1K8W Lyase Rna date Oct 25, 2001
title Crystal Structure Of The E. Coli Pseudouridine Synthase Trub Bound To A T Stem-Loop Rna
authors C.Hoang, A.R.Ferre-D'Amare
compound source
Molecule: 5'-R(Gpgpcpapapcpgpgpup(Fhu) Pcpgpapupcpcpcpgpupupgpc)-3';
Chain: B
Engineered: Yes
Other_details: T Stem-Loop Rna
Synthetic: Yes

Molecule: Trna Pseudouridine Synthase B
Chain: A
Fragment: Residues 10-314
Synonym: Trub Pseudouridine Synthase, Trna Pseudouridine 55 Synthase, Pseudouridylate Synthase;
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.184 R_Free 0.211
length a length b length c angle alpha angle beta angle gamma
145.054 40.361 77.987 90.00 110.60 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand FHU, SO4 enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1R3F

Primary referenceCocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme., Hoang C, Ferre-D'Amare AR, Cell 2001 Dec 28;107(7):929-39. PMID:11779468
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1k8w.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1K8W
  • CSU: Contacts of Structural Units for 1K8W
  • Likely Quarternary Molecular Structure file(s) for 1K8W
  • Structure Factors (362 Kb)
  • Retrieve 1K8W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K8W from S2C, [Save to disk]
  • Re-refined 1k8w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K8W 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 1K8W
  • 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 1K8W, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k8wa3, region A:251-312 [Jmol] [rasmolscript] [script source]
        - Domain d1k8wa5, region A:9-250 [Jmol] [rasmolscript] [script source]
  • Fold representative 1k8w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k8w_A] [1k8w] [1k8w_B]
  • SWISS-PROT database: [P60340]
  • Domain organization of [TRUB_ECOLI] by SWISSPFAM
  • Other resources with information on 1K8W
  • Community annotation for 1K8W 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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