2QKK Hydrolase Dna Rna date Jul 11, 2007
title Human Rnase H Catalytic Domain Mutant D210n In Complex With 14-Mer Rnadna Hybrid
authors M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, W.Yang
compound source
Molecule: Ribonuclease H1
Chain: A, B, E, F, I, J, M, N, R, S, W
Fragment: C-Terminal Domain (Residues 134-286)
Synonym: Hs-Rnase Hc; Rnase H1; Ribonuclease H Type II
Ec: 3.1.26.4
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(Cpgpapcpapcpcpupgpapupupcpc)- 3';
Chain: C, G, K, O, T, X
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Gpgpapaptpcpapgpgptpgptpcpg)- 3';
Chain: D, H, L, P, U, Z
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.212 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
151.065 176.200 125.845 90.00 90.22 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand CA, CL, MES, TRS enzyme Hydrolase E.C.3.1.26.4 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] (338 Kb) [Save to disk]
  • Biological Unit Coordinates (2qkk.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (2qkk.pdb2.gz) 63 Kb
  • Biological Unit Coordinates (2qkk.pdb3.gz) 62 Kb
  • Biological Unit Coordinates (2qkk.pdb4.gz) 61 Kb
  • Biological Unit Coordinates (2qkk.pdb5.gz) 62 Kb
  • Biological Unit Coordinates (2qkk.pdb6.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2QKK
  • CSU: Contacts of Structural Units for 2QKK
  • Structure Factors (450 Kb)
  • Retrieve 2QKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QKK from S2C, [Save to disk]
  • Re-refined 2qkk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QKK 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 2QKK
  • 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 2QKK, from MSDmotif at EBI
  • Fold representative 2qkk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qkk_R] [2qkk] [2qkk_A] [2qkk_U] [2qkk_K] [2qkk_F] [2qkk_S] [2qkk_H] [2qkk_O] [2qkk_C] [2qkk_G] [2qkk_M] [2qkk_I] [2qkk_Z] [2qkk_W] [2qkk_B] [2qkk_P] [2qkk_E] [2qkk_N] [2qkk_J] [2qkk_D] [2qkk_T] [2qkk_L] [2qkk_X]
  • SWISS-PROT database: [O60930]
  • Domain organization of [RNH1_HUMAN] by SWISSPFAM
  • Other resources with information on 2QKK
  • Community annotation for 2QKK 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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