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(-) Description

Title :  STRUCTURE OF VASPIN MUTANT E379S
 
Authors :  J. Pippel, N. Strater, D. Ulbricht, S. Schultz, R. Meier, J. T. Heiker
Date :  10 Feb 15  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serpin, Adipokine, Exosite, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Ulbricht, J. Pippel, S. Schultz, R. Meier, N. Strater, J. T. Heiker
A Unique Serpin P1' Glutamate And A Conserved Beta-Sheet C Arginine Are Key Residues For Activity, Protease Recognitio And Stability Of Serpina12 (Vaspin).
Biochem. J. V. 470 357 2015
PubMed-ID: 26199422  |  Reference-DOI: 10.1042/BJ20150643

(-) Compounds

Molecule 1 - SERPIN A12
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 22-414
    GeneSERPINA12
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOL-64,VISCERAL ADIPOSE TISSUE-DERIVED SERINE PROTEASE INHIBITOR,VASPIN,VISCERAL ADIPOSE-SPECIFIC SERPIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:211 , LYS A:359 , ARG A:363binding site for residue SO4 A 501
02AC2SOFTWAREVAL A:222 , LYS A:224 , GLU A:226 , MET A:240 , PHE A:242 , SER A:307binding site for residue EDO A 502
03AC3SOFTWARETHR A:322 , TYR A:325 , HOH A:732binding site for residue EDO A 503
04AC4SOFTWARELYS A:61 , PHE A:65 , GLU A:284 , HOH A:608binding site for residue EDO A 504
05AC5SOFTWARETHR A:127 , GLN A:128 , LYS A:131 , ARG A:211 , ARG A:363binding site for residue EDO A 505
06AC6SOFTWAREGLN A:147 , GLY A:250 , TYR A:251 , LEU A:298 , HOH A:609 , HOH A:610binding site for residue EDO A 506
07AC7SOFTWARELYS A:281 , LYS A:285 , GLU A:333 , GLU A:334 , LYS A:348binding site for residue SO4 A 507
08AC8SOFTWARELYS A:126 , LYS A:131 , HIS A:186 , LYS A:188 , HOH A:708 , HOH A:734 , HIS B:186binding site for residue SO4 A 508
09AC9SOFTWARETHR B:94 , LYS B:330 , GLU B:333 , HIS B:335 , GLY B:336 , ASP B:337 , LEU B:338 , LEU B:347 , HOH B:636binding site for residue EDO B 501
10AD1SOFTWARELYS B:320 , HIS B:344 , ARG B:345 , SER B:346binding site for residue SO4 B 502
11AD2SOFTWAREGLN B:168 , LEU B:170 , GLN B:174 , ASN B:195 , ILE B:196binding site for residue SO4 B 503
12AD3SOFTWAREASP A:179 , LYS B:188 , ASN B:190 , LYS B:355binding site for residue EDO B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y3K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:399 -Pro A:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y3K)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhee...eeeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeee......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhhhhhh..hhhhhhh...eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh.................eeeeeeeeee........eeee....eeeeeee.....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y3k A  35 EVQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKLKHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTEGPLVVKIDKPYLLLIYSEKIPSVLFLGKIVNPIGK 414
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  ||   387       397       407       
                                                                                                                                                                                                                                                                                                                                                                      367|                                 
                                                                                                                                                                                                                                                                                                                                                                       381                                 

Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhee...eeeeeeeeeeee.hhh.hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeee...........eeeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhh...hhhhhhhh...eeeeeeeeee.eeeeeeeehhhhhhh...hhhhh.................eeeeeeeeee............eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y3k B  35 EVQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDELKHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTVVKIDKPYLLLIYSEKIPSVLFLGKIVNPIGK 414
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274  ||   286       296       306       316       326       336       346       356       383       393       403       413 
                                                                                                                                                                                                                                                                            277|                                                                                  365|                               
                                                                                                                                                                                                                                                                             280                                                                                   383                               

   Legend:   → Mismatch (orange background)
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  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 4Y3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y3K)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPA12_HUMAN | Q8IW754if8 4y40 5ei0

(-) Related Entries Specified in the PDB File

4if8 4IF8 CONTAINS THE WILD TYPE PROTEIN CRYSTALLIZED IN THE SAME SPACE GROUP.
4y40 4Y40 CONTAINS THE D305C V383C MUTANT CRYSTALLIZED IN THE SAME SPACE GROUP.