5N1B Hydrolase Hydrolase Inhibitor date Feb 06, 2017
title Hpad4 Crystal Complex With Afm-14a
authors E.Beaumont, P.Kerry, P.Thompson, A.Muth, V.Subramanian, M.Nagar, H K.Clancy, S.Parelkar
compound source
Molecule: Protein-Arginine Deiminase Type-4
Chain: A
Synonym: Hl-60 Pad,Peptidylarginine Deiminase Iv,Protein-Ar Deiminase Type Iv;
Ec: 3.5.3.15
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Padi4, Pad4, Padi5, Pdi5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
147.580 60.600 115.980 90.00 124.62 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 8FW, CA, SO4 enzyme Hydrolase E.C.3.5.3.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDevelopment of a Selective Inhibitor of Protein Arginine Deiminase 2., Muth A, Subramanian V, Beaumont E, Nagar M, Kerry P, McEwan P, Srinath H, Clancy K, Parelkar S, Thompson PR, J Med Chem. 2017 Apr 13;60(7):3198-3211. doi: 10.1021/acs.jmedchem.7b00274. Epub , 2017 Mar 31. PMID:28328217
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (5n1b.pdb1.gz) 208 Kb
  • LPC: Ligand-Protein Contacts for 5N1B
  • CSU: Contacts of Structural Units for 5N1B
  • Structure Factors (568 Kb)
  • Retrieve 5N1B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5N1B from S2C, [Save to disk]
  • Re-refined 5n1b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5N1B 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 5N1B
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5n1b_A] [5n1b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5N1B
  • Community annotation for 5N1B at PDBWiki (http://pdbwiki.org)

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