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 :  CRYSTAL STRUCTURE OF THE VACCINE ANTIGEN TRANSFERRIN BINDING PROTEIN B (TBPB) DOUBLE MUTANT TYR-167-ALA AND TRP-176-ALA FROM HAEMOPHILUS PARASUIS HP5
 
Authors :  C. Calmettes, R. H. Yu, A. B. Schryvers, T. F. Moraes
Date :  19 Dec 13  (Deposition) - 14 Jan 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structure-Based Vaccine Design, Transferrin Receptor, Iron Acquisition, Host Pathogen Interaction, Surface Lipoprotein, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Frandoloso, S. Martinez-Martinez, C. Calmettes, J. Fegan, E. Costa, D. Curran, R. H. Yu, C. B. Gutierrez-Martin, E. F. Rodriguez-Ferri, T. F. Moraes, A. B. Schryvers
Nonbinding Site-Directed Mutants Of Transferrin Binding Protein B Exhibit Enhanced Immunogenicity And Protective Capabilities.
Infect. Immun. V. 83 1030 2015
PubMed-ID: 25547790  |  Reference-DOI: 10.1128/IAI.02572-14

(-) Compounds

Molecule 1 - TBPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS PARASUIS
    Organism Taxid: 738

 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  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:77 , ILE A:79BINDING SITE FOR RESIDUE GOL A 601
02AC2SOFTWAREGLY A:228BINDING SITE FOR RESIDUE GOL A 602
03AC3SOFTWAREARG A:298 , ASP A:301 , SER A:303 , SER A:499 , GLN A:513 , HOH A:724BINDING SITE FOR RESIDUE GOL A 603
04AC4SOFTWAREVAL A:116 , TYR A:173BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWARELEU A:42 , GLN A:256BINDING SITE FOR RESIDUE GOL A 605
06AC6SOFTWARELYS A:192 , ASP A:214BINDING SITE FOR RESIDUE SO4 A 606
07AC7SOFTWARETHR A:72 , ASP A:73 , SO4 A:611BINDING SITE FOR RESIDUE SO4 A 607
08AC8SOFTWARESER A:322 , ALA A:334 , SER A:358 , LEU A:360 , GLU A:361 , LYS A:364BINDING SITE FOR RESIDUE GOL A 608
09AC9SOFTWARELYS A:211BINDING SITE FOR RESIDUE GOL A 609
10BC1SOFTWAREASN A:290 , ALA A:291BINDING SITE FOR RESIDUE NA A 610
11BC2SOFTWARELYS A:78 , PRO A:80 , ASN A:81 , SO4 A:607 , HOH A:719BINDING SITE FOR RESIDUE SO4 A 611
12BC3SOFTWARETYR A:112 , SER A:185 , GLY A:186 , ALA A:188 , HIS A:193BINDING SITE FOR RESIDUE SO4 A 612
13BC4SOFTWAREGLU B:95 , TYR B:117BINDING SITE FOR RESIDUE SO4 B 601
14BC5SOFTWARETYR B:93BINDING SITE FOR RESIDUE SO4 B 602
15BC6SOFTWARETHR B:100 , ALA B:101 , ALA B:102 , GLU B:103BINDING SITE FOR RESIDUE SO4 B 603
16BC7SOFTWAREARG B:298 , SER B:303 , ILE B:312 , GLU B:314BINDING SITE FOR RESIDUE SO4 B 604
17BC8SOFTWAREASN B:77 , ILE B:79 , TYR B:82BINDING SITE FOR RESIDUE SO4 B 605
18BC9SOFTWARELYS B:192 , HIS B:193 , ASP B:214BINDING SITE FOR RESIDUE SO4 B 606
19CC1SOFTWAREVAL B:116 , TYR B:117 , TYR B:173BINDING SITE FOR RESIDUE GOL B 607
20CC2SOFTWAREARG B:62 , THR B:104 , LYS B:288BINDING SITE FOR RESIDUE GOL B 608

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:356 -A:357
2B:356 -B:357

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:58 -Gly A:59
2Cys A:356 -Cys A:357
3Asn A:520 -Gly A:521
4Ile B:326 -Asp B:327
5Cys B:356 -Cys B:357
6Asn B:520 -Gly B:521

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O4X)

(-) Exons   (0, 0)

(no "Exon" information available for 4O4X)

(-) 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:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...................eeeee.........ee.....eee.........hhhhhhhhhh.....eeee........eeeeeeee.........eeeeeee.....eeee...eeeeeeeeeee.ee..........................hhhhh......eeeeeeee....eeeeeeee..eeeeeeeeeee..eeeeeeee......hhhhh......eeeeeeeee.....eeeeeee.....eeeeeeeee.....eeee.eeeeeee.....eee........eeee..eeee......eeeeeeee..eeeeeeee......eeeeeeeee....eeeeeeeeeee...........eeeeeeeeeeeeee..eeeee..........eeeeeee....eeeeee.........eeeeeeee..eeeeeee..............eeeeeeee.....eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o4x A  25 EYKDVETDKKVKEQLGELMEPALGYVVKVPVSQSGVKRTEISNPEAITDEDLNKIPNYEIIKGVAYPNYGELVDKTAAETMKYVRSGYVIDVYHSGTRDKGYVFYKGITPSKELPQGPALTYQGEWDFTSDANLNNEEGRPTALNDDYYTTAIGKRAGLVSGDAKPSKHKYTSQFKVDFATKKMTGKLSDKEKTIYTVNADIRGNRFTGSATASDKDKGKGASYNFFSVDSQSLEGGFYGPKAEEMAGKFVADDKSLFAVFSAKHNASNVNTVRIIDASKIDLTNFSISELTNFGDASVLIIDGKKMELAGSEFTNKHTIDINGKKMVAVACCSNLEYMKFGQLWQQTEKQVKDNSLFLQGERTATDKMPKDGNYKYIGTWDAQVSKENNYWVATADDDRKAGYRTEFDVDFGSKNLSGKLFDKNGVNPVFTVNAKIDGNGFTGEAKTSDAGFVLNVKFSDVAVSGGFYGPTAAELGGQFRYQSDNGSVGVGAVFGAKQQVKK 537
                                    34        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       376       386       396       406       416       426       436       446       456       466       476    || 494       504       514       524       534   
                                                                                                                                                                                                                                                                                                                                                                                      373|                                                                                                      481|                                               
                                                                                                                                                                                                                                                                                                                                                                                       376                                                                                                       490                                               


Chain B from PDB  Type:PROTEIN  Length:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...........hhhhh...eeeee.........ee.....eee.........hhhhhhhhhhhhh..eeee........eeeeeeee.........eeeeeee.....eee....eeeeeeeeeee.ee..........................hhhhh......eeeeeeee....eeeeeeee..eeeeeeeeeee..eeeeeeee......hhhhh......eeeeeeeee.....eeeeeee.....eeeeeeeee......eee.eeeeeee.....eee........eee....eee......eeeeeee....eeeeeee......eeeeeeee....eeeeeeeeee..hhhhh....eeeeeeeeeeeeee..eeeee..........eeeeeee....eeeeee.........eeeeeeee..eeeeeee...............eeeeeeee.....eeeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o4x B  25 EYKDVETDKKVKEQLGELMEPALGYVVKVPVSQSGVKRTEISNPEAITDEDLNKIPNYEIIKGVAYPNYGELVDKTAAETMKYVRSGYVIDVYHSGTRDKGYVFYKGITPSKELPQGPALTYQGEWDFTSDANLNNEEGRPTALNDDYYTTAIGKRAGLVSGDAKPSKHKYTSQFKVDFATKKMTGKLSDKEKTIYTVNADIRGNRFTGSATASDKDKGKGASYNFFSVDSQSLEGGFYGPKAEEMAGKFVADDKSLFAVFSAKHNASNVNTVRIIDASKIDLTNFSISELTNFGDASVLIIDGKKMELAGSEFTNKHTIDINGKKMVAVACCSNLEYMKFGQLWQQTQVKDNSLFLQGERTATDKMPKDGNYKYIGTWDAQVSKENNYWVATADDDRKAGYRTEFDVDFGSKNLSGKLFDKNGVNPVFTVNAKIDGNGFTGEAKTSDAGFVLDNVKFSDVAVSGGFYGPTAAELGGQFRYQSDNGSVGVGAVFGAKQQVKK 537
                                    34        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       378       388       398       408       418       428       438       448       458       468       478  ||   495       505       515       525       535  
                                                                                                                                                                                                                                                                                                                                                                                     372|                                                                                                     481|                                                
                                                                                                                                                                                                                                                                                                                                                                                      377                                                                                                      489
   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 4O4X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O4X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O4X)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4O4X)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:520 - Gly A:521   [ RasMol ]  
    Asn B:520 - Gly B:521   [ RasMol ]  
    Cys A:356 - Cys A:357   [ RasMol ]  
    Cys B:356 - Cys B:357   [ RasMol ]  
    Ile B:326 - Asp B:327   [ RasMol ]  
    Ser A:58 - Gly A:59   [ 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
[ 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
  4o4x
    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
  A0A0H2UKY6_H | A0A0H2UKY6
    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
  A0A0H2UKY6_H | A0A0H2UKY6
    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 4O4X)

(-) Related Entries Specified in the PDB File

4o3w 4o3x 4o3y 4o3z 4o49 4o4u