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Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' P guide DNA in the presence of MG2+

Analyse Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' P guide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R8J
Type: protein + DNA
Length: 777 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Argonaute; DNA (5'- D(*TP*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)-3')
UniProt: A0A2M8J4C7
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Argonaute	protein	764	27% helix, 28% strand	A0A2M8J4C7
T	DNA (5'- D(TPTPAPCPTPGPCPAPCPAPGPGPTPGPAPCPGPA)-3')	dna	13	—	—

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.79	0.82	91	empty
2	677	0.74	0.80	57	empty
3	120	0.66	0.89	24	empty
4	76	0.52	0.84	17	empty
5	94	0.43	0.79	19	empty

Interfaces

1 interface between chains.

A–T · 2178 Å² buried · 41 hydrogen bonds · protein-nucleic

Compared structures

7R8J · Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt A0A2M8J4C7
Elsewhere: RCSB PDB 7R8J · PDBe 7R8J · UniProt A0A2M8J4C7

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