MolNFT v1 · #190931 · protein

Structure of ADP-ribosylated F-actin

7Z7I · Actin, alpha skeletal muscle: “Structure of ADP-ribosylated F-actin”. Electron microscopy, 3 ligands (ADP, AR6, MG), 14 pockets (best druggability 0.81). MolNFT v1 #190931 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7Z7I
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, AR6, MG
Pockets: 14 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B, E, C, A	Actin, alpha skeletal muscle	protein	371	42% helix, 19% strand	P68135

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains D, B, E, C, A
AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 5 copies · chains D, B, E, C, A
MG · Magnesium ion · metal · 5 copies · chains D, B, E, C, A

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	865	0.81	0.84	99	empty
2	712	0.79	0.83	86	empty
3	352	0.78	0.89	43	ADP, MG
4	341	0.77	0.88	45	ADP, MG
5	371	0.77	0.87	47	ADP, MG

Interfaces

7 interfaces between chains.

D–B · 1119 Å² buried · 6 hydrogen bonds · protein-protein
C–A · 1116 Å² buried · 6 hydrogen bonds · protein-protein
E–C · 1114 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 451 Å² buried · 4 hydrogen bonds · protein-protein
D–C · 409 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7Z7I · Structure of ADP-ribosylated F-actin · the same entry in another collection · chain A against A, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain C 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 7Z7I · PDBe 7Z7I · UniProt P68135

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