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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (500 UM 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 :  1.94
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
    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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:216 , GLU A:218 , HIS A:237 , VAL A:239 , LYS A:240 , PHE A:250BINDING SITE FOR RESIDUE MPD A 701
2AC2SOFTWARESER A:434 , PRO A:436 , GLU A:461 , LEU A:462 , TRP A:550 , HOH A:987 , HOH A:1165BINDING SITE FOR RESIDUE MPD A 702
3AC3SOFTWAREGLU A:199 , VAL A:238 , LEU A:282 , HOH A:1185BINDING SITE FOR RESIDUE MPD A 703
4AC4SOFTWAREARG A:448 , GLU A:461BINDING SITE FOR RESIDUE ACT A 704
5AC5SOFTWAREASP A:123 , ASP A:125 , ASP A:127 , VAL A:129 , GLU A:131 , HOH A:1266BINDING SITE FOR RESIDUE CA A 705
6AC6SOFTWAREASN A:154 , ASP A:156 , GLU A:158 , ASP A:166 , ASP A:177 , ASP A:180BINDING SITE FOR RESIDUE CA A 706
7AC7SOFTWAREASP A:156 , GLU A:158 , ASP A:180 , ASP A:389 , HOH A:948 , HOH A:1090BINDING SITE FOR RESIDUE CA A 707
8AC8SOFTWAREASP A:166 , ASP A:169 , LYS A:171 , HOH A:993 , HOH A:1013 , HOH A:1156 , HOH A:1182BINDING SITE FOR RESIDUE CA A 708
9AC9SOFTWAREGLU A:354 , PHE A:408 , LEU A:411 , GLU A:412 , HOH A:860 , HOH A:1170BINDING SITE FOR RESIDUE CA A 709

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N26)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:11 -Gly A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N26)

(-) Exons   (0, 0)

(no "Exon" information available for 4N26)

(-) 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:655
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee...eeeee..........eeeeee....eeeeee..eeeee.......ee....eeeeee..........eeeeeeee........eeeeeeeeeeeeeeee..........................eee.............hhhhh....hhhhhhhheeeeeeeee.......eeeeee..hhhhh.eeeeeee......eeeeee.....eeee....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...ee......eeeeeee....hhhhhhhhhhhhhh...eeeee....hhhhhheeeeeee....eeeeeee................eeee......hhhhhhh.eee...eee..eee....eeeee..........hhhhhhhhhhh.....eeee.......hhhh.eeeee......eeeeeeehhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee..eee.....eee........eee..eeeee.....ee..eehhhhhhhhhhhhhh.eeeee..hhhhh........eeeeee.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n26 A   3 RERTVRLQYGSRVEAVYVLGTYLWTDVYSAAPAGAQTFSLKHSEHVWVEVVRDGEAEEVATNGKQRWLLSPSTTLRVTMSQASTEASSDKVTVNYYDEEGSIPIDQAGLFLTAIEISLDVDADRDGVVEKNNPKKASWTWGPEGQGAILLVNCDRETPWLPKEDCRDEKVYSKEDLKDMSQMILRTKGPDRLPAGYEIVLYISMSDSDKVGVFYVENPFFGQRYIHILGRRKLYHVVKYTGGSAELLFFVEGLCFPDEGFSGLVSIHVSLLEYMAQDIPLTPIFTDTVIFRIAPWIMTPNILPPVSVFVCCMKDNYLFLKEVKNLVEKTNCELKVCFRGDRWIQDEIEFGYIEAPHKGFPVVLDSPRKDFPVKELLGPDFGYVTREPESVTSLDSFGNLEVSPPVTVNGKTYPLGRILIGSSFPLSGGRRMTKVVRDFLKAQQVQAPVELYSDWLTVGHVDEFMSFVPIPGTKKFLLLMASTSACYKLFREKQKDGHGEAIMFKGLGGMSSKRITINKILSNESLVQENLYFQRCLDWNRDILKKELGLTEQDIIDLPALFKMDEDHRARAFFPNMVNMIVLDKDLGIPKPFGPQVEEECCLEMHVRGLLEPLGLECTFIDDISAYHKFLGEVHCGTNVRRKPFTFKWWHMVPSR 667
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332      |346       356       366      |380       390      |402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662     
                                                                                                                                                                                                                                                                                                                                                                          339|                          373|                397|                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                           344                           378                 400                                                                                                                                                                                                                                                                           

   Legend:   → Mismatch (orange background)
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    → 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 4N26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N26)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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    Tyr A:11 - Gly A:12   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        PADI2_HUMAN | Q9Y2J84n20 4n22 4n24 4n25 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n

(-) Related Entries Specified in the PDB File

4n20 4n22 4n24 4n25 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n