MolNFT v1 · #47811 · protein

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

2P9P · Actin-like protein 3: “Crystal structure of bovine ARP2/3 complex co-crystallized with ADP”. X-ray diffraction, 2 ligands (ADP, CA), 18 pockets (best druggability 0.83). MolNFT v1 #47811 on GenesisL1: 3D structure, binding sites and…

PDB: 2P9P
Type: protein
Length: 1,653 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 0.83

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin-like protein 3	protein	388	43% helix, 20% strand	P61157
B	Actin-like protein 2	protein	184	48% helix, 12% strand	A7MB62
C	Actin-related protein 2/3 complex subunit 1B	protein	341	2% helix, 50% strand	Q58CQ2
D	Actin-related protein 2/3 complex subunit 2	protein	273	46% helix, 23% strand	Q3MHR7
E	Actin-related protein 2/3 complex subunit 3	protein	174	45% helix, 2% strand	Q3T035
F	Actin-related protein 2/3 complex subunit 4	protein	165	49% helix, 16% strand	Q148J6
G	Actin-related protein 2/3 complex subunit 5	protein	128	63% helix, 0% strand	Q3SYX9

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

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	706	0.83	0.87	71	empty
2	221	0.77	0.91	40	empty
3	95	0.76	0.97	23	empty
4	578	0.75	0.82	52	empty
5	424	0.72	0.83	55	CA, ADP

Interfaces

12 interfaces between chains.

D–F · 2232 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1722 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 1219 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 959 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 933 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2P9P · Crystal Structure of bovine Arp2/3 complex co-crystallized with ADP · 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
Q3SYX9 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 5 (Q3SYX9) · a predicted model of the same protein · chain G 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 0.99
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
A7MB62 · AlphaFold monomer V2.0 prediction for actin-related protein 2 (A7MB62) · a predicted model of the same protein · chain B 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 2P9P · PDBe 2P9P · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9

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