MolNFT v1 · #171185 · protein

Cryo-EM structure of the ARP2/3 1B5CL isoform complex.

6YW6 · Actin-related protein 3: “Cryo-EM structure of the ARP2/3 1B5CL isoform complex.”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.85). MolNFT v1 #171185 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6YW6
Type: protein
Length: 1,722 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-related protein 3; ARPC1B; Actin-related protein 2/3 complex subunit 2…
UniProt: P61158, O15143, O15144, O15145, P61160, Q9BPX5, P59998
Ligands: ATP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-related protein 3	protein	396	36% helix, 15% strand	P61158
C	ARPC1B	protein	341	1% helix, 44% strand	O15143
D	Actin-related protein 2/3 complex subunit 2	protein	284	42% helix, 16% strand	O15144
E	Actin-related protein 2/3 complex subunit 3	protein	170	36% helix, 2% strand	O15145
B	Actin-related protein 2	protein	277	33% helix, 11% strand	P61160
G	Actin-related protein 2/3 complex subunit 5-like protein	protein	89	53% helix, 0% strand	Q9BPX5
F	Actin-related protein 2/3 complex subunit 4	protein	165	48% helix, 13% strand	P59998

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.85	0.88	84	empty
2	165	0.79	0.94	34	empty
3	986	0.78	0.80	95	ATP
4	143	0.77	0.94	25	empty
5	96	0.77	0.97	31	empty

Interfaces

12 interfaces between chains.

D–F · 2044 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 1907 Å² buried · 20 hydrogen bonds · protein-protein
G–F · 1069 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 1066 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 990 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6YW6 · Cryo-EM structure of the ARP2/3 1B5CL isoform complex. · the same entry in another collection · chain B against B, 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 0.98
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
P61158 · AlphaFold monomer V2.0 prediction for actin-related protein 3 (P61158) · a predicted model of the same protein · chain A against A, TM-score 0.97
P59998 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 4 (P59998) · a predicted model of the same protein · chain F against A, TM-score 0.96
Q9BPX5 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 5-like… · a predicted model of the same protein · chain G against A, TM-score 0.90

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 O15143
Every structure of UniProt O15144
Every structure of UniProt O15145
Every structure of UniProt P61160
Every structure of UniProt Q9BPX5
Every structure of UniProt P59998
Elsewhere: RCSB PDB 6YW6 · PDBe 6YW6 · UniProt P61158 · UniProt O15143 · UniProt O15144 · UniProt O15145 · UniProt P61160 · UniProt Q9BPX5 · UniProt P59998

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