac muscles; Troponin T, cardiac muscle; Troponin I…
- UniProt
- P63316, P45379, P19429
- Ligands
- CA
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Troponin C, slow skeletal and cardiac muscles | protein | 155 | 59% helix, 4% strand | P63316 |
| B | Troponin T, cardiac muscle | protein | 74 | 82% helix, 0% strand | P45379 |
| C | Troponin I, cardiac muscle | protein | 126 | 76% helix, 0% strand | P19429 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.55 | 0.76 | 30 | empty |
| 2 | 63 | 0.53 | 0.87 | 16 | DMS |
| 3 | 115 | 0.46 | 0.79 | 20 | DMS |
| 4 | 93 | 0.44 | 0.79 | 17 | DMS |
| 5 | 110 | 0.35 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2410 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2391 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4Y99 · Core domain of human cardiac troponin · the same entry in another collection · chain A against A, TM-score 1.00
- P45379 · AlphaFold monomer V2.0 prediction for troponin T, cardiac muscle (P45379) · a predicted model of the same protein · chain B against A, TM-score 0.79
- P19429 · AlphaFold monomer V2.0 prediction for troponin I, cardiac muscle (P19429) · a predicted model of the same protein · chain C against A, TM-score 0.78
- P63316 · AlphaFold monomer V2.0 prediction for troponin C, slow skeletal and cardiac muscles… · a predicted model of the same protein · chain A against A, TM-score 0.53
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 P63316
- Every structure of UniProt P45379
- Every structure of UniProt P19429
- Elsewhere: RCSB PDB 4Y99 · PDBe 4Y99 · UniProt P63316 · UniProt P45379 · UniProt P19429
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