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 PROTEIN ARGININE DEIMINASE 2 (D177A, 0 MM CA2+)
 
Authors :  D. J. Slade, X. Zhang, P. Fang, C. J. Dreyton, Y. Zhang, M. L. Gross, M. Guo S. A. Coonrod, P. R. Thompson
Date :  04 Oct 13  (Deposition) - 04 Feb 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Deiminase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Slade, P. Fang, C. J. Dreyton, Y. Zhang, J. Fuhrmann, D. Rempel, B. D. Bax, S. A. Coonrod, H. D. Lewis, M. Guo, M. L. Gross, P. R. Thompson
Protein Arginine Deiminase 2 Binds Calcium In An Ordered Fashion: Implications For Inhibitor Design.
Acs Chem. Biol. V. 10 1043 2015
PubMed-ID: 25621824  |  Reference-DOI: 10.1021/CB500933J

(-) Compounds

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE-2
    ChainsA
    EC Number3.5.3.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePADI2, KIAA0994, PDI2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPAD-H19, PEPTIDYLARGININE DEIMINASE II, PROTEIN-ARGININE DEIMINASE TYPE II

 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
1CA2Ligand/IonCALCIUM ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:199 , LEU A:282 , LEU A:437 , HOH A:1117BINDING SITE FOR RESIDUE MPD A 701
2AC2SOFTWAREILE A:280 , HOH A:892 , HOH A:1464BINDING SITE FOR RESIDUE MPD A 702
3AC3SOFTWAREASP A:123 , ASP A:125 , ASP A:127 , VAL A:129 , GLU A:131 , HOH A:857BINDING SITE FOR RESIDUE CA A 704
4AC4SOFTWAREGLU A:354 , PHE A:408 , LEU A:411 , HOH A:1157 , HOH A:1211 , HOH A:1233BINDING SITE FOR RESIDUE CA A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N2H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2H)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2H)

(-) 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:639
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeeee...eeee...........eeeeee....eeeeee..eeeee.......ee....eeeeee..........eeeeeeee........eeeeeeeeeeeeeee...........................eee.......hhhhhh..eeeeeeeee.......eeeeee..hhhhh.eeeee..........eeee.....eeee....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...ee......eeeeeee....hhhhhhhhhhhhh....eeeee........hhhhhheeeeeee....eeeeeee..............eeee..hhhhhhh.eee...eee..eee....eeeee..........hhhhhhhhhhh.....eeee.......hhhh.eeeee......eeeeeeehhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..eee.....eee........eee..eeeee.....ee..eehhhhhhhhhhhhhh.eeeee..hhhhh........eeeeee.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n2h A   3 RERTVRLQYGSRVEAVYVLGTYLWTDVYSAAPAGAQTFSLKHSEHVWVEVVRDGEAEEVATNGKQRWLLSPSTTLRVTMSQASTEASSDKVTVNYYDEEGSIPIDQAGLFLTAIEISLDVDADRDGVVEKNNPKKASWTWGPEGQGAILLVNCDVYSKEALKDMSQMILRTKGPDRLPAGYEIVLYISMSDSDKVGVFYVENPFFGQRYIHILGRRKLYHVVKYTGGSAELLFFVEGLCFPDEGFSGLVSIHVSLLEYMAQDIPLTPIFTDTVIFRIAPWIMTPNILPPVSVFVCCMKDNYLFLKEVKNLVEKTNCELKVCFQYLNRGDRWIQDEIEFGYIEAPHKGFPVVLDSPRDGNLELLGPDFGYVTRVTSLDSFGNLEVSPPVTVNGKTYPLGRILIGSSFPLSGGRRMTKVVRDFLKAQQVQAPVELYSDWLTVGHVDEFMSFVPIPGTKKFLLLMASTSACYKLFREKQKDGHGEAIMFKGLGGMSSKRITINKILSNESLVQENLYFQRCLDWNRDILKKELGLTEQDIIDLPALFKMDEDHRARAFFPNMVNMIVLDKDLGIPKPFGPQVEEECCLEMHVRGLLEPLGLECTFIDDISAYHKFLGEVHCGTNVRRKPFTFKWWHMVPSRR 668
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   ||  177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377|      393 ||    409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659         
                                                                                                                                                                                   156|                                                                                                                                                                                                          377|        395|                                                                                                                                                                                                                                                                          
                                                                                                                                                                                    172                                                                                                                                                                                                           384         402                                                                                                                                                                                                                                                                          

   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 4N2H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2H)

(-) Gene Ontology  (17, 17)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4n2h)
 
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
  4n2h
    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
  PADI2_HUMAN | Q9Y2J8
    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
  PADI2_HUMAN | Q9Y2J8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PADI2_HUMAN | Q9Y2J84n20 4n22 4n24 4n25 4n26 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2i 4n2k 4n2l 4n2m 4n2n

(-) Related Entries Specified in the PDB File

4n20 4n22 4n24 4n25 4n26 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2i 4n2k 4n2l 4n2m 4n2n