Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF UNCHARACTERIZED PROTEIN ATU2773 FROM AGROBACTERIUM TUMEFACIENS C58
 
Authors :  Y. Patskovsky, J. B. Bonanno, S. Sojitra, M. Dickey, K. T. Bain, M. Iizuk D. Smith, L. Rodgers, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Alm York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  07 Aug 07  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, J. B. Bonanno, S. Sojitra, M. Dickey, D. Smith, K. T. Bain, M. Iizuka, L. Rodgers, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Uncharacterized Protein Atu2773 From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN ATU2773
    Atcc: 33970
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: ATU2773, AGR_C_5032
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: AGR_C_5032P

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:168 , TRP A:169 , GLY A:171 , HOH A:572BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QV5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:238 -Pro A:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QV5)

(-) Exons   (0, 0)

(no "Exon" information available for 2QV5)

(-) 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:246
 aligned with A9CHD2_AGRFC | A9CHD2 from UniProtKB/TrEMBL  Length:399

    Alignment length:246
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      
         A9CHD2_AGRFC   148 FGQLPVVGADGLRPMEQYARPWSGARGTRVAIVVGGLGLSQTGSQKAIRDLPPEVTLGFAASGNSLQRWMQDARREGHEILLQIPLEPFGYPGTNPGPDTLLAGDPAKVNIDRLHRSMAKITNYTGVMNYLGGRFLAEQSALEPVMRDIGKRGLLFLDDGSSAQSLSGGIAKAISAPQGFADVLLDGEVTEASILRKLDDLERIARRNGQAIGVASAFDESIAAISKWSREAGGRGIEIVGVSALV 393
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------2qv5A01 A:160-393 Glycoside hydrolase/deacetylase                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhh.........eeeeeeeeee..hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh..eeeeeee...................hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhh..eee..ee.....hhhhhhhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhhhhhhh.eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qv5 A 148 LGQLPVVGADGLRPMEQYARPWSGARGTRVAIVVGGLGLSQTGSQKAIRDLPPEVTLGFAASGNSLQRWMQDARREGHEILLQIPLEPFGYPGTNPGPDTLLAGDPAKVNIDRLHRSMAKITNYTGVMNYLGGRFLAEQSALEPVMRDIGKRGLLFLDDGSSAQSLSGGIAKAISAPQGFADVLLDGEVTEASILRKLDDLERIARRNGQAIGVASAFDESIAAISKWSREAGGRGIEIVGVSALV 393
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with A9CHD2_AGRFC | A9CHD2 from UniProtKB/TrEMBL  Length:399

    Alignment length:246
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      
         A9CHD2_AGRFC   148 FGQLPVVGADGLRPMEQYARPWSGARGTRVAIVVGGLGLSQTGSQKAIRDLPPEVTLGFAASGNSLQRWMQDARREGHEILLQIPLEPFGYPGTNPGPDTLLAGDPAKVNIDRLHRSMAKITNYTGVMNYLGGRFLAEQSALEPVMRDIGKRGLLFLDDGSSAQSLSGGIAKAISAPQGFADVLLDGEVTEASILRKLDDLERIARRNGQAIGVASAFDESIAAISKWSREAGGRGIEIVGVSALV 393
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------2qv5B01 B:160-393 Glycoside hydrolase/deacetylase                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhh.........eeeeeeeeee..hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh..eeeeeee...................hhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhh..eee..ee.....hhhhhhhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhhhhh...eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qv5 B 148 LGQLPVVGADGLRPMEQYARPWSGARGTRVAIVVGGLGLSQTGSQKAIRDLPPEVTLGFAASGNSLQRWMQDARREGHEILLQIPLEPFGYPGTNPGPDTLLAGDPAKVNIDRLHRSMAKITNYTGVMNYLGGRFLAEQSALEPVMRDIGKRGLLFLDDGSSAQSLSGGIAKAISAPQGFADVLLDGEVTEASILRKLDDLERIARRNGQAIGVASAFDESIAAISKWSREAGGRGIEIVGVSALV 393
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
   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 2QV5)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QV5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A9CHD2_AGRFC | A9CHD2)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:238 - Pro A:239   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2qv5
    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
  A9CHD2_AGRFC | A9CHD2
    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
  A9CHD2_AGRFC | A9CHD2
    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 2QV5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QV5)