MolNFT v1 · #76851 · protein

Crystal structure of mid domain from HAGO2 in complex with ATP

3QX9 · Protein argonaute-2: “Crystal structure of mid domain from HAGO2 in complex with ATP”. X-ray diffraction, 1 ligand (ATP), 3 pockets (best druggability 0.42). MolNFT v1 #76851 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3QX9
Type: protein
Length: 400 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2
UniProt: Q9UKV8
Ligands: ATP
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2	protein	135	47% helix, 16% strand	Q9UKV8
B	Protein argonaute-2	protein	132	47% helix, 16% strand	Q9UKV8
C	Protein argonaute-2	protein	133	47% helix, 17% strand	Q9UKV8

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.42	0.74	23	empty
2	62	0.31	0.75	16	ATP
3	53	0.27	0.74	12	empty

Interfaces

2 interfaces between chains.

B–C · 714 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 637 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3QX9 · Crystal structure of MID domain from hAGO2 in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
Q9UKV8 · AlphaFold monomer V2.0 prediction for protein argonaute-2 (Q9UKV8) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q9UKV8
Elsewhere: RCSB PDB 3QX9 · PDBe 3QX9 · UniProt Q9UKV8

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