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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PEPTIDYLARGININE DEIMINASE TYPE4 (PAD4) IN COMPLEX WITH GSK199
 
Authors :  H. D. Lewis, B. D. Bax, C. -W. Chung, O. Polyakova, J. Thorpe
Date :  10 Dec 14  (Deposition) - 28 Jan 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. D. Lewis, J. Liddle, J. E. Coote, S. J. Atkinson, M. D. Barker, B. D. Bax, K. L. Bicker, R. P. Bingham, M. Campbell, Y. H. Chen, C. W. Chung, P. D. Craggs, R. P. Davis, D. Eberhard, G. Joberty, K. E. Lind, K. Locke, C. Maller, K. Martinod, C. Patten, O. Polyakova, C. E. Rise, M. Rudiger, R. J. Sheppard, D. J. Slade, P. Thomas, J. Thorpe G. Yao, G. Drewes, D. D. Wagner, P. R. Thompson, R. K. Prinjha, D. M. Wilson
Inhibition Of Pad4 Activity Is Sufficient To Disrupt Mouse And Human Net Formation.
Nat. Chem. Biol. V. 11 189 2015
PubMed-ID: 25622091  |  Reference-DOI: 10.1038/NCHEMBIO.1735

(-) Compounds

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE-4
    Chains: A
    EC Number: 3.5.3.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Gene: PADI4, 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
13Z01Ligand/Ion[(3R)-3-AMINOPIPERIDIN-1-YL][2-(1-ETHYL-1H-PYRROLO[2,3-B]PYRIDIN-2-YL)-7-METHOXY-1-METHYL-1H-BENZIMIDAZOL-5-YL]METHANONE
2CA4Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13Z02Ligand/Ion[(3R)-3-AMINOPIPERIDIN-1-YL][2-(1-ETHYL-1H-PYRROLO[2,3-B]PYRIDIN-2-YL)-7-METHOXY-1-METHYL-1H-BENZIMIDAZOL-5-YL]METHANONE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:353 , PHE A:407 , LEU A:410 , GLU A:411 , HOH A:818 , HOH A:819binding site for residue CA A 701
2AC2SOFTWAREASN A:153 , ASP A:155 , ASP A:157 , ASP A:165 , ASP A:176 , ASP A:179binding site for residue CA A 702
3AC3SOFTWAREASP A:155 , ASP A:157 , ASP A:179 , LYS A:362 , ASP A:388binding site for residue CA A 703
4AC4SOFTWAREASP A:165 , ASP A:168 , GLU A:170 , HOH A:813 , HOH A:821 , HOH A:822binding site for residue CA A 704
5AC5SOFTWAREVAL A:469 , HIS A:471 , ASP A:473 , GLU A:474 , ALA A:581 , PHE A:582 , PHE A:583 , PRO A:584 , ASN A:585 , ASN A:588 , VAL A:643binding site for residue 3Z0 A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X8G)

(-) Exons   (0, 0)

(no "Exon" information available for 4X8G)

(-) 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:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......eeeeee...eeeee..........eeeeee...eeeeee.........eeeeee.........eeeeeeee.eeeeeeeeeeeeeeee...........................eee.............hhhhh....hhhhh...eeeeeeeeehhhhhh.eeeeeee.......eeeee....eeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...........eeeee....hhhhhhhhhhhhhhh..eee....eeeeeee....eeeeeee...........eee...........eee...eee..eee....eeeee...........hhhhhhhhhhh.....eeee............eeeee......eeeeeeehhhhhhhhhhhhhh.....ee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee..eee.hhh.eee.......................ee..eehhhhhhhhhhhhhh..........eee..eee...eeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x8g A   3 QGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIASTWPLDPGVEVTLTMKVASGSTGDQKVQISYYPVKALLYLTGVEISLCADITRTGKVKPTAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACFENEDFLKSVTTLAMKAKCKLTIQDEMEIGYIQAPHKTLPVVFDSPRKRVMGPDFGYVTRISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIGEVHAGTNVRRKPFSFKWWNMVP 663
                                    12        22        32        42        52||      74        84        94  ||   109       119       129||     140       150       160       170       180       190       200       210      |226       236       246       256       266       276       286       296       306    || 318       328       350       360       370 ||    389    || 405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635  ||   647       657      
                                                                             53|                             97|                        130|                                                                                  217|                                                                                    311|                   336|                    372|         394|                                                                                                                                                                                                                                          638|                      
                                                                              66                             103                         132                                                                                   224                                                                                     314                    349                     382          401                                                                                                                                                                                                                                           641
   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 4X8G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X8G)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  4x8g
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  PADI4_HUMAN | Q9UM07
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  3.5.3.15
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PADI4_HUMAN | Q9UM07: 1wd8 1wd9 1wda 2dew 2dex 2dey 2dw5 3apm 3apn 3b1t 3b1u 4dkt 4x8c 5n0m 5n0y 5n0z 5n1b

(-) Related Entries Specified in the PDB File

4x8c