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Isolated S3D-cofilin bound to an actin filament

Analyse Isolated S3D-cofilin bound to an actin filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UC0
Type: protein
Length: 2,754 residues
Chains: 8
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 0.83

Structure

electron microscopy · 2 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Actin, alpha skeletal muscle	protein	370	40% helix, 18% strand	P68135
I	Cofilin-1	protein	164	27% helix, 29% strand	P23528

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1018	0.83	0.84	110	empty
2	1004	0.83	0.84	114	empty
3	1065	0.81	0.82	111	MG, ADP
4	555	0.77	0.84	62	empty
5	265	0.76	0.89	50	MG, ADP

Interfaces

13 interfaces between chains.

C–D · 1258 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1254 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 1253 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1251 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1241 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6UC0 · Isolated S3D-cofilin bound to an actin filament · the same entry in another collection · chain I against I, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · 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 P68135
Every structure of UniProt P23528
Elsewhere: RCSB PDB 6UC0 · PDBe 6UC0 · UniProt P68135 · UniProt P23528

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