Research workbench

Cryo-EM structure of F-actin in complex with ADP-BeFx

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

PDB: 5OOF
Type: protein
Length: 1,855 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Oryctolagus cuniculus
Molecule: Actin, alpha skeletal muscle
UniProt: P68135
Ligands: ADP, MG
Pockets: 16 · best druggability 0.83

Structure

electron microscopy · resolution 3.4 · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Actin, alpha skeletal muscle	protein	371	44% helix, 20% 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

16 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	1047	0.83	0.84	109	empty
2	839	0.81	0.84	85	empty
3	399	0.79	0.88	53	ADP, MG
4	347	0.78	0.89	55	ADP, MG
5	396	0.78	0.87	55	ADP, MG

Interfaces

7 interfaces between chains.

A–C · 1102 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 1102 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1101 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 492 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 492 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (methylation).

Compared structures

5OOF · Cryo-EM structure of F-actin in complex with ADP-befx · 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 E 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 5OOF · PDBe 5OOF · UniProt P68135

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