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Crystal structure of the 46KDA domain of human cardiac troponin in the CA2+ saturated form

Analyse Crystal structure of the 46KDA domain of human cardiac troponin in the CA2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1J1D
Type: protein
Length: 698 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Troponin C; Troponin T; Troponin I
UniProt: P63316, P45379, P19429
Ligands: CA
Pockets: 9 · best druggability 0.49

Structure

x-ray diffraction · 6 distinct chains · 71% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Troponin C	protein	159	55% helix, 4% strand	P63316
B	Troponin T	protein	70	89% helix, 0% strand	P45379
C	Troponin I	protein	118	77% helix, 0% strand	P19429
D	Troponin C	protein	160	58% helix, 5% strand	P63316
E	Troponin T	protein	75	87% helix, 0% strand	P45379
F	Troponin I	protein	116	82% helix, 0% strand	P19429

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.49	0.79	20	empty
2	258	0.47	0.73	28	empty
3	117	0.45	0.78	19	empty
4	148	0.42	0.74	18	empty
5	70	0.39	0.79	19	empty

Interfaces

8 interfaces between chains.

A–C · 2372 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 2233 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2106 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 2081 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 449 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1J1D · Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form · the same entry in another collection · chain F against F, TM-score 1.00
P19429 · AlphaFold monomer V2.0 prediction for troponin I, cardiac muscle (P19429) · a predicted model of the same protein · chain F against A, TM-score 0.82
P45379 · AlphaFold monomer V2.0 prediction for troponin T, cardiac muscle (P45379) · a predicted model of the same protein · chain E against A, TM-score 0.71
P63316 · AlphaFold monomer V2.0 prediction for troponin C, slow skeletal and cardiac muscles… · a predicted model of the same protein · chain D 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 1J1D · PDBe 1J1D · UniProt P63316 · UniProt P45379 · UniProt P19429

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