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Cryo-EM structure of ADP-pi-actin filaments

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

PDB: 6DJN
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: P68139
Ligands: ADP, MG, PO4
Pockets: 15 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Actin, alpha skeletal muscle	protein	372	36% helix, 20% strand	P68139

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
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

15 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	266	0.75	0.89	54	MG, ADP, PO4
2	243	0.75	0.89	49	MG, ADP, PO4
3	264	0.74	0.88	47	MG, ADP, PO4
4	257	0.74	0.88	50	MG, ADP, PO4
5	172	0.67	0.87	24	empty

Interfaces

5 interfaces between chains.

A–C · 1241 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 1237 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 471 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 469 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 466 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

6DJN · Cryo-EM structure of ADP-Pi-actin filaments · the same entry in another collection · chain B against B, TM-score 1.00
P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain C 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 6DJN · PDBe 6DJN · UniProt P68139

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