1M5R Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex date
authors Lariviere, L., Morera, S.
compound source
symmetry
R_factor
R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand 3DR, MPD, TRS, UDP enzyme
related structures by homologous chain: 1J39, 1SXQ
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog., Lariviere L, Morera S, J Mol Biol 2002 Nov 29;324(3):483-90. PMID:12445783
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (1m5r.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (1m5r.pdb2.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 1M5R
  • CSU: Contacts of Structural Units for 1M5R
  • Likely Quarternary Molecular Structure file(s) for 1M5R
  • Structure Factors (663 Kb)
  • Retrieve 1M5R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M5R from S2C, [Save to disk]
  • Re-refined 1m5r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M5R 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 1M5R
  • 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 1M5R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m5ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m5rb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m5r_A] [1m5r_E] [1m5r_D] [1m5r_F] [1m5r] [1m5r_B] [1m5r_C]
  • SWISS-PROT database: [P04547]
  • Domain organization of [GSTB_BPT4] by SWISSPFAM
  • Other resources with information on 1M5R
  • Community annotation for 1M5R 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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