2QFD	Hydrolase	date	Jun 27, 2007
title	Crystal Structure Of The Regulatory Domain Of Human Rig-I With Bound Hg
authors	S.Cui, A.Lammens, K.Lammens, K.P.Hopfner
compound		source
Molecule: Probable Atp-Dependent Rna Helicase Ddx58 Chain: A, B, C, D, E, F, G, H, I, J Fragment: Regulatory Domain Synonym: Dead-Box Protein 58, Retinoic Acid-Inducible Gene Protein, Rig-1, Rig-I; Ec: 3.6.1.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ddx58 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
symmetry	Space Group: P 1 21 1	R_factor 0.241 R_Free 0.276
crystal cell	length a length b length c angle alpha angle beta angle gamma 97.150 76.540 137.900 90.00 93.07 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	HG	enzyme	Hydrolase E.C.3.6.1 BRENDA
Primary reference	The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I., Cui S, Eisenacher K, Kirchhofer A, Brzozka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP, Mol Cell. 2008 Feb 1;29(2):169-179. PMID:18243112

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk] Biological Unit Coordinates (2qfd.pdb1.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb2.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb3.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb4.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb5.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb6.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb7.gz) 24 Kb Biological Unit Coordinates (2qfd.pdb8.gz) 23 Kb Biological Unit Coordinates (2qfd.pdb9.gz) 24 Kb LPC: Ligand-Protein Contacts for 2QFD CSU: Contacts of Structural Units for 2QFD Likely Quarternary Molecular Structure file(s) for 2QFD Structure Factors (362 Kb) Retrieve 2QFD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2QFD from S2C, [Save to disk] Re-refined 2qfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2QFD 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 2QFD

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 3D motif for 2QFD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2qfd_D] [2qfd_F] [2qfd_G] [2qfd_B] [2qfd_J] [2qfd] [2qfd_I] [2qfd_A] [2qfd_H] [2qfd_E] [2qfd_C] SWISS-PROT database: [O95786] Domain organization of [DDX58_HUMAN] by SWISSPFAM

Other resources with information on 2QFD

Community annotation for 2QFD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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