Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) 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
    ChainsA
    EC Number3.5.3.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-GOLD(DE3)PLYSS AG
    Expression System Taxid866768
    GenePADI4, PADI5, PDI5
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHL-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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3Z0  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4x8g)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4x8g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PADI4_HUMAN | Q9UM07
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.3.15
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PADI4_HUMAN | Q9UM07
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PADI4_HUMAN | Q9UM071wd8 1wd9 1wda 2dew 2dex 2dey 2dw5 3apm 3apn 3b1t 3b1u 4dkt 4x8c 5n0m 5n0y 5n0z 5n1b

(-) Related Entries Specified in the PDB File

4x8c