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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (D169A, 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 :  1.80
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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:199 , TYR A:236 , VAL A:238 , LEU A:282 , LEU A:437 , HOH A:1223BINDING SITE FOR RESIDUE MPD A 701
2AC2SOFTWAREVAL A:446BINDING SITE FOR RESIDUE MPD A 702
3AC3SOFTWAREGLU A:354 , PHE A:408 , LEU A:411 , HOH A:982 , HOH A:1014 , HOH A:1039BINDING SITE FOR RESIDUE CA A 703
4AC4SOFTWAREASP A:123 , ASP A:125 , ASP A:127 , VAL A:129 , GLU A:131 , HOH A:960BINDING SITE FOR RESIDUE CA A 704
5AC5SOFTWARESER A:434 , PHE A:435 , PRO A:436 , GLU A:461 , LEU A:462 , TRP A:550 , HOH A:934 , HOH A:1054BINDING SITE FOR RESIDUE MPD A 705
6AC6SOFTWAREPHE A:320 , GLN A:350 , ASN A:590 , ILE A:592 , PRO A:601 , ASP A:634 , THR A:649BINDING SITE FOR RESIDUE MPD A 706
7AC7SOFTWAREGLY A:128 , MET A:181 , SER A:182 , GLN A:183BINDING SITE FOR RESIDUE ACT A 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2F)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2F)

(-) 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    
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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:633
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......eeeeeee..eeeee...........eeeeee....eeeeee..eeee........ee....eeeeee..........eeeeeeee........eeeeeeeeeeeeeee...........................eee.........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
                 4n2f A   2 LRERTVRLQYGSRVEAVYVLGTYLWTDVYSAAPAGAQTFSLKHSEHVWVEVVRDGEAEEVATNGKQRWLLSPSTTLRVTMSQASTEASSDKVTVNYYDEEGSIPIDQAGLFLTAIEISLDVDADRDGVVEKNNPKKASWTWGPEGQGAILLVNCDLKDMSQMILRTKGPDRLPAGYEIVLYISMSDSDKVGVFYVENPFFGQRYIHILGRRKLYHVVKYTGGSAELLFFVEGLCFPDEGFSGLVSIHVSLLEYMAQDIPLTPIFTDTVIFRIAPWIMTPNILPPVSVFVCCMKDNYLFLKEVKNLVEKTNCELKVCFQYLNRGDRWIQDEIEFGYIEAPHKGFPVVLDSPRDGELLGPDFGYVTRESVTSLDSFGNLEVSPPVTVNGKTYPLGRILIGSSFPLSGGRRMTKVVRDFLKAQQVQAPVELYSDWLTVGHVDEFMSFVPIPGTKKFLLLMASTSACYKLFREKQKDGHGEAIMFKGLGGMSSKRITINKILSNESLVQENLYFQRCLDWNRDILKKELGLTEQDIIDLPALFKMDEDHRARAFFPNMVNMIVLDKDLGIPKPFGPQVEEECCLEMHVRGLLEPLGLECTFIDDISAYHKFLGEVHCGTNVRRKPFTFKWWHMVPSR 667
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    || 182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372  ||   390     ||404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664   
                                                                                                                                                                                    156|                                                                                                                                                                                                  375|         396|                                                                                                                                                                                                                                                                          
                                                                                                                                                                                     178                                                                                                                                                                                                   384          401                                                                                                                                                                                                                                                                          

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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 4N2F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2F)

(-) 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 | Q9Y2J84n20 4n22 4n24 4n25 4n26 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n

(-) Related Entries Specified in the PDB File

4n20 4n22 4n24 4n25 4n26 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2g 4n2h 4n2i 4n2k 4n2l 4n2m 4n2n