Research workbench

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

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

PDB: 6KLL
Type: protein
Length: 1,488 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle
UniProt: P68134
Ligands: ADP, MG
Pockets: 13 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Actin, alpha skeletal muscle	protein	372	40% 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

13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	695	0.78	0.83	77	empty
2	290	0.76	0.88	52	MG, ADP
3	306	0.75	0.88	52	MG, ADP
4	327	0.75	0.87	58	MG, ADP
5	306	0.75	0.87	49	MG, ADP

Interfaces

5 interfaces between chains.

B–D · 1234 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1234 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 445 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 445 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 428 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

6KLL · F-actin of cardiac thin filament in low-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 A 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 6KLL · PDBe 6KLL · UniProt P68134

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