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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
 
Authors :  T. A. Binkowski, R. Wu, S. F. Moy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  09 Aug 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  B  (3x)
Keywords :  Structural Genomics, Mcsg, Hypothetical Protein, Protein Structure Initiative, Psi, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Binkowski, R. Wu, S. F. Moy, A. Joachimiak
Hypothetical Protein From Vibrio Cholerae O1 Biovar Eltor Str. N16961
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN VC0714
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: VC0714
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
    Organism Taxid: 243277
    Strain: O1 BIOVAR ELTOR STR. N16961

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): A 
Biological Unit 3 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:82 , SER A:86 , ARG B:62 , GLU B:63 , THR B:66BINDING SITE FOR RESIDUE PO4 B 201
2AC2SOFTWAREARG A:62 , GLU A:63 , THR A:66 , HOH A:236 , HOH A:245 , HOH A:280 , ASP B:85 , SER B:86BINDING SITE FOR RESIDUE PO4 A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U9D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U9D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U9D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U9D)

(-) Exons   (0, 0)

(no "Exon" information available for 1U9D)

(-) 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:122
 aligned with Q9KU16_VIBCH | Q9KU16 from UniProtKB/TrEMBL  Length:107

    Alignment length:122
                                           1                                                                                                          
                                     -     |   5        15        25        35        45        55        65        75        85        95       105  
         Q9KU16_VIBCH     - ---------------MPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGVYPMVEVLWFGREQQTQDQIAQVITDQIRQLLGADSHLAVVFIPLQRTAYYLDGQHF 107
               SCOP domains d1u9da_ A: Hypothetical protein VC0714                                                                                     SCOP domains
               CATH domains 1u9dA00 A:-14-107 Macrophage Migration Inhibitory Factor                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhheeee.............eeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhh.ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9d A -14 GVDLGTENLYFSSNAmPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGVYPmVEVLWFGREQQTQDQIAQVITDQIRQLLGADSHLAVVFIPLQRTAYYLDGQHF 107
                                    -5     |   5        15        25        35        45        55        65        75        85        95       105  
                                           1-MSE                                               54-MSE                                                 


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with Q9KU16_VIBCH | Q9KU16 from UniProtKB/TrEMBL  Length:107

    Alignment length:122
                                           1                                                                                                          
                                     -     |   5        15        25        35        45        55        65        75        85        95       105  
         Q9KU16_VIBCH     - ---------------MPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGVYPMVEVLWFGREQQTQDQIAQVITDQIRQLLGADSHLAVVFIPLQRTAYYLDGQHF 107
               SCOP domains d1u9db_ B: Hypothetical protein VC0714                                                                                     SCOP domains
               CATH domains 1u9dB00 B:-14-107 Macrophage Migration Inhibitory Factor                                                                   CATH domains
           Pfam domains (1) ---------------DUF1904-1u9dB01 B:1-106                                                                                   - Pfam domains (1)
           Pfam domains (2) ---------------DUF1904-1u9dB02 B:1-106                                                                                   - Pfam domains (2)
         Sec.struct. author .................eeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhheeee.............eeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhh.ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9d B -14 GVDLGTENLYFSSNAmPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGVYPmVEVLWFGREQQTQDQIAQVITDQIRQLLGADSHLAVVFIPLQRTAYYLDGQHF 107
                                    -5     |   5        15        25        35        45        55        65        75        85        95       105  
                                           1-MSE                                               54-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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: MIF (36)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9KU16_VIBCH | Q9KU16)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1u9d)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  1u9d
    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
  Q9KU16_VIBCH | Q9KU16
    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
  Q9KU16_VIBCH | Q9KU16
    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 1U9D)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1U9D)