5CVD Transferase Peptide date Jul 26, 2015
title Crystal Structure Of Human Nrmt1 In Complex With Alpha-N-Dim Human Cenp-A Peptide
authors R.Wu, H.Li
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, Nrmt1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: N-Teminal Peptide From Histone H3-Like Centromeri A;
Chain: D, E
Fragment: Unp Residues 2-10
Synonym: Centromere Autoantigen A,Centromere Protein A,Cenp
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cenpa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: C 1 2 1
R_factor 0.132 R_Free 0.160
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.839 66.245 68.998 90.00 106.69 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand DMG, SAH enzyme Transferase E.C.2.1.1.244 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMolecular basis for histone N-terminal methylation by NRMT1., Wu R, Yue Y, Zheng X, Li H, Genes Dev. 2015 Nov 15;29(22):2337-42. doi: 10.1101/gad.270926.115. Epub 2015 Nov, 5. PMID:26543159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (253 Kb) [Save to disk]
  • Biological Unit Coordinates (5cvd.pdb1.gz) 126 Kb
  • Biological Unit Coordinates (5cvd.pdb2.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 5CVD
  • CSU: Contacts of Structural Units for 5CVD
  • Structure Factors (1428 Kb)
  • Retrieve 5CVD in mmCIF format [Save to disk]
  • Re-refined 5cvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CVD 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 5CVD
  • 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 5cvd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cvd_A] [5cvd_E] [5cvd] [5cvd_D] [5cvd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CVD
  • Community annotation for 5CVD at PDBWiki (http://pdbwiki.org)

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