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

(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION FROM PORPHYROMONAS GINGIVALIS W83
 
Authors :  T. A. Binkowski, E. Duggan, M. Shui, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  31 Jul 07  (Deposition) - 25 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Mcsg, Structural Genomics, Porphyromonas Gingivalis W83, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Binkowski, E. Duggan, M. Shui, A. Joachimiak
Protein Of Unknown Function From Porphyromonas Gingivalis W83.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Atcc: BAA-308
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PG_0320
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2NA1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2QSV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QSV)

(-) 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:220
 aligned with Q7MX90_PORGI | Q7MX90 from UniProtKB/TrEMBL  Length:362

    Alignment length:220
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
         Q7MX90_PORGI   143 GPLQVSNARLLFPISMPEDEGVVRLVVNNTDESDLQVAVVSLPSFVSLDDRAFRLQAREPRELNLSLAVPRNMPPGMKDEPLVLEVTSPETGKKAVDSVMVSLPLVDNFPALTAAQTGVMELSTYLDMGQLDGETTKAAIEIRNVGAGPLRLHSVTTRNPALTAVPDRTEIKPGGSTLLRIAVDPQVMKAEGWQSIAADISIICNDPQAPLRRIKVKAEL 362
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qsvA01 A:1-112 PapD-like                                                                                       2qsvA02 A:113-220 PapD-like                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee..........eeeeeeee.....eeeeeee....ee....eeee.....eeeeeee........eeeeeeeeeeee......eeeeeeeeeeee..hhhhhhhhhh..ee...eeeeee.....eeeeeeeee.....eeeeeeee....eeeee...ee....eeeeeeeehhhhhhhh...eeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qsv A   1 GPLQVSNARLLFPISmPEDEGVVRLVVNNTDESDLQVAVVSLPSFVSLDDRAFRLQAREPRELNLSLAVPRNmPPGmKDEPLVLEVTSPETGKKAVDSVmVSLPLVDNFPALTAAQTGVmELSTYLDmGQLDGETTKAAIEIRNVGAGPLRLHSVTTRNPALTAVPDRTEIKPGGSTLLRIAVDPQVmKAEGWQSIAADISIICNDPQAPLRRIKVKAEL 220
                                    10     |  20        30        40        50        60        70  |   | 80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
                                          16-MSE                                                   73-MSE                    100-MSE             120-MSE 128-MSE                                                     188-MSE                            
                                                                                                       77-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 2QSV)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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 ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2qsv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qsv)
 

(-) 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
  2qsv
    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
  Q7MX90_PORGI | Q7MX90
    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
  Q7MX90_PORGI | Q7MX90
    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 2QSV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QSV)