Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF VASPIN MUTANT D305C V383C
 
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, Signaling Protein, Hydrolase Inhibitor, Hydrloase 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
    Expression System Taxid511693
    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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:127 , GLN A:128 , LYS A:131 , ARG A:211 , ARG A:363binding site for residue EDO A 501
2AC2SOFTWARETHR A:223 , LYS A:224 , GLU A:225 , PRO A:239 , ARG A:310binding site for residue SO4 A 502
3AC3SOFTWAREHIS A:113 , ASP A:153 , PHE A:157binding site for residue EDO A 503
4AC4SOFTWAREPHE A:317 , ASP A:318 , THR A:322binding site for residue EDO A 504
5AC5SOFTWARELEU A:48 , GLN A:51 , ASN A:52 , SER A:80 , PHE A:102 , PHE A:104 , PHE A:116 , HOH A:746binding site for residue EDO A 505
6AC6SOFTWAREARG A:143 , CYS A:383 , VAL A:384 , LYS A:385binding site for residue EDO A 506
7AC7SOFTWARETHR B:162 , HOH B:676binding site for residue EDO B 501
8AC8SOFTWARELEU B:48 , GLN B:51 , ASN B:52 , SER B:80 , PHE B:102 , PHE B:104 , PHE B:116binding site for residue EDO B 502

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:305 -A:383
2B:305 -B:383

(-) 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 4Y40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y40)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y40)

(-) 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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhee...eeeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeee...........eeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh.................eeeeeeeeee........eeee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y40 A  36 VQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKLKHLEKGLQVDTFSRWKTLLSRRVVCVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTETPLCVKIDKPYLLLIYSEKIPSVLFLGKIVNPIGK 414
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365||     388       398       408      
                                                                                                                                                                                                                                                                                                                                                                    366|                                  
                                                                                                                                                                                                                                                                                                                                                                     380                                  

Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhee...eeeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeee...........eeeee.......eeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhh.hhhhhhhhhh..eeeeeeeeee.eeeeeeeehhhhhhh...hhhhh.................eeeeeeeeee.......ee....eeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y40 B  34 SEVQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEKHLEKGLQVDTFSRWKTLLSRRVVCVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTLCVKIDKPYLLLIYSEKIPSVLFLGKIVNPIG 413
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   ||  286       296       306       316       326       336       346       356       382       392       402       412 
                                                                                                                                                                                                                                                                             277|                                                                                 365|                               
                                                                                                                                                                                                                                                                              281                                                                                  382                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4Y40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y40)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:399 - Pro A:400   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4y40
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPA12_HUMAN | Q8IW75
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPA12_HUMAN | Q8IW75
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPA12_HUMAN | Q8IW754if8 4y3k 5ei0

(-) Related Entries Specified in the PDB File

4if8 4IF8 CONTAINS THE WILD TYPE PROTEIN CRYSTALLIZED IN THE SAME SPACE GROUP.
4y3k 4Y3K CONTAINS THE E379S MUTANT CRYSTALLIZED IN THE SAME SPACE GROUP.