MolNFT v1 · #178913 · protein

Cryo-EM structure of arpin-bound ARP2/3 complex

7JPN · Actin-related protein 3: “Cryo-EM structure of arpin-bound ARP2/3 complex”. Electron microscopy, 2 ligands (ATP, MG), 18 pockets (best druggability 0.83). MolNFT v1 #178913 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7JPN
Type: protein
Length: 1,885 residues
Chains: 8
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: P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, G3MXC8, Q7Z6K5
Ligands: ATP, MG
Pockets: 18 · best druggability 0.83

Structure

electron microscopy · 8 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	399	42% helix, 19% strand	P61157
B	Actin-related protein 2	protein	345	41% helix, 19% strand	A7MB62
C	Actin-related protein 2/3 complex subunit 1B	protein	339	2% helix, 50% strand	Q58CQ2
D	Actin-related protein 2/3 complex subunit 2	protein	284	49% helix, 20% strand	Q3MHR7
E	Actin-related protein 2/3 complex subunit 3	protein	174	44% helix, 6% strand	Q3T035
F	Actin-related protein 2/3 complex subunit 4	protein	167	49% helix, 15% strand	Q148J6
G	Actin-related protein 2/3 complex subunit 5	protein	143	59% helix, 0% strand	G3MXC8
H	Arpin	protein	34	32% helix, 0% strand	Q7Z6K5

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

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	682	0.83	0.87	59	empty
2	1024	0.80	0.81	100	MG, ATP
3	949	0.77	0.79	93	empty
4	165	0.76	0.93	39	empty
5	555	0.76	0.83	80	MG, ATP

Interfaces

13 interfaces between chains.

D–F · 2231 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1766 Å² buried · 28 hydrogen bonds · protein-protein
A–H · 1402 Å² buried · 13 hydrogen bonds · protein-protein
C–F · 1204 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1015 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7JPN · Cryo-EM structure of Arpin-bound Arp2/3 complex · the same entry in another collection · chain H against H, 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 0.99
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 0.98
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
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

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 G3MXC8
Every structure of UniProt Q7Z6K5
Elsewhere: RCSB PDB 7JPN · PDBe 7JPN · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt G3MXC8 · UniProt Q7Z6K5

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