MolNFT v1 · #186276 · protein + DNA

Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' P guide DNA

7R8H: “Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' P guide DNA”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #186276 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7R8H
Type: protein + DNA
Length: 787 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: 6 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Argonaute	protein	769	28% helix, 28% strand	A0A2M8J4C7
T	DNA (5'- D(TPTPAPCPTPGPCPAPCPAPGPGPTPGPAPCPGPA)-3')	dna	18	—	—

Pockets

6 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	514	0.79	0.86	60	empty
2	274	0.75	0.88	33	empty
3	222	0.68	0.86	26	empty
4	115	0.60	0.86	24	empty
5	128	0.47	0.78	20	empty

Interfaces

1 interface between chains.

A–T · 2623 Å² buried · 46 hydrogen bonds · protein-nucleic

Compared structures

7R8H · Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A2M8J4C7
Elsewhere: RCSB PDB 7R8H · PDBe 7R8H · UniProt A0A2M8J4C7

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