Research workbench

Human cofilin-1 decorated actin filament

Analyse Human cofilin-1 decorated actin filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VAO
Type: protein
Length: 2,600 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Cofilin-1
UniProt: P68135, P23528
Ligands: ADP, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, E	Actin, alpha skeletal muscle	protein	356	41% helix, 19% strand	P68135
J, F, G, H, I	Cofilin-1	protein	164	27% helix, 29% strand	P23528

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains D, A, B, C, E
MG · Magnesium ion · metal · 5 copies · chains D, A, B, C, 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	938	0.84	0.86	101	MG, ADP
2	967	0.84	0.85	109	MG, ADP
3	818	0.81	0.84	77	empty
4	237	0.78	0.92	41	MG, ADP
5	881	0.77	0.80	92	MG, ADP

Interfaces

15 interfaces between chains.

D–G · 1123 Å² buried · 9 hydrogen bonds · protein-protein
A–I · 1104 Å² buried · 7 hydrogen bonds · protein-protein
H–E · 1098 Å² buried · 7 hydrogen bonds · protein-protein
J–C · 1095 Å² buried · 8 hydrogen bonds · protein-protein
E–I · 881 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6VAO · Human cofilin-1 decorated actin filament · the same entry in another collection · chain I against I, TM-score 1.00
P23528 · AlphaFold monomer V2.0 prediction for cofilin-1 (P23528) · a predicted model of the same protein · chain H 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
Every structure of UniProt P23528
Elsewhere: RCSB PDB 6VAO · PDBe 6VAO · UniProt P68135 · UniProt P23528

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