Research workbench

Structure of bare actin filament

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

PDB: 6BNO
Type: protein
Length: 2,936 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle
UniProt: P68135
Ligands: ADP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Actin, alpha skeletal muscle	protein	367	39% helix, 19% strand	P68135

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.83	0.86	96	empty
2	985	0.83	0.84	95	empty
3	619	0.78	0.84	50	empty
4	290	0.75	0.88	44	MG, ADP
5	450	0.75	0.84	63	empty

Interfaces

13 interfaces between chains.

A–C · 1152 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 1120 Å² buried · 18 hydrogen bonds · protein-protein
E–G · 1116 Å² buried · 14 hydrogen bonds · protein-protein
F–H · 1107 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 1079 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6BNO · Structure of bare actin filament · the same entry in another collection · chain H against H, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain H against A, TM-score 0.95

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 6BNO · PDBe 6BNO · UniProt P68135

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