MolNFT v1 · #81240 · protein

Structure of ARP2/3 complex with bound inhibitor ck-869

3UKU · Actin-like protein 3: “Structure of ARP2/3 complex with bound inhibitor ck-869”. X-ray diffraction, 1 ligand (C69), 18 pockets (best druggability 0.84). MolNFT v1 #81240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UKU
Type: protein
Length: 1,689 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-like protein 3; Actin-like protein 2; Actin-related protein 2/3 complex subunit 1B…
UniProt: P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, Q3SYX9
Ligands: C69
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-like protein 3	protein	399	41% helix, 18% strand	P61157
B	Actin-like protein 2	protein	195	45% helix, 15% strand	A7MB62
C	Actin-related protein 2/3 complex subunit 1B	protein	341	3% helix, 48% strand	Q58CQ2
D	Actin-related protein 2/3 complex subunit 2	protein	277	42% helix, 21% strand	Q3MHR7
E	Actin-related protein 2/3 complex subunit 3	protein	173	47% helix, 5% strand	Q3T035
F	Actin-related protein 2/3 complex subunit 4	protein	166	49% helix, 19% strand	Q148J6
G	Actin-related protein 2/3 complex subunit 5	protein	138	56% helix, 0% strand	Q3SYX9

Ligands and binding sites

C69 · (2S)-2-(3-bromophenyl)-3-(2,4-dimethoxyphenyl)-1,3-thiazolidin-4-one · ligand · chains A

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

Pockets

18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1141	0.84	0.85	107	empty
2	790	0.81	0.84	79	C69
3	778	0.78	0.82	100	empty
4	700	0.73	0.79	60	empty
5	230	0.51	0.76	27	empty

Interfaces

12 interfaces between chains.

D–F · 2201 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1741 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 1188 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 941 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 940 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3UKU · Structure of Arp2/3 complex with bound inhibitor CK-869 · the same entry in another collection · chain G against G, TM-score 1.00
Q58CQ2 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 1B… · a predicted model of the same protein · chain C against A, TM-score 1.00
Q3MHR7 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 2 (Q3MHR7) · a predicted model of the same protein · chain D against A, TM-score 0.99
Q3T035 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 3 (Q3T035) · a predicted model of the same protein · chain E against A, TM-score 0.98
Q3SYX9 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 5 (Q3SYX9) · a predicted model of the same protein · chain G against A, TM-score 0.98
Q148J6 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 4 (Q148J6) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 P61157
Every structure of UniProt A7MB62
Every structure of UniProt Q58CQ2
Every structure of UniProt Q3MHR7
Every structure of UniProt Q3T035
Every structure of UniProt Q148J6
Every structure of UniProt Q3SYX9
Elsewhere: RCSB PDB 3UKU · PDBe 3UKU · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9

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