5DST Transferase date Sep 17, 2015
title Crystal Structure Of Human Prmt8 In Complex With Sah
authors S.Toma-Fukai, T.Shimizu
compound source
Molecule: Protein Arginine N-Methyltransferase 8
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
Fragment: Unp Residues 68-394
Synonym: Heterogeneous Nuclear Ribonucleoprotein Methyltran Like Protein 4;
Ec: 2.1.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prmt8, Hrmt1l3, Hrmt1l4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.224 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
199.983 130.943 294.377 90.00 106.48 90.00
method X-Ray Diffractionresolution 2.96 Å
ligand SAH enzyme Transferase E.C.2.1.1 BRENDA
Primary referenceNovel helical assembly in arginine methyltransferase 8., Toma-Fukai S, Kim JD, Park KE, Kuwabara N, Shimizu N, Krayukuhina E, Uchiyama S, Fukamizu A, Shimizu T, J Mol Biol. 2016 Feb 11. pii: S0022-2836(16)00112-1. doi:, 10.1016/j.jmb.2016.02.007. PMID:26876602
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (801 Kb) [Save to disk]
  • Biological Unit Coordinates (5dst.pdb1.gz) 121 Kb
  • Biological Unit Coordinates (5dst.pdb2.gz) 121 Kb
  • Biological Unit Coordinates (5dst.pdb3.gz) 122 Kb
  • Biological Unit Coordinates (5dst.pdb4.gz) 121 Kb
  • Biological Unit Coordinates (5dst.pdb5.gz) 122 Kb
  • Biological Unit Coordinates (5dst.pdb6.gz) 121 Kb
  • Biological Unit Coordinates (5dst.pdb7.gz) 122 Kb
  • Biological Unit Coordinates (5dst.pdb8.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 5DST
  • CSU: Contacts of Structural Units for 5DST
  • Structure Factors (2864 Kb)
  • Retrieve 5DST in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DST from S2C, [Save to disk]
  • Re-refined 5dst structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DST 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 5DST
  • 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 5dst from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dst_H] [5dst_J] [5dst_E] [5dst_D] [5dst_G] [5dst_N] [5dst] [5dst_C] [5dst_I] [5dst_O] [5dst_M] [5dst_L] [5dst_A] [5dst_K] [5dst_F] [5dst_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DST
  • Community annotation for 5DST at PDBWiki (http://pdbwiki.org)

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