3LLM Hydrolase date Jan 29, 2010
title Crystal Structure Analysis Of A Rna Helicase
authors P.Schutz, T.Karlberg, R.Collins, C.H.Arrowsmith, H.Berglund, C.Bo S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Jo A.Kallas, P.Kraulis, T.Kotenyova, A.Kotzsch, N.Markova, M.Moche, T.K.Nielsen, P.Nordlund, T.Nyman, C.Persson, A.K.Roos, M.I.Sipon L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlb J.Weigelt, M.Welin, M.Wisniewska, H.M.Schuler, Structural Genom Consortium (Sgc)
compound source
Molecule: Atp-Dependent Rna Helicase A
Chain: A, B
Fragment: Nucleotide Binding Domain (Unp Residues 329-563)
Synonym: Nuclear Dna Helicase II, Ndh II, Deah Box Protein
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx9, Dhx9, Lkp, Ndh2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)R3 Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 32 2 1
R_factor 0.211 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
113.700 113.700 141.650 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand ADP, CAC, GOL, MN, MSE enzyme Hydrolase E.C.3.6.1 BRENDA
A, B

Primary referenceCrystal structure of human RNA helicase A (DHX9): Structural basis for unselective nucleotide base binding in a DEAD-box variant protein., Schutz P, Wahlberg E, Karlberg T, Hammarstrom M, Collins R, Flores A, Schuler H, J Mol Biol. 2010 May 24. PMID:20510246
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (3llm.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 3LLM
  • CSU: Contacts of Structural Units for 3LLM
  • Structure Factors (390 Kb)
  • Retrieve 3LLM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LLM from S2C, [Save to disk]
  • Re-refined 3llm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LLM 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 3LLM
  • 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 3LLM, from MSDmotif at EBI
  • Fold representative 3llm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3llm_A] [3llm] [3llm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LLM: [DEXDc ] by SMART
  • Other resources with information on 3LLM
  • Community annotation for 3LLM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science