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
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELLED RAFE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  N. G. Paterson, A. Riboldi-Tunnicliffe, T. J. Mitchell, N. W. Isaacs
Date :  23 Jun 06  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Periplasmic Binding Protein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. Paterson, A. Riboldi-Tunnicliffe, T. J. Mitchell, N. W. Isaacs
Crystal Structure Of Selenomethionine-Labelled Rafe From Streptococcus Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE-10
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RAFE
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 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, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE22Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2HFB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HFB)

(-) 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:383
 aligned with A0A0H2URJ7_S | A0A0H2URJ7 from UniProtKB/TrEMBL  Length:419

    Alignment length:383
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412   
         A0A0H2URJ7_S    33 TVTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPMK 415
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh....eee......hhhhhhh...........hhhhh..hhhhhhh.......ee.....eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.....eeee...........eee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh............................eee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hfb A   5 TVTIEYFNQKKEmTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPImKDDIKVmDILRINGSKQKNWEGAGYTDVIGAFARGDVLmTPNGSWAITAINEQKPNFKIGTFmIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYmTRPEVmQKYYDVDGSPTAIEGVKQAGEDSPLAGmTEYAFTDRHLVWLQQYWTSEADFHTLTmNYVLTGDKQGmVNDLNAFFNPmK 387
                                    14  |     24        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       374|      384 | 
                                       17-MSE                                                                                                                                                                                 201-MSE  |                             240-MSE                 264-MSE                               302-MSE |                         336-MSE                     364-MSE    375-MSE    386-MSE
                                                                                                                                                                                                                                     208-MSE                                                                                             308-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:381
 aligned with A0A0H2URJ7_S | A0A0H2URJ7 from UniProtKB/TrEMBL  Length:419

    Alignment length:381
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413 
         A0A0H2URJ7_S    34 VTIEYFNQKKEMTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPIMKDDIKVMDILRINGSKQKNWEGAGYTDVIGAFARGDVLMTPNGSWAITAINEQKPNFKIGTFMIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYMTRPEVMQKYYDVDGSPTAIEGVKQAGEDSPLAGMTEYAFTDRHLVWLQQYWTSEADFHTLTMNYVLTGDKQGMVNDLNAFFNPM 414
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhhh........eeee...hhhhhhhhhhhhh....eee....hhhhhhhh...........hhhhhh..hhhhhhh.......ee.......eeee.hhhhhh.......hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....eee...hhhhhhhhh.....eeee...........eee....eeee......hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........eee.hhhhh..hhhhhhhhhhhhhhh....hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hfb B   6 VTIEYFNQKKEmTKTLEEITRDFEKENPKIKVKVVNVPNAGEVLKTRVLAGDVPDVVNIYPQSIELQEWAKAGVFEDLSNKDYLKRVKNGYAEKYAVNEKVYNVPFTANAYGIYYNKDKFEELGLKVPETWDEFEQLVKDIVAKGQTPFGIAGADAWTLNGYNQLAFATATGGGKEANQYLRYSQPNAIKLSDPImKDDIKVmDILRINGSKQKNWEGAGYTDVIGAFARGDVLmTPNGSWAITAINEQKPNFKIGTFmIPGKEKGQSLTVGAGDLAWSISATTKHPKEANAFVEYmTRPEVmQKYYDVDGSPTAIEGVKQAGEDSPLAGmTEYAFTDRHLVWLQQYWTSEADFHTLTmNYVLTGDKQGmVNDLNAFFNPm 386
                                    15 |      25        35        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       375       385|
                                      17-MSE                                                                                                                                                                                 201-MSE  |                             240-MSE                 264-MSE                               302-MSE |                         336-MSE                     364-MSE    375-MSE    386-MSE
                                                                                                                                                                                                                                    208-MSE                                                                                             308-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 2HFB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2HFB)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2hfb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hfb)
 
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 | Biol. Unit 1 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
  2hfb
    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
  A0A0H2URJ7_S | A0A0H2URJ7
    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
  A0A0H2URJ7_S | A0A0H2URJ7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2URJ7_S | A0A0H2URJ7: 2heu 2hq0 2i58

(-) Related Entries Specified in the PDB File

2heu ATOMIC RESOLUTION CRYSTAL FORM OF PROTEIN