MolNFT v1 · #81238 · protein

Crystal structure of bos taurus ARP2/3 complex with bound inhibitor ck-666

3UKR · Actin-related protein 3: “Crystal structure of bos taurus ARP2/3 complex with bound inhibitor ck-666”. X-ray diffraction, 1 ligand (CKH), 20 pockets (best druggability 0.84). MolNFT v1 #81238 on GenesisL1: 3D structure, binding…

PDB: 3UKR
Type: protein
Length: 1,701 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-related protein 3; Actin-related protein 2; Actin-related protein 2/3 complex…
UniProt: P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, Q3SYX9
Ligands: CKH
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	401	43% helix, 19% strand	P61157
B	Actin-related protein 2	protein	193	44% helix, 16% strand	A7MB62
C	Actin-related protein 2/3 complex subunit 1B	protein	349	5% helix, 50% strand	Q58CQ2
D	Actin-related protein 2/3 complex subunit 2	protein	282	45% helix, 22% strand	Q3MHR7
E	Actin-related protein 2/3 complex subunit 3	protein	173	48% helix, 6% strand	Q3T035
F	Actin-related protein 2/3 complex subunit 4	protein	167	51% helix, 17% strand	Q148J6
G	Actin-related protein 2/3 complex subunit 5	protein	136	62% helix, 0% strand	Q3SYX9

Ligands and binding sites

CKH · 2-fluoro-N-[2-(2-methyl-1H-indol-3-yl)ethyl]benzamide · ligand · chains A, B

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

Pockets

20 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	1134	0.84	0.85	109	empty
2	103	0.79	0.98	22	empty
3	336	0.77	0.88	50	CKH
4	539	0.73	0.81	48	empty
5	585	0.72	0.80	54	empty

Interfaces

12 interfaces between chains.

D–F · 2207 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 1788 Å² buried · 28 hydrogen bonds · protein-protein
C–F · 1178 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 929 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 922 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3UKR · Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666 · 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 3UKR · PDBe 3UKR · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9

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