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(-) Description

Title :  HPAD4 CRYSTAL COMPLEX WITH AFM-30A
 
Authors :  E. Beaumont, P. Kerry, P. Thompson, A. Muth, V. Subramanian, M. Nagar, H K. Clancy, S. Parelkar
Date :  03 Feb 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Muth, V. Subramanian, E. Beaumont, M. Nagar, P. Kerry, P. Mcewan, H. Srinath, K. Clancy, S. Parelkar, P. R. Thompson
Development Of A Selective Inhibitor Of Protein Arginine Deiminase 2.
J. Med. Chem. V. 60 3198 2017
PubMed-ID: 28328217  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00274

(-) Compounds

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE-4
    Chains: A
    EC Number: 3.5.3.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PADI4, PAD4, PADI5, PDI5
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HL-60 PAD,PEPTIDYLARGININE DEIMINASE IV,PROTEIN-ARGININE DEIMINASE TYPE IV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
18FQ1Ligand/Ion~{N}-[(1~{S})-4-(2-FLUORANYLETHANIMIDOYLAMINO)-1-(4-METHOXY-1-METHYL-BENZIMIDAZOL-2-YL)BUTYL]-3-OXIDANYLIDENE-1,2-DIHYDROISOINDOLE-4-CARBOXAMIDE
2CA5Ligand/IonCALCIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
18FQ2Ligand/Ion~{N}-[(1~{S})-4-(2-FLUORANYLETHANIMIDOYLAMINO)-1-(4-METHOXY-1-METHYL-BENZIMIDAZOL-2-YL)BUTYL]-3-OXIDANYLIDENE-1,2-DIHYDROISOINDOLE-4-CARBOXAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:402 , GLY A:403 , ARG A:441 , 8FQ A:707 , HOH A:834binding site for residue SO4 A 701
2AC2SOFTWAREGLN A:349 , GLU A:353 , PHE A:407 , LEU A:410 , GLU A:411 , HOH A:827 , HOH A:893binding site for residue CA A 702
3AC3SOFTWAREGLU A:351 , ASP A:369 , SER A:370 , ASN A:373 , HOH A:805 , HOH A:913binding site for residue CA A 703
4AC4SOFTWAREASN A:153 , ASP A:155 , ASP A:157 , ASP A:165 , ASP A:176 , ASP A:179binding site for residue CA A 704
5AC5SOFTWAREASP A:155 , ASP A:157 , ASP A:179 , ASP A:388 , HOH A:932binding site for residue CA A 705
6AC6SOFTWAREASP A:165 , ASP A:168 , GLU A:170 , HOH A:804 , HOH A:845 , HOH A:970binding site for residue CA A 706
7AC7SOFTWARETRP A:347 , ASP A:350 , ARG A:374 , VAL A:469 , HIS A:471 , ASP A:473 , ARG A:639 , HIS A:640 , CYS A:645 , SO4 A:701 , HOH A:803 , HOH A:870 , HOH A:878binding site for residue 8FQ A 707
8AC8SOFTWARELYS A:525 , LYS A:527 , ASN A:528binding site for residue SO4 A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N0Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5N0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5N0Y)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:635
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee...eeeee..........eeeeee...eeeeee...ee.....eeeeee.........eeeeeeeee..eeeeeeeeeeeeeeeeeee...................eee.............hhhhh......hhhhhheeeeeeeee..hhhhheeeeee....hhh.eeeeee...eeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...........eeeeeee....hhhhhhhhhhhhhhh..eeeeehhhhhh........eeeeeeee..eeeeeeee........hhhhhhh.....eeee........hhhhhhh.eee...eee..eee....eeeee...........hhhhhhhhhhh.....eeee.......hhhh.eeeee......eeeeeeehhhhhhhhhhhhhh.....ee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..eee.hhh.eee........eee..eeeee.....ee..eehhhhhhhhhhhhhh.eeeee.....hhhhh..hhh.eeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n0y A   3 QGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCADITRTGKVRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP 663
                                    12        22        32        42        52 ||     73        83        93       103       113       123   ||  142       152       162       172       182       192       202       212    || 228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658     
                                                                              54|                                                          127|                                                                             217|                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                               66                                                           137                                                                              224
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5N0Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N0Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N0Y)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        PADI4_HUMAN | Q9UM07: 1wd8 1wd9 1wda 2dew 2dex 2dey 2dw5 3apm 3apn 3b1t 3b1u 4dkt 4x8c 4x8g 5n0m 5n0z 5n1b

(-) Related Entries Specified in the PDB File

5n0m