MolNFT v1 · #146510 · protein

Cryo-EM structure of ADP-actin filaments

6DJO · Actin, alpha skeletal muscle: “Cryo-EM structure of ADP-actin filaments”. Electron microscopy, 2 ligands (ADP, MG), 12 pockets (best druggability 0.81). MolNFT v1 #146510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DJO
Type: protein
Length: 1,488 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle
UniProt: P68139
Ligands: ADP, MG
Pockets: 12 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Actin, alpha skeletal muscle	protein	372	34% helix, 19% strand	P68139

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

12 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	794	0.81	0.84	77	empty
2	283	0.76	0.89	49	MG, ADP
3	263	0.76	0.89	47	MG, ADP
4	273	0.75	0.88	48	MG, ADP
5	290	0.75	0.88	51	MG, ADP

Interfaces

5 interfaces between chains.

B–D · 1250 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1243 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 510 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 504 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 502 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation).

Compared structures

6DJO · Cryo-EM structure of ADP-actin filaments · the same entry in another collection · chain D against D, 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
Elsewhere: RCSB PDB 6DJO · PDBe 6DJO · UniProt P68139

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