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Crystal structure of bovine ARP2/3 complex co-crystallized with ADP and crosslinked with gluteraldehyde

Analyse Crystal structure of bovine ARP2/3 complex co-crystallized with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P9I
Type: protein
Length: 1,764 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin-like protein 3; Actin-like protein 2; Actin-related protein 2/3 complex subunit 1B…
UniProt: P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, Q3SYX9
Ligands: ADP, CA
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-like protein 3	protein	393	45% helix, 19% strand	P61157
B	Actin-like protein 2	protein	272	42% helix, 18% strand	A7MB62
C	Actin-related protein 2/3 complex subunit 1B	protein	341	3% helix, 51% strand	Q58CQ2
D	Actin-related protein 2/3 complex subunit 2	protein	280	44% helix, 23% strand	Q3MHR7
E	Actin-related protein 2/3 complex subunit 3	protein	174	47% helix, 5% strand	Q3T035
F	Actin-related protein 2/3 complex subunit 4	protein	167	51% helix, 16% strand	Q148J6
G	Actin-related protein 2/3 complex subunit 5	protein	137	66% helix, 0% strand	Q3SYX9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
CA · Calcium 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	639	0.82	0.87	59	empty
2	378	0.79	0.88	62	CA, ADP
3	771	0.78	0.82	87	CA, ADP
4	516	0.71	0.80	80	empty
5	550	0.71	0.80	62	empty

Interfaces

12 interfaces between chains.

D–F · 2218 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 1727 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 1235 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 972 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 941 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2P9I · Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with… · 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
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
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 0.98

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 2P9I · PDBe 2P9I · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9

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