Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - 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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A CUPIN DOMAIN (BP2299) FROM BORDETELLA PERTUSSIS TOHAMA I AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Jan 06  (Deposition) - 16 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Double-Stranded Beta-Helix Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of (Np_880937. 1) From Bordetella Pertussi At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN BP2299
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_880937.1
    Organism Scientific: BORDETELLA PERTUSSIS TOHAMA I
    Organism Taxid: 257313
    Strain: TOHAMA I

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ACT4Ligand/IonACETATE ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2ACT2Ligand/IonACETATE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ACT2Ligand/IonACETATE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ACT2Ligand/IonACETATE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , HIS A:35 , HIS A:76 , HOH A:164 , HOH A:165 , HOH A:166BINDING SITE FOR RESIDUE ZN A 100
2AC2SOFTWAREHIS B:33 , HIS B:35 , HIS B:76 , HOH B:169 , HOH B:170 , HOH B:171BINDING SITE FOR RESIDUE ZN B 100
3AC3SOFTWAREHIS C:33 , HIS C:35 , HIS C:76 , HOH C:174 , HOH C:175 , HOH C:176BINDING SITE FOR RESIDUE ZN C 100
4AC4SOFTWAREHIS D:33 , HIS D:35 , HIS D:76 , ACT D:101BINDING SITE FOR RESIDUE ZN D 100
5AC5SOFTWARETYR A:39 , TYR A:68 , HIS A:76 , HOH A:119 , HOH A:166BINDING SITE FOR RESIDUE ACT A 101
6AC6SOFTWARETYR B:39 , TYR B:68 , ARG B:70 , HIS B:76 , PHE B:88 , HOH B:170BINDING SITE FOR RESIDUE ACT B 101
7AC7SOFTWARETYR C:39 , TYR C:68 , HIS C:76 , PHE C:88 , HOH C:176BINDING SITE FOR RESIDUE ACT C 101
8AC8SOFTWARETYR D:39 , TYR D:68 , ARG D:70 , HIS D:76 , PHE D:88 , ZN D:100BINDING SITE FOR RESIDUE ACT D 101
9AC9SOFTWARETYR B:68 , THR B:69 , ARG B:70 , HOH B:162 , ASP C:13 , ASN C:14 , HOH C:103 , HOH C:133BINDING SITE FOR RESIDUE 1PE C 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FQP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FQP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FQP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FQP)

(-) Exons   (0, 0)

(no "Exon" information available for 2FQP)

(-) 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:96
 aligned with Q7VWF8_BORPE | Q7VWF8 from UniProtKB/TrEMBL  Length:96

    Alignment length:96
                             1                                                                                              
                             |       9        19        29        39        49        59        69        79        89      
          Q7VWF8_BORPE    - -MKRPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSMDYVVVPMTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKA 95
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee...eeeeeeee........ee....eeeee...eeeeeee..eeeeeee.....eee....eeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  2fqp A  0 GmKRPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSmDYVVVPmTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKA 95
                             |       9        19        29       |39    |   49        59        69        79        89      
                             |                                  37-MSE 44-MSE                                               
                             1-MSE                                                                                          


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with Q7VWF8_BORPE | Q7VWF8 from UniProtKB/TrEMBL  Length:96

    Alignment length:92
                                    12        22        32        42        52        62        72        82        92  
          Q7VWF8_BORPE    3 RPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSMDYVVVPMTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIK 94
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeeee........ee....eeeee...eeeeeee..eeeeeee.....eee....eeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2fqp B  3 RPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSmDYVVVPmTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIK 94
                                    12        22        32    |   42 |      52        62        72        82        92  
                                                             37-MSE 44-MSE                                              


Chain C from PDB  Type:PROTEIN  Length:96
 aligned with Q7VWF8_BORPE | Q7VWF8 from UniProtKB/TrEMBL  Length:96

    Alignment length:96
                             1                                                                                              
                             |       9        19        29        39        49        59        69        79        89      
          Q7VWF8_BORPE    - -MKRPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSMDYVVVPMTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKA 95
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee...eeeeeeee........ee....eeeee...eeeeeee..eeeeeee.....eee....eeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  2fqp C  0 GmKRPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSmDYVVVPmTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKA 95
                             |       9        19        29       |39    |   49        59        69        79        89      
                             1-MSE                              37-MSE 44-MSE                                               


Chain D from PDB  Type:PROTEIN  Length:94
 aligned with Q7VWF8_BORPE | Q7VWF8 from UniProtKB/TrEMBL  Length:96

    Alignment length:94
                                    12        22        32        42        52        62        72        82        92    
          Q7VWF8_BORPE    3 RPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSMDYVVVPMTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKAA 96
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeeee........ee....eeeee...eeeeeee..eeeeeee.....eee....eeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  2fqp D  3 RPGAIPTVQIDNERVKVTEWRFPPGGETGWHRHSmDYVVVPmTTGPLLLETPEGSVTSQLTRGVSYTRPEGVEHNVINPSDTEFVFVEIEIKAA 96
                                    12        22        32    |   42 |      52        62        72        82        92    
                                                             37-MSE 44-MSE
   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 2FQP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FQP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FQP)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7VWF8_BORPE | Q7VWF8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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 ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fqp)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  2fqp
    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
  Q7VWF8_BORPE | Q7VWF8
    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
  Q7VWF8_BORPE | Q7VWF8
    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 2FQP)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FQP)