Research workbench

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

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

PDB: 5ONV
Type: protein
Length: 1,855 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle
UniProt: P68135
Ligands: ADP, MG
Pockets: 17 · best druggability 0.83

Structure

electron microscopy · 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

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	1116	0.83	0.84	100	empty
2	314	0.81	0.91	58	ADP, MG
3	527	0.80	0.86	65	empty
4	273	0.80	0.92	48	ADP, MG
5	288	0.79	0.90	47	ADP, MG

Interfaces

7 interfaces between chains.

B–D · 1198 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1197 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 1193 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 485 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 484 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (methylation).

Compared structures

5ONV · Cryo-EM structure of F-actin in complex with ADP · 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 0.96

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 P68135
Elsewhere: RCSB PDB 5ONV · PDBe 5ONV · UniProt P68135

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