Research workbench

Actin phalloidin at befx state

Analyse Actin phalloidin at befx state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U96
Type: protein
Length: 1,890 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Phalloidin derivative
UniProt: P68135
Ligands: ADP
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 2 distinct chains · 35% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Actin, alpha skeletal muscle	protein	371	36% helix, 15% strand	P68135
F, G, H, I, J	Phalloidin derivative	protein	7	0% helix, 14% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.79	0.96	29	empty
2	566	0.78	0.85	58	ADP
3	589	0.78	0.84	64	ADP
4	549	0.78	0.85	60	ADP
5	805	0.78	0.82	66	empty

Interfaces

20 interfaces between chains.

A–D · 1078 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 1067 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 1049 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 320 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 319 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (nonstandard, hydroxylation, methylation).

Compared structures

6U96 · Actin phalloidin at BeFx state · the same entry in another collection · chain J against J, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain D against A, TM-score 0.92

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 6U96 · PDBe 6U96 · UniProt P68135

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