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
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF YIBA_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET31.
 
Authors :  A. Kuzin, A. Semesi, T. Skarina, A. Savchenko, C. Arrowsmith, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  07 Apr 03  (Deposition) - 12 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, A. Semesi, T. Skarina, A. Savchenko, C. Arrowsmith, L. Tong
X-Ray Structure Of Yiba_ecoli Northeast Structural Genomics Consortium Target Et31.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YIBA
    Chains: A
    Engineered: YES
    Gene: YIBA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1OYZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OYZ)

(-) 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:273
 aligned with YIBA_ECO57 | P0ADK7 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:276
                                    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      
           YIBA_ECO57     5 YQKRKASKEYGLYNQCKKLNDDELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQIKICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVINDKATIPLLINLLKDPNGDVRNWAAFAININKYDNSDIRDCFVEMLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDTMLYKFDDNEIITSAIDKLKRS 280
               SCOP domains d1oyza_ A: Hypothetical protein YibA                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1oyzA00 A:5-280 Leucine-rich Repeat Variant                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------HEAT_2-1oyzA01 A:130-191                                      ----------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------HEAT_2-1oyzA02 A:130-191                                      ----------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhh.---.hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oyz A   5 YQKRKASKEYGLYNQCKKLNDDELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQIKICKKCEDNVFNILNNmALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVI---ATIPLLINLLKDPNGDVRNWAAFAININKYDNSDIRDCFVEmLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDTmLYKFDDNEIITSAIDKLKRS 280
                                    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      
                                                                                                                        98-MSE                                                  155 159                                      200-MSE                                                     260-MSE                


Chain A from PDB  Type:PROTEIN  Length:273
 aligned with YIBA_ECOLI | P0ADK6 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:276
                                    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      
           YIBA_ECOLI     5 YQKRKASKEYGLYNQCKKLNDDELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQIKICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVINDKATIPLLINLLKDPNGDVRNWAAFAININKYDNSDIRDCFVEMLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDTMLYKFDDNEIITSAIDKLKRS 280
               SCOP domains d1oyza_ A: Hypothetical protein YibA                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1oyzA00 A:5-280 Leucine-rich Repeat Variant                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------HEAT_2-1oyzA01 A:130-191                                      ----------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------HEAT_2-1oyzA02 A:130-191                                      ----------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhh.---.hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oyz A   5 YQKRKASKEYGLYNQCKKLNDDELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQIKICKKCEDNVFNILNNmALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVI---ATIPLLINLLKDPNGDVRNWAAFAININKYDNSDIRDCFVEmLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDTmLYKFDDNEIITSAIDKLKRS 280
                                    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      
                                                                                                                        98-MSE                                                  155 159                                      200-MSE                                                     260-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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YIBA_ECO57 | P0ADK7)

Chain A   (YIBA_ECOLI | P0ADK6)
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1oyz)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1oyz)
 

(-) 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 ](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
  1oyz
    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
  YIBA_ECO57 | P0ADK7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  YIBA_ECOLI | P0ADK6
    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
  YIBA_ECO57 | P0ADK7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  YIBA_ECOLI | P0ADK6
    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 1OYZ)

(-) Related Entries Specified in the PDB File

et31