5YJF Transferase date Oct 10, 2017
title Co-Crystal Structure Of Human Nicotinamide N-Methyltransfera With Small Molecule Analog Of Nicotinamide
authors S.Swaminathan, S.Birudukota, M.K.Thakur, R.Parveen, S.Kandan, M.S S.Rajagopal, S.Ruf, S.Dhakshinamoorthy, A.Kannt, R.Gosu
compound source
Molecule: Nicotinamide N-Methyltransferase
Chain: A, B, C, D
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nnmt
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.224 R_Free 0.286
length a length b length c angle alpha angle beta angle gamma
60.323 132.976 61.317 90.00 103.57 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand 8WO, SAH enzyme Transferase E.C. BRENDA
A, D, C, B

Primary referenceA small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders., Kannt A, Rajagopal S, Kadnur SV, Suresh J, Bhamidipati RK, Swaminathan S, Hallur MS, Kristam R, Elvert R, Czech J, Pfenninger A, Rudolph C, Schreuder H, Chandrasekar DV, Mane VS, Birudukota S, Shaik S, Zope BR, Burri RR, Anand NN, Thakur MK, Singh M, Parveen R, Kandan S, Mullangi R, Yura T, Gosu R, Ruf S, Dhakshinamoorthy S, Sci Rep. 2018 Feb 26;8(1):3660. doi: 10.1038/s41598-018-22081-7. PMID:29483571
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (340 Kb) [Save to disk]
  • Biological Unit Coordinates (5yjf.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (5yjf.pdb2.gz) 86 Kb
  • Biological Unit Coordinates (5yjf.pdb3.gz) 86 Kb
  • Biological Unit Coordinates (5yjf.pdb4.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 5YJF
  • CSU: Contacts of Structural Units for 5YJF
  • Structure Factors (948 Kb)
  • Retrieve 5YJF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YJF from S2C, [Save to disk]
  • View 5YJF 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 5YJF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5yjf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yjf_A] [5yjf_D] [5yjf_B] [5yjf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YJF
  • Community annotation for 5YJF at PDBWiki (http://pdbwiki.org)

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