Research workbench

F-actin of cardiac thin filament in high-calcium state

Analyse F-actin of cardiac thin filament in high-calcium state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KLN
Type: protein
Length: 1,488 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Mus musculus
Molecule: Actin, alpha skeletal muscle
UniProt: P68134
Ligands: ADP, MG
Pockets: 11 · best druggability 0.79

Structure

electron microscopy · resolution 3.4 · 1 distinct chain · 35% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Actin, alpha skeletal muscle	protein	372	35% helix, 19% strand	P68134

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	689	0.79	0.83	79	empty
2	261	0.76	0.89	47	MG, ADP
3	278	0.76	0.89	48	MG, ADP
4	290	0.75	0.88	50	MG, ADP
5	264	0.75	0.89	45	MG, ADP

Interfaces

5 interfaces between chains.

B–D · 1269 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1259 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 445 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 421 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 407 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

6KLN · F-actin of cardiac thin filament in high-calcium state · the same entry in another collection · chain D against D, TM-score 1.00
P68134 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68134) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P68134
Elsewhere: RCSB PDB 6KLN · PDBe 6KLN · UniProt P68134

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