5C1D Transferase date Jun 13, 2015
title Human Ogt In Complex With Udp-5s-Glcnac And Substrate Peptid
authors M.Schimpl, K.Rafie, D.M.F.Van Aalten
compound source
Molecule: Udp-N-Acetylglucosamine--Peptide N- Acetylglucosaminyltransferase 110 Kda Subunit;
Chain: A
Fragment: Unp Residues 313-1031
Synonym: O-Glcnac Transferase, O-Glcnac Transferase Subunit Linked N-Acetylglucosamine Transferase 110 Kda Subunit,Ogt;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ogt
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693

Molecule: Retinoblastoma-Like Protein 2
Chain: C
Fragment: Unp Residues 416-423
Synonym: 130 Kda Retinoblastoma-Associated Protein,P130, Retinoblastoma-Related Protein 2,Rbr-2,Prb2;
Engineered: Yes
Other_details: Nitrogen From Residue 8 Results From An Acet During Chemical Synthesis Of The Compound And Is Part Of Re But Needed A Different Residue Number In The Pdb

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: F 2 2 2
R_factor 0.195 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
138.527 151.611 200.429 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand 12V, PO4 enzyme Transferase E.C. BRENDA

Primary referenceThe active site of O-GlcNAc transferase imposes constraints on substrate sequence., Pathak S, Alonso J, Schimpl M, Rafie K, Blair DE, Borodkin VS, Schuttelkopf AW, Albarbarawi O, van Aalten DM, Nat Struct Mol Biol. 2015 Aug 3. doi: 10.1038/nsmb.3063. PMID:26237509
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (5c1d.pdb1.gz) 119 Kb
  • LPC: Ligand-Protein Contacts for 5C1D
  • CSU: Contacts of Structural Units for 5C1D
  • Structure Factors (1230 Kb)
  • Retrieve 5C1D in mmCIF format [Save to disk]
  • Re-refined 5c1d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C1D 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 5C1D
  • 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
  • Fold representative 5c1d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c1d_C] [5c1d] [5c1d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5C1D: [TPR ] by SMART
  • Other resources with information on 5C1D
  • Community annotation for 5C1D at PDBWiki (http://pdbwiki.org)

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