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Near-atomic resolution for one state of F-actin

Analyse Near-atomic resolution for one state of F-actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J8I
Type: protein
Length: 1,875 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: 19 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 33% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F, G, H	Actin, alpha skeletal muscle	protein	375	33% helix, 13% strand	P68135

Ligands and binding sites

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

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	803	0.81	0.84	84	empty
2	509	0.72	0.81	50	empty
3	325	0.72	0.84	35	empty
4	326	0.72	0.84	33	empty
5	267	0.71	0.85	36	ADP, MG

Interfaces

7 interfaces between chains.

F–H · 1225 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 1225 Å² buried · 7 hydrogen bonds · protein-protein
E–G · 1223 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 439 Å² buried · 7 hydrogen bonds · protein-protein
F–G · 437 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3J8I · Near-Atomic Resolution for One State of F-Actin · 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 E against A, TM-score 0.94

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 3J8I · PDBe 3J8I · UniProt P68135

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