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Crystal structure of mid domain from HAGO2 in complex with ump

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

PDB: 3LUJ
Type: protein
Length: 399 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2
UniProt: Q9UKV8
Ligands: U5P
Pockets: 5 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2	protein	134	47% helix, 16% strand	Q9UKV8
B	Protein argonaute-2	protein	133	47% helix, 17% strand	Q9UKV8
C	Protein argonaute-2	protein	132	48% helix, 17% strand	Q9UKV8

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · 3 copies · chains A, B, C

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

Pockets

5 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	90	0.37	0.75	19	U5P
2	68	0.35	0.77	18	U5P
3	59	0.33	0.77	15	U5P
4	80	0.32	0.74	21	empty
5	66	0.28	0.73	13	empty

Interfaces

2 interfaces between chains.

B–C · 695 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 640 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3LUJ · Crystal structure of MID domain from hAGO2 in complex with UMP · 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 3LUJ · PDBe 3LUJ · UniProt Q9UKV8

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