Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  CRYSTAL STRUCTURE OF SERPIN FROM TICK IXODES RICINUS
 
Authors :  P. Rezacova, Z. Kovarova, J. Chmelar, M. Mares
Date :  07 Jun 10  (Deposition) - 27 Oct 10  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serpin, Vaccination Target, Tick, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Chmelar, C. J. Oliveira, P. Rezacova, I. M. Francischetti, Z. Kovarova, G. Pejler, P. Kopacek, J. M. Ribeiro, M. Mares, J. Kopecky M. Kotsyfakis
A Tick Salivary Protein Targets Cathepsin G And Chymase And Inhibits Host Inflammation And Platelet Aggregation.
Blood V. 117 736 2011
PubMed-ID: 20940421  |  Reference-DOI: 10.1182/BLOOD-2010-06-293241

(-) Compounds

Molecule 1 - SERPIN-2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-LIKE
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SHEEP TICK
    Organism Scientific: IXODES RICINUS
    Organism Taxid: 34613

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:111 , SER A:112 , LEU A:122 , HOH A:668 , PHE B:213 , GLU B:220 , LYS B:239 , HOH B:455 , HOH B:570 , HOH B:816BINDING SITE FOR RESIDUE 1PE B 5002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NDA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NDA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NDA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NDA)

(-) Exons   (0, 0)

(no "Exon" information available for 3NDA)

(-) 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:374
 aligned with Q06B74_IXORI | Q06B74 from UniProtKB/TrEMBL  Length:397

    Alignment length:377
                                    30        40        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       380       390       
         Q06B74_IXORI    21 AQEEAKLTKANNRFGLRLLRALPSGPEKNVFFSPYSVSAAMGMAFAGARGQTQQELSQGLGFSDVDLTDAGVLDAYTHHTERLKSTPSNSTLDVANAAAIQRTLALLNSYESALQSSFGAELHKVDFAGEPQAAVDFVNNWVKRKTHDKIEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARIKYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNLTVDRFQNYLSDLRERKITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDERLRVSAVEHKAVVEVNEEGTVAAATTGVVIVPYSLGPEPVVFRVDHPFLFFIRNTRTDDIFFVGQVNKL 397
               SCOP domains d3ndaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.................eeeeeeeeeeee.....hhhhheeeeeeehhheeeeeeeeeeeeeeeeeee....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh....hhhhhh..eeeeeeeeeeeeee...eeeeeeeeeeeeee.---....eee....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nda A   1 MQEEAKLTKANNRFGLRLLRALPSGPEKNVFFSPYSVSTAMGMAFAGARGQTQQELSQGLGFSDVDLTDAGVLDAYTHHTERLKSTPSNSTLDVANAAAIQRTLALLNSYESALQSSFGAELHKVDFAGEPQAAVDFVNNWVKRKTHDKIEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARIKYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNLTIDRFQNYLSDLRERKITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDGSLRVSAVEHKAVVEVNEEGTVAAATTGVVIVPY---PEPVVFRVDHPFLFFIRNTRTDDIFFVGQVNKL 377
                                    10        20        30        40        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       
                                                                                                                                                                                                                                                                                                                                                                              341 345                                


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with Q06B74_IXORI | Q06B74 from UniProtKB/TrEMBL  Length:397

    Alignment length:377
                                    30        40        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       380       390       
         Q06B74_IXORI    21 AQEEAKLTKANNRFGLRLLRALPSGPEKNVFFSPYSVSAAMGMAFAGARGQTQQELSQGLGFSDVDLTDAGVLDAYTHHTERLKSTPSNSTLDVANAAAIQRTLALLNSYESALQSSFGAELHKVDFAGEPQAAVDFVNNWVKRKTHDKIEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARIKYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNLTVDRFQNYLSDLRERKITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDERLRVSAVEHKAVVEVNEEGTVAAATTGVVIVPYSLGPEPVVFRVDHPFLFFIRNTRTDDIFFVGQVNKL 397
               SCOP domains d3ndab_ B: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Serpin-3ndaB01 B:9-377                                                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) --------Serpin-3ndaB02 B:9-377                                                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.................eeeeeeeeeeee.....hhhhheeeeeeehhheeeeeeeeeeeeeeeeeee....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh....hhhhhh..eeeeeeeeeeeeee...eeeeeeeeeeeeee.-----.eeee....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nda B   1 MQEEAKLTKANNRFGLRLLRALPSGPEKNVFFSPYSVSTAMGMAFAGARGQTQQELSQGLGFSDVDLTDAGVLDAYTHHTERLKSTPSNSTLDVANAAAIQRTLALLNSYESALQSSFGAELHKVDFAGEPQAAVDFVNNWVKRKTHDKIEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARIKYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNLTIDRFQNYLSDLRERKITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDGSLRVSAVEHKAVVEVNEEGTVAAATTGVVIVPY-----PVVFRVDHPFLFFIRNTRTDDIFFVGQVNKL 377
                                    10        20        30        40        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       
                                                                                                                                                                                                                                                                                                                                                                              341   347
   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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NDA)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Serpin] (63)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q06B74_IXORI | Q06B74)
cellular component
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nda)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3nda
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q06B74_IXORI | Q06B74
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q06B74_IXORI | Q06B74
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3NDA)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NDA)