5E1D Transferase date Sep 29, 2015
title Ntmt1 In Complex With Ypkria Peptide
authors C.Dong, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, S Genomics Consortium (Sgc)
compound source
Molecule: N-Terminal Xaa-Pro-Lys N-Methyltransferase 1
Chain: A, B
Synonym: Alpha N-Terminal Protein Methyltransferase 1a, Methyltransferase-Like Protein 11a,N-Terminal Rcc1 Methyltr X-Pro-Lys N-Terminal Protein Methyltransferase 1a,Ntm1a;
Ec: 2.1.1.244
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ntmt1, C9orf32, Mettl11a, Nrmt, Nrmt1, Ad-003
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-V3r
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Lic

Molecule: Rcc1
Chain: D, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: P 65 2 2
R_factor 0.154 R_Free 0.169
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.082 107.082 205.946 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.45 Å
ligand GOL, SAH, UNX enzyme Transferase E.C.2.1.1.244 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for substrate recognition by the human N-terminal methyltransferase 1., Dong C, Mao Y, Tempel W, Qin S, Li L, Loppnau P, Huang R, Min J, Genes Dev. 2015 Nov 15;29(22):2343-8. doi: 10.1101/gad.270611.115. Epub 2015 Nov , 5. PMID:26543161
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (5e1d.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (5e1d.pdb2.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 5E1D
  • CSU: Contacts of Structural Units for 5E1D
  • Structure Factors (35493 Kb)
  • Retrieve 5E1D in mmCIF format [Save to disk]
  • Re-refined 5e1d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E1D 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 5E1D
  • 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 5e1d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e1d_E] [5e1d] [5e1d_D] [5e1d_B] [5e1d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5E1D
  • Community annotation for 5E1D at PDBWiki (http://pdbwiki.org)

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