2QK9 Hydrolase Dna Rna date Jul 10, 2007
title Human Rnase H Catalytic Domain Mutant D210n In Complex With Rnadna Hybrid
authors M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crou
compound source
Molecule: Ribonuclease H1
Chain: A
Fragment: C-Terminal Domain (Residues 134-286)
Synonym: Hs-Rnase Hc; Rnase H1; Ribonuclease H Type II
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnaseh1, Rnh1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15

Molecule: 5'-R(Apgpupgpcpgpapcpapcpcpupgpapu -3';
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Gpgpapaptpcpapgpgptpgptpcpgpc -3';
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: H 3 2
R_factor 0.190 R_Free 0.216
length a length b length c angle alpha angle beta angle gamma
158.578 158.578 142.055 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.55 Å
ligand 16D, FLC, GOL, NA, SO4 enzyme Hydrolase E.C. BRENDA

Primary referenceStructure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription., Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W, Mol Cell. 2007 Oct 26;28(2):264-76. PMID:17964265
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (2qk9.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 2QK9
  • CSU: Contacts of Structural Units for 2QK9
  • Likely Quarternary Molecular Structure file(s) for 2QK9
  • Structure Factors (212 Kb)
  • Retrieve 2QK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QK9 from S2C, [Save to disk]
  • Re-refined 2qk9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QK9 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 2QK9
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2QK9, from MSDmotif at EBI
  • Fold representative 2qk9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qk9_A] [2qk9_C] [2qk9_B] [2qk9]
  • SWISS-PROT database: [O60930]
  • Domain organization of [RNH1_HUMAN] by SWISSPFAM
  • Other resources with information on 2QK9
  • Community annotation for 2QK9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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