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 :  PUTATIVE SOLUTE-BINDING PROTEIN FROM YERSINIA PESTIS.
 
Authors :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  10 May 11  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Idp00509, Center For Structural Genomics Of Infectious Diseases, Csgid, Solute-Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
Putative Solute-Binding Protein From Yersinia Pestis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SOLUTE-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OPPA4, Y1231, YPO2660, YP_2461
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: PUTATIVE SUBSTRATE-BINDING PERIPLASMIC PROTEIN OF ABC TRANSPORTER

 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, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:135 , HOH A:533 , ARG B:180 , TYR B:197BINDING SITE FOR RESIDUE ACT B 701
2AC2SOFTWARETHR B:455 , TRP B:456 , HOH B:606BINDING SITE FOR RESIDUE ACT B 702

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:497 -A:497
2B:497 -B:497

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RY3)

(-) Exons   (0, 0)

(no "Exon" information available for 3RY3)

(-) 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:489
 aligned with Q7CJS8_YERPE | Q7CJS8 from UniProtKB/TrEMBL  Length:525

    Alignment length:492
                                    39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519  
         Q7CJS8_YERPE    30 TLQLAIGDEPTEGFDPMLGWSHGSYLLLHSPLLKQNEDFSWDSLLLSQYQPSDDGKTWLLTLKPDLKFSDGSPLTAKDVAFTYNNAAASGGKVDMGNFLSAEVIDPLNVRIHLKAPQSTFVNVLGSLGIVSADKYNAKTYAQKPIGAGPYRLVSFQPGQQMIVEANPYYAGNKNDFDKLIFVFLDEDSAFAAAQSGQLGVVRIPPSMAVGSVNNMKLWVRPSVENRGIVFPTTPAGKKDAHGYPIGNDVTADVAIRRAINYAINRQLLADQIMEGHAIPAYTGVQGLPWNNPDSAIKDGDIDKAKQILEQAGWQLNSQGTREKNGLPAKITLWYTSGDTTRRDLAQALRSMLKPIGIDVDLKSGSWETVERNMHANPTLFGWGSLDPMELYHHYSSNAAGVEYYNPGYYKNPMVDKHLQQALDAPTWQQAVPFWQQVDWDGTTGAGIRGDAAWAWLLNIQHTYLANNCVDLGKGTPEIHGSWSLLNSIDSWK 521
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....---..hhhhh...hhhhhh....eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhh..........eeeeeeee..eeeeee.....hhhhhhh........................eeeeeee...eeeeee............eeeee..hhhhhhhhhhh....eeee...........eeeeeeeeeeeeeee......................hhhhhhhhhhhhhhhhhhhhhh...eee....................hhhhhhhhhhhh..ee.....eee..ee.eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhh....eee......hhhhhhhhhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.............eeeeeeeeeeeeee...............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ry3 A  30 TLQLAIGDE---GFDPmLGWSHGSYLLLHSPLLKQNEDFSWDSLLLSQYQPSDDGKTWLLTLKPDLKFSDGSPLTAKDVAFTYNNAAASGGKVDmGNFLSAEVIDPLNVRIHLKAPQSTFVNVLGSLGIVSADKYNAKTYAQKPIGAGPYRLVSFQPGQQmIVEANPYYAGNKNDFDKLIFVFLDEDSAFAAAQSGQLGVVRIPPSmAVGSVNNmKLWVRPSVENRGIVFPTTPAGKKDAHGYPIGNDVTADVAIRRAINYAINRQLLADQImEGHAIPAYTGVQGLPWNNPDSAIKDGDIDKAKQILEQAGWQLNSQGTREKNGLPAKITLWYTSGDTTRRDLAQALRSmLKPIGIDVDLKSGSWETVERNmHANPTLFGWGSLDPmELYHHYSSNAAGVEYYNPGYYKNPmVDKHLQQALDAPTWQQAVPFWQQVDWDGTTGAGIRGDAAWAWLLNIQHTYLANNCVDLGKGTPEIHGSWSLLNSIDSWK 521
                                    |-  |   | 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       379|      389       399  |    409       419       429       439  |    449       459       469       479       489       499       509       519  
                                   38  42   |                                                                           124-MSE                                                           190-MSE                                       236-MSE 244-MSE                                                   302-MSE                                                                       380-MSE               402-MSE        417-MSE                  442-MSE                                                                           
                                           46-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:490
 aligned with Q7CJS8_YERPE | Q7CJS8 from UniProtKB/TrEMBL  Length:525

    Alignment length:492
                                    39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519  
         Q7CJS8_YERPE    30 TLQLAIGDEPTEGFDPMLGWSHGSYLLLHSPLLKQNEDFSWDSLLLSQYQPSDDGKTWLLTLKPDLKFSDGSPLTAKDVAFTYNNAAASGGKVDMGNFLSAEVIDPLNVRIHLKAPQSTFVNVLGSLGIVSADKYNAKTYAQKPIGAGPYRLVSFQPGQQMIVEANPYYAGNKNDFDKLIFVFLDEDSAFAAAQSGQLGVVRIPPSMAVGSVNNMKLWVRPSVENRGIVFPTTPAGKKDAHGYPIGNDVTADVAIRRAINYAINRQLLADQIMEGHAIPAYTGVQGLPWNNPDSAIKDGDIDKAKQILEQAGWQLNSQGTREKNGLPAKITLWYTSGDTTRRDLAQALRSMLKPIGIDVDLKSGSWETVERNMHANPTLFGWGSLDPMELYHHYSSNAAGVEYYNPGYYKNPMVDKHLQQALDAPTWQQAVPFWQQVDWDGTTGAGIRGDAAWAWLLNIQHTYLANNCVDLGKGTPEIHGSWSLLNSIDSWK 521
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------SBP_bac_5-3ry3B01 B:69-431                                                                                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------SBP_bac_5-3ry3B02 B:69-431                                                                                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeee.........hhhhh....hhhhhh....ee.....ee...eeeeee.....eeeeee............hhhhhhhhhhhhh.--.......eeeeeeee..eeeeee.....hhhhhhh........................eeeeeee...eeeeee............eeeee..hhhhhhhhhhh....eeee...........eeeeee....eeeee.......ee.....ee......hhhhhhhhhhhhhhhhhhhhhh...eee....................hhhhhhhhhhhh..ee.....eee..ee.eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhh....eee......hhhhhhhhhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhh................eeeeeee.eeeeee...............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ry3 B  30 TLQLAIGDEPTEGFDPmLGWSHGSYLLLHSPLLKQNEDFSWDSLLLSQYQPSDDGKTWLLTLKPDLKFSDGSPLTAKDVAFTYNNAAA--GKVDmGNFLSAEVIDPLNVRIHLKAPQSTFVNVLGSLGIVSADKYNAKTYAQKPIGAGPYRLVSFQPGQQmIVEANPYYAGNKNDFDKLIFVFLDEDSAFAAAQSGQLGVVRIPPSmAVGSVNNmKLWVRPSVENRGIVFPTTPAGKKDAHGYPIGNDVTADVAIRRAINYAINRQLLADQImEGHAIPAYTGVQGLPWNNPDSAIKDGDIDKAKQILEQAGWQLNSQGTREKNGLPAKITLWYTSGDTTRRDLAQALRSmLKPIGIDVDLKSGSWETVERNmHANPTLFGWGSLDPmELYHHYSSNAAGVEYYNPGYYKNPmVDKHLQQALDAPTWQQAVPFWQQVDWDGTTGAGIRGDAAWAWLLNIQHTYLANNCVDLGKGTPEIHGSWSLLNSIDSWK 521
                                    39      | 49        59        69        79        89        99       109       | -|   |  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       379|      389       399  |    409       419       429       439  |    449       459       469       479       489       499       509       519  
                                           46-MSE                                                                117  |   |                                                               190-MSE                                       236-MSE 244-MSE                                                   302-MSE                                                                       380-MSE               402-MSE        417-MSE                  442-MSE                                                                           
                                                                                                                    120   |                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                        124-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 3RY3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RY3)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7CJS8_YERPE | Q7CJS8)
molecular function
    GO:0015197    peptide transporter activity    Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
biological process
    GO:0015833    peptide transport    The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ry3)
 
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
  3ry3
    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
  Q7CJS8_YERPE | Q7CJS8
    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
  Q7CJS8_YERPE | Q7CJS8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7CJS8_YERPE | Q7CJS8: 4ofl 4ofo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RY3)