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

(-) Description

Title :  THE CRYSTAL STRUCTURE OF NUDIX HYDROLASE FROM RHODOSPIRILLUM RUBRUM
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  07 Mar 11  (Deposition) - 11 May 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi2, Hydrolase, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Nudix Hydrolase From Rhodospirillu Rubrum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUDIX HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3 (BC)
    Expression System Strain: BL21(DE3)-CODON+RIL(P)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 18-151
    Gene: RRU_A0393
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Organism Taxid: 269796
    Strain: STRAIN ATCC 11170

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:42 , SER A:47 , GLU A:53 , LYS A:58 , MSE A:103 , ASP A:140BINDING SITE FOR RESIDUE ADP A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R03)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:44 -Gly A:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R03)

(-) Exons   (0, 0)

(no "Exon" information available for 3R03)

(-) 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:131
 aligned with Q2RXE7_RHORT | Q2RXE7 from UniProtKB/TrEMBL  Length:151

    Alignment length:131
                                    30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q2RXE7_RHORT    21 PILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHSYDTFHLLMPLYACRSWRGRATAREGQTLAWVRAERLREYPMPPADLPLIPILQDWL 151
               SCOP domains d3r03a_ A: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeee..........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeee....eeeeeeeee.............eeeeehhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r03 A  21 PILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHSYDTFHLLmPLYACRSWRGRATAREGQTLAWVRAERLREYPmPPADLPLIPILQDWL 151
                                    30        40        50        60        70        80        90       100  |    110       120       130     | 140       150 
                                                                                                            103-MSE                          136-MSE           


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q2RXE7_RHORT | Q2RXE7 from UniProtKB/TrEMBL  Length:151

    Alignment length:134
                                    27        37        47        57        67        77        87        97       107       117       127       137       147    
         Q2RXE7_RHORT    18 LGLPILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHSYDTFHLLMPLYACRSWRGRATAREGQTLAWVRAERLREYPMPPADLPLIPILQDWL 151
               SCOP domains d3r03b_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----NUDIX-3r03B01 B:23-148                                                                                                        --- Pfam domains (1)
           Pfam domains (2) -----NUDIX-3r03B02 B:23-148                                                                                                        --- Pfam domains (2)
         Sec.struct. author ....eee..eeee.....eeeeee....-----.ee..........hhhhhhhhhhhhhhh...hhhhheeeeeeeee....eeeeeeeee.............eeeeee.hhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r03 B  18 LGLPILLVTAAALIDPDGRVLLAQRPPG-----LWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHSYDTFHLLmPLYACRSWRGRATAREGQTLAWVRAERLREYPmPPADLPLIPILQDWL 151
                                    27        37       | -   |    57        67        77        87        97     | 107       117       127       137       147    
                                                      45    51                                                 103-MSE                          136-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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R03)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2RXE7_RHORT | Q2RXE7)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:44 - Gly A:45   [ RasMol ]  
 

(-) 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 | Asym./Biol. Unit - 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
  3r03
    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
  Q2RXE7_RHORT | Q2RXE7
    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
  Q2RXE7_RHORT | Q2RXE7
    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 3R03)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R03)