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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (5 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 :  1.70
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
    Chains: A
    EC Number: 3.5.3.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PADI2, KIAA0994, PDI2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAD-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, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:216 , GLU A:218 , HIS A:237 , VAL A:239 , LYS A:240 , PHE A:250 , HOH A:1235BINDING SITE FOR RESIDUE MPD A 701
02AC2SOFTWARESER A:433 , SER A:434 , PRO A:436 , GLU A:461 , LEU A:462 , TRP A:550 , HOH A:1300BINDING SITE FOR RESIDUE MPD A 702
03AC3SOFTWAREGLU A:199BINDING SITE FOR RESIDUE MPD A 703
04AC4SOFTWAREASP A:166 , ASP A:169 , LYS A:171 , HOH A:835 , HOH A:878 , HOH A:894 , HOH A:917BINDING SITE FOR RESIDUE CA A 704
05AC5SOFTWAREASN A:154 , ASP A:156 , GLU A:158 , ASP A:166 , ASP A:177 , ASP A:180 , CA A:706BINDING SITE FOR RESIDUE CA A 705
06AC6SOFTWAREASP A:156 , GLU A:158 , ASP A:180 , ASP A:389 , CA A:705 , HOH A:872 , HOH A:888BINDING SITE FOR RESIDUE CA A 706
07AC7SOFTWAREGLN A:350 , ASN A:590 , ILE A:592 , THR A:649BINDING SITE FOR RESIDUE ACT A 707
08AC8SOFTWAREASP A:123 , ASP A:125 , ASP A:127 , VAL A:129 , GLU A:131 , HOH A:890BINDING SITE FOR RESIDUE CA A 708
09AC9SOFTWAREGLN A:350 , GLU A:354 , PHE A:408 , LEU A:411 , GLU A:412 , HOH A:814 , HOH A:861BINDING SITE FOR RESIDUE CA A 709
10BC1SOFTWAREILE A:526 , LYS A:530 , ASN A:534 , PHE A:584 , HOH A:1179BINDING SITE FOR RESIDUE MPD A 710
11BC2SOFTWAREARG A:448BINDING SITE FOR RESIDUE ACT A 711

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N2A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2A)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2A)

(-) 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 .eee.......eeeeeee...eeee...........eeeeee....eeeeee..eeeee.......ee....eeeeee..........eeeeeeee........eeeeeeeeeeeeeeee..........................eee.............hhhhh....hhhhhhhheeeeeeeee.......eeeeee..hhhhh.eeeeeee......eeeeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...ee......eeeeeee....hhhhhhhhhhhhhh...eeeee..hhhhhheeeeeeee..eeeeeeee................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
                 4n2a A   3 RERTVRLQYGSRVEAVYVLGTYLWTDVYSAAPAGAQTFSLKHSEHVWVEVVRDGEAEEVATNGKQRWLLSPSTTLRVTMSQASTEASSDKVTVNYYDEEGSIPIDQAGLFLTAIEISLDVDADRDGVVEKNNPKKASWTWGPEGQGAILLVNCDRETPWLPKEDCRDEKVYSKEDLKDMSQMILRTKGPDRLPAGYEIVLYISMSDSDKVGVFYVENPFFGQRYIHILGRRKLYHVVKYTGGSAELLFFVEGLCFPDEGFSGLVSIHVSLLEYMAQDIPLTPIFTDTVIFRIAPWIMTPNILPPVSVFVCCMKDNYLFLKEVKNLVEKTNCELKVCFDRWIQDEIEFGYIEAPHKGFPVVLDSPRKDFPVKELLGPDFGYVTREPLFESVTSLDSFGNLEVSPPVTVNGKTYPLGRILIGSSFPLSGGRRMTKVVRDFLKAQQVQAPVELYSDWLTVGHVDEFMSFVPIPGTKKFLLLMASTSACYKLFREKQKDGHGEAIMFKGLGGMSSKRITINKILSNESLVQENLYFQRCLDWNRDILKKELGLTEQDIIDLPALFKMDEDHRARAFFPNMVNMIVLDKDLGIPKPFGPQVEEECCLEMHVRGLLEPLGLECTFIDDISAYHKFLGEVHCGTNVRRKPFTFKWWHMVPSR 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      |348       358       368    || 382       392       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|                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                           346                         378
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  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 4N2A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2A)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PADI2_HUMAN | Q9Y2J8: 4n20 4n22 4n24 4n25 4n26 4n28 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n

(-) Related Entries Specified in the PDB File

4n20 4n22 4n24 4n25 4n26 4n28 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n