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Cryo-EM structure of F-actin stabilized by trans-optojasp-8

Analyse Cryo-EM structure of F-actin stabilized by trans-optojasp-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AHQ
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, RLZ, MG, PO4
Pockets: 17 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Actin, alpha skeletal muscle	protein	371	42% helix, 18% strand	P68135

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
RLZ · ~{N}-[4-[(4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15, 19-tetramethyl-2,6,9,12-tetrakis(oxidanylidene)-1-oxa-5,8,11-triazacyclononadec-15-en-10-yl]butyl]-~{N}'-[5-methoxy-2-[(~{Z})-(3,4,5-trimethoxyphenyl) diazenyl]phenyl]butanediamide · ligand · 5 copies · chains A, B, C, D, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
PO4 · Phosphate ion · ion · 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	262	0.78	0.91	43	ADP, PO4, MG
2	269	0.78	0.91	44	ADP, PO4, MG
3	294	0.77	0.89	49	ADP, PO4, MG
4	266	0.77	0.90	44	ADP, PO4, MG
5	263	0.77	0.90	46	ADP, PO4, MG

Interfaces

7 interfaces between chains.

B–D · 1170 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1165 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 1164 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 516 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 496 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified, 3 covalent (methylation, covalent ligand).

Compared structures

7AHQ · Cryo-EM structure of F-actin stabilized by trans-optoJASP-8 · 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 7AHQ · PDBe 7AHQ · UniProt P68135

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