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Structure of DIP1-activated ARP2/3 complex with nucleated actin filament

Analyse Structure of DIP1-activated ARP2/3 complex with nucleated actin filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W17
Type: protein
Length: 3,518 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-related protein 3; Actin-related protein 2; Actin-related protein 2/3 complex…
UniProt: P32390, Q9UUJ1, P78774, O14241, Q9Y7J4, Q92352, Q10316, O74771, P68135
Ligands: ADP, ATP, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	380	39% helix, 15% strand	P32390
B	Actin-related protein 2	protein	364	41% helix, 14% strand	Q9UUJ1
C	Actin-related protein 2/3 complex subunit 1	protein	333	0% helix, 46% strand	P78774
D	Actin-related protein 2/3 complex subunit 2	protein	301	43% helix, 18% strand	O14241
E	Actin-related protein 2/3 complex subunit 3	protein	174	42% helix, 2% strand	Q9Y7J4
F	Actin-related protein 2/3 complex subunit 4	protein	168	48% helix, 17% strand	Q92352
G	Actin-related protein 2/3 complex subunit 5	protein	150	53% helix, 0% strand	Q10316
H	Protein DIP1	protein	132	58% helix, 0% strand	O74771
I	Actin, alpha skeletal muscle	protein	371	42% helix, 18% strand	P68135
J, K, L	Actin, alpha skeletal muscle	protein	370	43% helix, 17% strand	P68135
M, N, O, P, Q	Phalloidin	protein	7	0% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains I, J, K, L
ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B, I, J, K, L

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	584	0.84	0.90	86	ADP, MG
2	1164	0.84	0.85	128	MG, ATP
3	1047	0.81	0.82	140	empty
4	478	0.81	0.88	63	empty
5	361	0.80	0.90	56	empty

Interfaces

37 interfaces between chains.

D–F · 2162 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1520 Å² buried · 19 hydrogen bonds · protein-protein
A–I · 1498 Å² buried · 17 hydrogen bonds · protein-protein
I–K · 1238 Å² buried · 10 hydrogen bonds · protein-protein
C–F · 1167 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 modified (nonstandard, hydroxylation, methylation).

Compared structures

6W17 · Structure of Dip1-activated Arp2/3 complex with nucleated actin filament · the same entry in another collection · chain J against J, TM-score 1.00

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 P32390
Every structure of UniProt Q9UUJ1
Every structure of UniProt P78774
Every structure of UniProt O14241
Every structure of UniProt Q9Y7J4
Every structure of UniProt Q92352
Every structure of UniProt Q10316
Every structure of UniProt O74771
Every structure of UniProt P68135
Elsewhere: RCSB PDB 6W17 · PDBe 6W17 · UniProt P32390 · UniProt Q9UUJ1 · UniProt P78774 · UniProt O14241 · UniProt Q9Y7J4 · UniProt Q92352 · UniProt Q10316 · UniProt O74771 · UniProt P68135

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