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

(-) Description

Title :  STRUCTURE OF RCL-CLEAVED VASPIN (SERPINA12)
 
Authors :  J. Pippel, B. E. Kuettner, D. Ulbricht, J. Daberger, S. Schultz, J. T. He N. Strater
Date :  29 Oct 15  (Deposition) - 11 Nov 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  E  (1x)
Keywords :  Serpin, Cleaved, Adipokine, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Pippel, E. B. Kuettner, D. Ulbricht, J. Daberger, S. Schultz, J. T. Heiker, N. Strater
Crystal Structure Of Cleaved Vaspin (Serpina12).
Biol. Chem. V. 397 111 2016
PubMed-ID: 26529565  |  Reference-DOI: 10.1515/HSZ-2015-0229
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERPIN A12
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 22-414
    GeneSERPINA12
    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 AE
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5EI0)

(-) Sites  (0, 0)

(no "Site" information available for 5EI0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EI0)

(-) Exons   (0, 0)

(no "Exon" information available for 5EI0)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhheee..eeeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeeee..........eeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhhhhh...hhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh..............eeeeeeeeeeeee...eeeeeeeeeeeee....eeee....eeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ei0 A  40 KQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKLKHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTEGAAGTGAQTLPETPLVVKIDKPYLLLIYSEKIPSVLFLGKIVNPI 412
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       380       390       400       410  
                                                                                                                                                                                                                                                                                                                                                                           377|                                 
                                                                                                                                                                                                                                                                                                                                                                            379                                 

Chain E from PDB  Type:PROTEIN  Length:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeeeee..........eeeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee...hhhhhhhh...hhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh...hhhhh.....eeeeeeeeeeeeee...eeeeeeeeeeeeee..eeee....eeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ei0 E  41 QRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKLKHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTEGAAGTGAQTLPMPLVVKIDKPYLLLIYSEKIPSVLFLGKIVNPIG 413
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       382       392       402       412 
                                                                                                                                                                                                                                                                                                                                                                           378|                                
                                                                                                                                                                                                                                                                                                                                                                            381                                

   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 5EI0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EI0)

(-) 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
(no "Ligands, Modified Residues, Ions" information available for 5ei0)
 
  Sites
(no "Sites" information available for 5ei0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ei0)
 
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
  5ei0
    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 4y40

(-) Related Entries Specified in the PDB File

4if8 4IF8 CONTAINS THE NATIVE STRUCTURE OF VASPIN
4y3k 4Y3K CONTAINS THE STRUCTURE OF THE VASPIN MUTANT E379S IN THE UNCLEAVED STATE
4y40 4Y40 CONTAINS THE STRUCTURE OF THE VASPIN MUTANT D305C V383C IN THE UNCLEAVED STATE