MolNFT v1 · #23527 · protein

Crystal structure of ARP2/3 complex with bound ADP and calcium

1U2V · Actin-related protein 3: “Crystal structure of ARP2/3 complex with bound ADP and calcium”. X-ray diffraction, 2 ligands (ADP, CA), 20 pockets (best druggability 0.82). MolNFT v1 #23527 on GenesisL1: 3D structure, binding sites and…

PDB: 1U2V
Type: protein
Length: 1,714 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-related protein 3; Actin-related protein 2; ARP2/3 complex 41KDA subunit; ARP2/3…
UniProt: P61157
Ligands: ADP, CA
Pockets: 20 · best druggability 0.82

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	402	43% helix, 19% strand	P61157
B	Actin-related protein 2	protein	204	41% helix, 16% strand	—
C	ARP2/3 complex 41KDA subunit	protein	357	4% helix, 49% strand	—
D	ARP2/3 complex 34KDA subunit	protein	282	45% helix, 22% strand	—
E	ARP2/3 complex 21KDA subunit	protein	168	49% helix, 4% strand	—
F	ARP2/3 complex 20KDA subunit	protein	166	49% helix, 16% strand	—
G	ARP2/3 complex 16KDA subunit	protein	135	67% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	661	0.82	0.87	58	empty
2	238	0.79	0.92	45	empty
3	90	0.76	0.97	23	empty
4	764	0.73	0.79	72	empty
5	711	0.72	0.79	63	empty

Interfaces

12 interfaces between chains.

D–F · 2194 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 1748 Å² buried · 30 hydrogen bonds · protein-protein
C–F · 1221 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 946 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 941 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1U2V · Crystal structure of Arp2/3 complex with bound ADP and calcium · the same entry in another collection · chain G against G, TM-score 1.00
P61157 · AlphaFold monomer V2.0 prediction for actin-related protein 3 (P61157) · a predicted model of the same protein · chain A against A, TM-score 0.95

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
Elsewhere: RCSB PDB 1U2V · PDBe 1U2V · UniProt P61157

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.