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Cryo-EM structure of amppnp-actin filaments

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

PDB: 6DJM
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: ANP, MG
Pockets: 14 · best druggability 0.77

Structure

electron microscopy · 1 distinct chain · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Actin, alpha skeletal muscle	protein	372	37% helix, 19% strand	P68139

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

14 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	277	0.77	0.90	52	MG, ANP
2	266	0.76	0.89	47	MG, ANP
3	275	0.76	0.89	48	MG, ANP
4	259	0.74	0.88	45	MG, ANP
5	272	0.71	0.86	52	empty

Interfaces

5 interfaces between chains.

B–D · 1269 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1266 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 468 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 468 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 465 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

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

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