Research workbench

Cryoem structure of human ARP2/3 complex with bound npfs

Analyse Cryoem structure of human ARP2/3 complex with bound npfs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UHC
Type: protein
Length: 1,940 residues
Chains: 9
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: P61158, P61160, O15143, O15144, O15145, P59998, O15511, Q91YD9
Ligands: ATP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 9 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	404	41% helix, 18% strand	P61158
B	Actin-related protein 2	protein	374	39% helix, 18% strand	P61160
C	Actin-related protein 2/3 complex subunit 1B	protein	354	3% helix, 48% strand	O15143
D	Actin-related protein 2/3 complex subunit 2	protein	283	43% helix, 22% strand	O15144
E	Actin-related protein 2/3 complex subunit 3	protein	173	45% helix, 3% strand	O15145
F	Actin-related protein 2/3 complex subunit 4	protein	166	49% helix, 16% strand	P59998
G	Actin-related protein 2/3 complex subunit 5	protein	141	59% helix, 0% strand	O15511
H	Neural wiskott-aldrich syndrome protein	protein	21	38% helix, 0% strand	Q91YD9
I	Neural wiskott-aldrich syndrome protein	protein	24	63% helix, 0% strand	Q91YD9

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.83	0.84	134	MG, ATP
2	694	0.83	0.87	71	empty
3	1033	0.82	0.83	108	empty
4	590	0.79	0.85	60	empty
5	603	0.73	0.81	60	MG, ATP

Interfaces

15 interfaces between chains.

D–F · 2053 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 1594 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 1084 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 893 Å² buried · 4 hydrogen bonds · protein-protein
F–G · 880 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6UHC · CryoEM structure of human Arp2/3 complex with bound NPFs · the same entry in another collection · chain I against I, TM-score 1.00
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 0.99
O15145 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 3 (O15145) · a predicted model of the same protein · chain E against A, TM-score 0.98
O15143 · 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 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 P61158
Every structure of UniProt P61160
Every structure of UniProt O15143
Every structure of UniProt O15144
Every structure of UniProt O15145
Every structure of UniProt P59998
Every structure of UniProt O15511
Every structure of UniProt Q91YD9
Elsewhere: RCSB PDB 6UHC · PDBe 6UHC · UniProt P61158 · UniProt P61160 · UniProt O15143 · UniProt O15144 · UniProt O15145 · UniProt P59998 · UniProt O15511 · UniProt Q91YD9

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