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Crystal structure of mid domain from HAGO2 in complex with AMP

Analyse Crystal structure of mid domain from HAGO2 in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LUD
Type: protein
Length: 398 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2
UniProt: Q9UKV8
Ligands: AMP, PO4
Pockets: 3 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein argonaute-2	protein	133	49% helix, 17% strand	Q9UKV8
B	Protein argonaute-2	protein	132	45% helix, 17% strand	Q9UKV8

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 6 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	92	0.39	0.77	17	empty
2	97	0.35	0.74	23	empty
3	53	0.25	0.72	13	empty

Interfaces

2 interfaces between chains.

B–C · 728 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 674 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3LUD · Crystal structure of MID domain from hAGO2 in complex with AMP · 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 A 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 3LUD · PDBe 3LUD · UniProt Q9UKV8

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