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Structure of the F-actin-tropomyosin complex

Analyse Structure of the F-actin-tropomyosin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J8A
Type: protein
Length: 2,105 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tropomyosin alpha-1; Actin, alpha skeletal muscle
UniProt: P68135
Ligands: ADP, MG
Pockets: 18 · best druggability 0.83

Structure

electron microscopy · 2 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, G	Tropomyosin alpha-1	protein	135	99% helix, 0% strand	—
A, B, C, D, E	Actin, alpha skeletal muscle	protein	367	31% helix, 16% strand	P68135

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

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.83	0.84	86	empty
2	359	0.81	0.90	55	MG, ADP
3	325	0.79	0.90	52	MG, ADP
4	345	0.79	0.89	56	MG, ADP
5	342	0.79	0.89	53	MG, ADP

Interfaces

11 interfaces between chains.

F–G · 1813 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1138 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 1127 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 1126 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 462 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (methylation).

Compared structures

3J8A · Structure of the F-actin-tropomyosin complex · the same entry in another collection · chain E against E, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P68135
Elsewhere: RCSB PDB 3J8A · PDBe 3J8A · UniProt P68135

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