Research workbench

F-actin-utrophin complex

Analyse F-actin-utrophin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M5G
Type: protein
Length: 2,204 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Utrophin
UniProt: P68139, P46939
Ligands: ADP, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 2 distinct chains · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Actin, alpha skeletal muscle	protein	370	39% helix, 18% strand	P68139
F, G, H	Utrophin	protein	118	59% helix, 0% strand	P46939

Ligands and binding sites

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

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	878	0.81	0.83	104	empty
2	309	0.78	0.90	46	MG, ADP
3	340	0.77	0.88	53	MG, ADP
4	280	0.77	0.89	45	MG, ADP
5	465	0.74	0.83	71	MG, ADP

Interfaces

13 interfaces between chains.

C–H · 1414 Å² buried · 18 hydrogen bonds · protein-protein
B–F · 1406 Å² buried · 21 hydrogen bonds · protein-protein
A–G · 1364 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1194 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 1172 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6M5G · F-actin-Utrophin complex · the same entry in another collection · chain H against H, TM-score 1.00
P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain C 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
Every structure of UniProt P46939
Elsewhere: RCSB PDB 6M5G · PDBe 6M5G · UniProt P68139 · UniProt P46939

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