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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN ARGININE DEIMINASE 2 (D177A, 10 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 :  1.90
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, 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 , HIS A:237 , VAL A:239 , LYS A:240BINDING 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:1082 , HOH A:1238BINDING SITE FOR RESIDUE MPD A 702
03AC3SOFTWAREGLU A:199 , LEU A:282 , HOH A:1198 , HOH A:1209BINDING SITE FOR RESIDUE MPD A 703
04AC4SOFTWAREGLN A:350 , GLU A:354 , PHE A:408 , LEU A:411 , GLU A:412 , HOH A:846 , HOH A:1247BINDING SITE FOR RESIDUE CA A 704
05AC5SOFTWAREASN A:154 , ASP A:156 , GLU A:158 , ASP A:166 , ASP A:180 , CA A:706 , HOH A:969BINDING SITE FOR RESIDUE CA A 705
06AC6SOFTWAREASP A:156 , GLU A:158 , ASP A:180 , ASP A:389 , CA A:705 , HOH A:1235BINDING SITE FOR RESIDUE CA A 706
07AC7SOFTWAREASP A:166 , ASP A:169 , LYS A:171 , HOH A:1058BINDING SITE FOR RESIDUE CA A 707
08AC8SOFTWAREARG A:448BINDING SITE FOR RESIDUE ACT A 708
09AC9SOFTWARETYR A:98 , GLY A:197 , HOH A:1051BINDING SITE FOR RESIDUE ACT A 709
10BC1SOFTWAREPHE A:320 , ARG A:347 , GLN A:350 , ASN A:590 , ILE A:592 , GLY A:599 , PRO A:601 , ILE A:632 , ASP A:634 , THR A:649BINDING SITE FOR RESIDUE MPD A 710
11BC2SOFTWAREASP A:123 , ASP A:125 , ASP A:127 , VAL A:129 , GLU A:131 , HOH A:1253BINDING SITE FOR RESIDUE CA A 711

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N2I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N2I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N2I)

(-) Exons   (0, 0)

(no "Exon" information available for 4N2I)

(-) 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........eeeeee..eeeee...........eeeeee....eeeeee..eeee........ee....eeeeee..........eeeeeeee........eeeeeeeeeeeeeee...........................eee..........hhhhh.....hhhhhhheeeeeeeee.......eeeeee..hhhhh.eeeeeee......eeeeee.....eeee....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...ee......eeeeeee....hhhhhhhhhhhhhh...eeeee......hhhhhheeeeeeee..eeeeeeee....................eeee........hhhhhhh.eee...eee..eee....eeeee..........hhhhhhhhhhhh....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
                 4n2i A   2 LRERTVRLQYGSRVEAVYVLGTYLWTDVYSAAPAGAQTFSLKHSEHVWVEVVRDGEAEEVATNGKQRWLLSPSTTLRVTMSQASTEASSDKVTVNYYDEEGSIPIDQAGLFLTAIEISLDVDADRDGVVEKNNPKKASWTWGPEGQGAILLVNCDRETPKEDCRDEKVYSKEALKDMSQMILRTKGPDRLPAGYEIVLYISMSDSDKVGVFYVENPFFGQRYIHILGRRKLYHVVKYTGGSAELLFFVEGLCFPDEGFSGLVSIHVSLLEYMAQDIPLTPIFTDTVIFRIAPWIMTPNILPPVSVFVCCMKDNYLFLKEVKNLVEKTNCELKVCFLNRGDRWIQDEIEFGYIEAPHKGFPVVLDSPRDGNLKDFPVKELLGPDFGYVTREPLFESVTSLDSFGNLEVSPPVTVNGKTYPLGRILIGSSFPLSGGRRMTKVVRDFLKAQQVQAPVELYSDWLTVGHVDEFMSFVPIPGTKKFLLLMASTSACYKLFREKQKDGHGEAIMFKGLGGMSSKRITINKILSNESLVQENLYFQRCLDWNRDILKKELGLTEQDIIDLPALFKMDEDHRARAFFPNMVNMIVLDKDLGIPKPFGPQVEEECCLEMHVRGLLEPLGLECTFIDDISAYHKFLGEVHCGTNVRRKPFTFKWWHMVPSRR 668
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334    || 346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666  
                                                                                                                                                                                        160|                                                                                                                                                                            339|                                                                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                         164                                                                                                                                                                             342                                                                                                                                                                                                                                                                                                                                      

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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 4N2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N2I)

(-) Gene Ontology  (17, 17)

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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 4n2f 4n2g 4n2h 4n2k 4n2l 4n2m 4n2n

(-) Related Entries Specified in the PDB File

4n20 4n22 4n24 4n25 4n26 4n28 4n2a 4n2b 4n2c 4n2d 4n2e 4n2f 4n2g 4n2h 4n2k 4n2l 4n2m 4n2n