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

(-) Description

Title :  THE STRUCTURE OF TRP REPRESSOR BINDING PROTEIN FROM BACILLUS SUBTILIS
 
Authors :  Y. Kim, P. Quartey, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  25 Nov 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Trp Repressor, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, P. Quartey, A. Joachimiak
Crystal Structure Analysis Of Trp Repressor Binding Protein From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRP REPRESSOR BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2PT11Ligand/IonPLATINUM (II) ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:83 , HOH A:607 , HOH A:646 , HOH A:689 , HOH A:690BINDING SITE FOR RESIDUE PT A 601
02AC2SOFTWAREHOH A:691 , HOH D:615 , HOH D:636 , HOH D:692 , HOH D:711BINDING SITE FOR RESIDUE PT D 602
03AC3SOFTWAREMET B:83 , GLN B:135 , HOH B:701 , HOH B:702 , HOH C:613 , HOH C:653BINDING SITE FOR RESIDUE PT B 603
04AC4SOFTWAREHOH B:703 , HOH C:614 , HOH C:623 , HOH C:636BINDING SITE FOR RESIDUE PT C 604
05AC5SOFTWARELYS A:2 , HIS A:70 , HOH A:705 , HOH A:707BINDING SITE FOR RESIDUE PT A 605
06AC6SOFTWARETHR A:16 , HOH A:672 , HOH A:709 , HOH A:710BINDING SITE FOR RESIDUE PT A 606
07AC7SOFTWARELYS D:2 , HIS D:70 , HOH D:736BINDING SITE FOR RESIDUE PT D 607
08AC8SOFTWAREHIS B:70 , PO4 B:614 , HOH B:726BINDING SITE FOR RESIDUE PT B 608
09AC9SOFTWAREASN C:15 , HOH C:697 , HOH C:699 , HOH C:700 , HOH C:715BINDING SITE FOR RESIDUE PT C 609
10BC1SOFTWARELYS C:2 , HIS C:70 , HOH C:694 , HOH C:695BINDING SITE FOR RESIDUE PT C 610
11BC2SOFTWAREHOH D:737 , HOH D:738 , HOH D:739 , HOH D:740BINDING SITE FOR RESIDUE PT D 611
12BC3SOFTWAREGLY B:14 , ASN B:15 , THR B:16 , PRO B:77 , PO4 B:613 , HOH B:624 , HOH B:626 , HOH B:673 , HOH B:733BINDING SITE FOR RESIDUE PO4 B 612
13BC4SOFTWAREASN B:7 , GLY B:9 , THR B:10 , ARG B:11 , THR B:16 , ASP B:17 , PO4 B:612 , HOH B:624 , HOH B:728BINDING SITE FOR RESIDUE PO4 B 613
14BC5SOFTWARELYS B:2 , ILE B:71 , PT B:608 , HOH B:708 , HOH B:726 , HOH B:727BINDING SITE FOR RESIDUE PO4 B 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RLI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RLI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RLI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RLI)

(-) Exons   (0, 0)

(no "Exon" information available for 1RLI)

(-) Sequences/Alignments

Asymmetric/Biological 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:156
 aligned with YWQN_BACSU | P96726 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           YWQN_BACSU     2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYPIQPIEDLRHAQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKRSDA 180
               SCOP domains d1rlia_ A: Hypothetical protein Y                       wqN                                                                                                                         SCOP domains
               CATH domains 1rliA00 A:2-180  [code=3.40.50.36                       0, no name defined]                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh....eeee.-----------------------hhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh......hhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rli A   2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYL-----------------------DYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKRSDA 180
                                    11        21        31  |      -         -      | 61        71        81        91       101       111       121       131       141       151       161       171         
                                                           34                      58                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with YWQN_BACSU | P96726 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
           YWQN_BACSU     2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYPIQPIEDLRHAQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKRSD 179
               SCOP domains d1rlib_ B: Hypothetical protein Yw                      qN                                                                                                                         SCOP domains
               CATH domains 1rliB00 B:2-179  [code=3.40.50.360                      , no name defined]                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh....eeee..----------------------hhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh......hhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rli B   2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQ----------------------DYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKRSD 179
                                    11        21        31   |     -         -      | 61        71        81        91       101       111       121       131       141       151       161       171        
                                                            35                     58                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:165
 aligned with YWQN_BACSU | P96726 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:174
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
           YWQN_BACSU     2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYPIQPIEDLRHAQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLL 175
               SCOP domains d1rlic_ C: Hypothetical protein YwqN                                                                                                                                           SCOP domains
               CATH domains 1rliC00 C:2-175  [code=3.40.50.360, n         o name defined]                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhh.....eeee..ee.---------.....ee...hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh......hhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rli C   2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYP---------AQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLL 175
                                    11        21        31      |  -      | 51        61        71        81        91       101       111       121       131       141       151       161       171    
                                                               38        48                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:168
 aligned with YWQN_BACSU | P96726 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
           YWQN_BACSU     2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYPIQPIEDLRHAQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKR 177
               SCOP domains d1rlid_ D: Hypothetical protein YwqN                                                                                                                                             SCOP domains
               CATH domains 1rliD00 D:2-177  [code=3.40.50.360, no         name defined]                                                                                                                     CATH domains
           Pfam domains (1) FMN_red-1rliD01 D:2-152                                                                                                                                ------------------------- Pfam domains (1)
           Pfam domains (2) FMN_red-1rliD02 D:2-152                                                                                                                                ------------------------- Pfam domains (2)
           Pfam domains (3) FMN_red-1rliD03 D:2-152                                                                                                                                ------------------------- Pfam domains (3)
           Pfam domains (4) FMN_red-1rliD04 D:2-152                                                                                                                                ------------------------- Pfam domains (4)
         Sec.struct. author .eeeee......hhhhhhhhhhhh....eeee..eee.--------....eee...hhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhh......hhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rli D   2 KIAVINGGTRSGGNTDVLAEKAVQGFDAEHIYLQKYPI--------AQGGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPDFKQQMSVKQAYVIAVGGDNPKIKGLPLIQQFEHIFHFMGMSFKGYVLGEGNRPGDILRDHQALSAASRLLKR 177
                                    11        21        31       | -      | 51        61        71        81        91       101       111       121       131       141       151       161       171      
                                                                39       48
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (YWQN_BACSU | P96726)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PT  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rli)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1rli
    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
  YWQN_BACSU | P96726
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  YWQN_BACSU | P96726
    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 1RLI)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RLI)