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

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

PDB: 7AHN
Type: protein
Length: 1,835 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: 15 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, E, D, B	Actin, alpha skeletal muscle	protein	367	44% helix, 19% strand	P68135

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains C, A, E, D, B
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 C, E, D, A, B
MG · Magnesium ion · metal · 5 copies · chains C, A, E, D, B
PO4 · Phosphate ion · ion · 5 copies · chains C, A, E, D, B

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

Pockets

15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.81	0.84	92	empty
2	298	0.77	0.89	48	ADP, MG, PO4
3	315	0.77	0.88	51	ADP, MG, PO4
4	305	0.77	0.89	50	ADP, MG, PO4
5	311	0.76	0.88	49	ADP, MG, PO4

Interfaces

7 interfaces between chains.

D–B · 1119 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 1104 Å² buried · 8 hydrogen bonds · protein-protein
C–A · 1103 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 493 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 485 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified, 2 covalent (methylation, covalent ligand).

Compared structures

7AHN · Cryo-EM structure of F-actin stabilized by cis-optoJASP-8 · the same entry in another collection · chain B against B, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · 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 P68135
Elsewhere: RCSB PDB 7AHN · PDBe 7AHN · UniProt P68135

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