Research workbench

Cryo-EM structure of the ARP2/3 1A5C isoform complex.

Analyse Cryo-EM structure of the ARP2/3 1A5C isoform complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YW7
Type: protein
Length: 1,788 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-related protein 3; Actin-related protein 2/3 complex subunit 2; Actin-related…
UniProt: P61158, O15144, O15145, P61160, P59998, O15511, Q92747
Ligands: ATP
Pockets: 17 · best druggability 0.67

Structure

electron microscopy · 7 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	396	0% helix, 0% strand	P61158
D	Actin-related protein 2/3 complex subunit 2	protein	284	0% helix, 0% strand	O15144
E	Actin-related protein 2/3 complex subunit 3	protein	170	0% helix, 0% strand	O15145
B	Actin-related protein 2	protein	286	0% helix, 0% strand	P61160
F	Actin-related protein 2/3 complex subunit 4	protein	165	0% helix, 0% strand	P59998
G	Actin-related protein 2/3 complex subunit 5	protein	139	0% helix, 0% strand	O15511
C	Actin-related protein 2/3 complex subunit 1A	protein	348	0% helix, 0% strand	Q92747

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.67	0.74	129	empty
2	822	0.65	0.73	136	empty
3	513	0.62	0.75	60	empty
4	515	0.61	0.75	67	empty
5	459	0.59	0.74	70	empty

Interfaces

8 interfaces between chains.

F–G · 219 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 135 Å² buried · 0 hydrogen bonds · protein-protein
D–F · 117 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 98 Å² buried · 0 hydrogen bonds · protein-protein
B–F · 49 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6YW7 · Cryo-EM structure of the ARP2/3 1A5C isoform complex. · the same entry in another collection · chain C against C, TM-score 1.00
O15511 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 5 (O15511) · a predicted model of the same protein · chain G against A, TM-score 0.98
P59998 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 4 (P59998) · a predicted model of the same protein · chain F against A, TM-score 0.98
O15144 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 2 (O15144) · a predicted model of the same protein · chain D against A, TM-score 0.97
P61158 · AlphaFold monomer V2.0 prediction for actin-related protein 3 (P61158) · a predicted model of the same protein · chain A against A, TM-score 0.97
Q92747 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 1A… · a predicted model of the same protein · chain C against A, TM-score 0.93

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 P61158
Every structure of UniProt O15144
Every structure of UniProt O15145
Every structure of UniProt P61160
Every structure of UniProt P59998
Every structure of UniProt O15511
Every structure of UniProt Q92747
Elsewhere: RCSB PDB 6YW7 · PDBe 6YW7 · UniProt P61158 · UniProt O15144 · UniProt O15145 · UniProt P61160 · UniProt P59998 · UniProt O15511 · UniProt Q92747

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