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

(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATOR FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.15 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jun 05  (Deposition) - 19 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Np_813211. 1, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Transcription Regulator From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 15 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTION REGULATOR, CRP FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_813211.1
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:64 , ASN A:65 , ALA A:96 , TRP A:145 , HOH A:237BINDING SITE FOR RESIDUE GOL A 221
2AC2SOFTWAREHIS A:36 , ILE A:42 , ILE A:43 , GLN A:51BINDING SITE FOR RESIDUE GOL A 222
3AC3SOFTWAREHIS A:-2 , MSE A:1 , GLU A:2 , PHE A:5 , HOH A:379BINDING SITE FOR RESIDUE GOL A 223
4AC4SOFTWAREHIS A:-1 , LYS A:-7 , HIS A:0 , THR A:3 , HOH A:388BINDING SITE FOR RESIDUE GOL A 224
5AC5SOFTWAREVAL A:175 , MSE A:177 , HIS A:207 , LYS A:209 , GLU A:210 , HOH A:311BINDING SITE FOR RESIDUE GOL A 225
6AC6SOFTWAREPHE A:114 , SER A:117 , ASP A:118 , LEU A:206 , HIS A:207 , HOH A:326 , HOH A:372 , HOH A:381BINDING SITE FOR RESIDUE GOL A 226
7AC7SOFTWAREARG A:136 , ASN A:139 , LEU A:140 , TYR A:141 , ARG A:143 , SER A:162 , CYS A:164 , GLU A:165 , HOH A:354BINDING SITE FOR RESIDUE GOL A 227

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:53 -A:109

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:79 -Pro A:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZYB)

(-) 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:230
 aligned with Q89ZS6_BACTN | Q89ZS6 from UniProtKB/TrEMBL  Length:220

    Alignment length:230
                                      1                                                                                                                                                                                                                           
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
         Q89ZS6_BACTN     - ----------METMFDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLLKGEISIVTNAKENIYTVIEQIEAPYLIEPQSLFGMNTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPDAQKLL 220
               SCOP domains ----------d1zyba2 A:1-147 Probable transcription regulator BT4300, N-terminal domain                                                                         d1zyba1 A:148-220                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------cNMP_binding-1zybA02 A:33-122                                                             -------------------------------HTH_Crp_2-1zybA01 A:154-220                                         Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeee....eee.......eeeeeee.eeeeeee.hhhh.eeeeeee..eeehhhhhh........eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh........eeee.hhhhhhhhhh.hhhhhhhhhhhhhhh...eee..eeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zyb A  -9 SDKIHHHHHHmETmFDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLLKGEISIVTNAKENIYTVIEQIEAPYLIEPQSLFGmNTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIFRLNYmNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSHCEKPQGEKTFKVKmDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPDAQKLL 220
                                     0|  |    10        20        30        40        50        60        70        80        90|      100       110       120       130       140       150       160       170      |180       190       200       210       220
                                      1-MSE                                                                                    91-MSE                                130-MSE                                        177-MSE                                       
                                         4-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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZYB)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q89ZS6_BACTN | Q89ZS6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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 ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:79 - Pro A:80   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1zyb
    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
  Q89ZS6_BACTN | Q89ZS6
    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
  Q89ZS6_BACTN | Q89ZS6
    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 1ZYB)

(-) Related Entries Specified in the PDB File

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