MolNFT v1 · #143293 · protein

Cryoem structure of mical oxidized actin (class 1)

6AVB · Actin, alpha skeletal muscle: “Cryoem structure of mical oxidized actin (class 1)”. Electron microscopy, 1 ligand (ADP), 7 pockets (best druggability 0.81). MolNFT v1 #143293 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6AVB
Type: protein
Length: 1,101 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle
UniProt: P68135
Ligands: ADP
Pockets: 7 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 34% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B	Actin, alpha skeletal muscle	protein	367	34% helix, 14% strand	P68135

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, A, B

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.81	0.82	106	empty
2	198	0.73	0.90	45	ADP
3	165	0.72	0.90	40	ADP
4	202	0.72	0.89	49	ADP
5	549	0.68	0.78	46	empty

Interfaces

3 interfaces between chains.

A–B · 1098 Å² buried · 10 hydrogen bonds · protein-protein
C–A · 439 Å² buried · 3 hydrogen bonds · protein-protein
C–B · 433 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (nonstandard, methylation).

Compared structures

6AVB · CryoEM structure of Mical Oxidized Actin (Class 1) · the same entry in another collection · chain C against C, 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 0.95

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 6AVB · PDBe 6AVB · UniProt P68135

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