2IYK	Hydrolase	date	Jul 18, 2006
title	Crystal Structure Of The Upf2-Interacting Domain Of Nonsense Mediated Mrna Decay Factor Upf1
authors	J.Kadlec, D.Guilligay, R.B.Ravelli, S.Cusack
compound		source
Molecule: Regulator Of Nonsense Transcripts 1 Chain: A, B Fragment: Upf2-Interacting Domain, Residues 115-272 Synonym: Atp-Dependent Helicase Rent1, Nonsense Mrna Reducing Factor 1, Norf1, Up-Frameshift Suppressor 1 Homolog, Hupf1, Upf1; Ec: 3.6.1.- Engineered: Yes Other_details: Cysteine-Histidine Rich		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pproexhtb
symmetry	Space Group: P 21 21 21	R_factor 0.221 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 64.560 72.980 73.210 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.95 Å
ligand	ZN	enzyme	Hydrolase E.C.3.6.1 BRENDA
Primary reference	Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1., Kadlec J, Guilligay D, Ravelli RB, Cusack S, RNA. 2006 Oct;12(10):1817-24. Epub 2006 Aug 24. PMID:16931876

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk] Biological Unit Coordinates (2iyk.pdb1.gz) 52 Kb Biological Unit Coordinates (2iyk.pdb2.gz) 52 Kb LPC: Ligand-Protein Contacts for 2IYK CSU: Contacts of Structural Units for 2IYK Likely Quarternary Molecular Structure file(s) for 2IYK Structure Factors (51 Kb) Retrieve 2IYK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2IYK from S2C, [Save to disk] Re-refined 2iyk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2IYK 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2IYK

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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 2IYK, from MSDmotif at EBI Fold representative 2iyk from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2iyk_A] [2iyk_B] SWISS-PROT database: [Q92900] Domain organization of [RENT1_HUMAN] by SWISSPFAM Alignments of the sequence of 2IYK with the sequences similar proteins can be viewed for 2IYK's classification [RENT1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [RENT1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2IYK

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

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