5KI6	Hydrolase Rna	date	Jun 16, 2016
title	Human Argonaute-2 Bound To A Guide Rna With A Nucleobase Mod At Position 1
authors	N.T.Schirle, I.J.Macrae
compound		source
Molecule: Protein Argonaute-2 Chain: A Synonym: Hago2,Argonaute Risc Catalytic Component 2,Eukaryo Translation Initiation Factor 2c 2,Eif2c 2,Paz Piwi Domain Ppd,Protein Slicer; Ec: 3.1.26.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ago2, Eif2c2 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_vector_type: Baculovirus
Molecule: Mir-122 Chain: B Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 1 21 1	R_factor 0.238 R_Free 0.270
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.276 107.297 68.855 90.00 107.44 90.00
method	X-Ray Diffraction	resolution	2.15 Å
ligand	6U0, IPH	enzyme	Hydrolase E.C.3.1.26 BRENDA
Gene Ontology	Chain Function Process Component A core promoter sequence-speci... translation initiation facto... endoribonuclease activity endoribonuclease activity, p... siRNA binding endoribonuclease activity, c...
Primary reference	Structure-Guided Control of siRNA Off-Target Effects., Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal PA, J Am Chem Soc. 2016 Jul 20;138(28):8667-9. doi: 10.1021/jacs.6b06137. Epub 2016, Jul 12. PMID:27387838

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk] Biological Unit Coordinates (5ki6.pdb1.gz) 136 Kb LPC: Ligand-Protein Contacts for 5KI6 CSU: Contacts of Structural Units for 5KI6 Structure Factors (3114 Kb) Retrieve 5KI6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5KI6 from S2C, [Save to disk] Re-refined 5ki6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5KI6 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5KI6

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5ki6_B] [5ki6] [5ki6_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5KI6: [DUF1785] [PAZ] [Piwi ] by SMART

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