Research workbench

Cryo-EM structure of the ADP state actin filament

Analyse Cryo-EM structure of the ADP state actin filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R8V
Type: protein
Length: 1,855 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle, intermediate form
UniProt: P68139
Ligands: ADP, MG
Pockets: 17 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, D, E	Actin, alpha skeletal muscle, intermediate form	protein	371	43% helix, 20% strand	P68139

Ligands and binding sites

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

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

Pockets

17 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	973	0.82	0.83	89	empty
2	765	0.80	0.83	81	empty
3	278	0.78	0.90	54	ADP, MG
4	285	0.77	0.89	55	ADP, MG
5	364	0.76	0.87	59	ADP, MG

Interfaces

7 interfaces between chains.

D–E · 1224 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1224 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 1217 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 446 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 445 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (methylation).

Compared structures

7R8V · Cryo-EM structure of the ADP state actin filament · the same entry in another collection · chain E against E, TM-score 1.00
P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain D 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 P68139
Elsewhere: RCSB PDB 7R8V · PDBe 7R8V · UniProt P68139

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.