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
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)

(-) Description

Title :  COCRYSTAL STRUCTURE OF NUDIX DOMAIN OF SHEWANELLA ONEIDENSIS NRTR COMPLEXED WITH ADP RIBOSE
 
Authors :  N. Huang, H. Zhang
Date :  06 Apr 09  (Deposition) - 09 Jun 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Binding Protein, Nudix Domain, Whth Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Huang, J. De Ingeniis, L. Galeazzi, C. Mancini, Y. D. Korostelev, A. B. Rakhmaninova, M. S. Gelfand, D. A. Rodionov, N. Raffaelli, H. Zhang
Structure And Function Of An Adp-Ribose-Dependent Transcriptional Regulator Of Nad Metabolism
Structure V. 17 939 2009
PubMed-ID: 19604474  |  Reference-DOI: 10.1016/J.STR.2009.05.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NRTR, SO_1979
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1APR4Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:19 , THR A:21 , ASP A:23 , ARG A:41 , ASN A:43 , PHE A:56 , LYS A:76 , ARG A:95 , ASP A:96 , ARG A:98 , PHE A:140 , HIS A:142 , HOH A:165 , HOH A:166 , HOH A:176 , HOH A:188 , HOH A:200 , TYR B:10 , PHE B:15BINDING SITE FOR RESIDUE APR A 302
2AC2SOFTWARETYR A:10 , PHE A:15 , LEU B:19 , THR B:21 , ASP B:23 , ARG B:41 , ASN B:43 , PHE B:56 , LYS B:76 , ARG B:95 , ASP B:96 , ARG B:98 , SER B:121 , HIS B:142 , HOH B:163 , HOH B:170 , HOH B:179 , HOH B:278 , HOH B:324BINDING SITE FOR RESIDUE APR B 302
3AC3SOFTWARELEU C:19 , THR C:21 , ASP C:23 , ARG C:41 , ASN C:43 , PHE C:56 , LYS C:76 , ARG C:95 , ASP C:96 , ARG C:98 , SER C:101 , SER C:121 , PHE C:140 , HIS C:142 , HOH C:180 , HOH C:188 , HOH C:211 , HOH C:238 , HOH C:489 , TYR D:10 , PHE D:15BINDING SITE FOR RESIDUE APR C 302
4AC4SOFTWARETYR C:10 , PHE C:15 , THR D:21 , ASP D:23 , ARG D:41 , ASN D:43 , PHE D:56 , LYS D:76 , ARG D:95 , ASP D:96 , ARG D:98 , THR D:103 , SER D:121 , PHE D:140 , HIS D:142 , HOH D:162 , HOH D:164 , HOH D:167 , HOH D:172 , HOH D:175 , HOH D:181 , HOH D:185BINDING SITE FOR RESIDUE APR D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GZ8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:44 -Pro A:45
2His B:44 -Pro B:45
3His C:44 -Pro C:45
4His D:44 -Pro D:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3GZ8)

(-) 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:154
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
         Q8EFJ3_SHEON     1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeee........ee..eee.......hhhhhhhhhhhhhhh......eeeeeeee........eeeeeeeeee...........eeeeeeeehhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz8 A   1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
         Q8EFJ3_SHEON     1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeee........ee..eee.......hhhhhhhhhhhhhhh......eeeeeeee........eeeeeeeee............eeeeeeeehhhhh......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz8 B   1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    


Chain C from PDB  Type:PROTEIN  Length:156
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:156
                             1                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      
         Q8EFJ3_SHEON     - -MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQ 155
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh.hhhhh...eeeeeeeeeeee..eeeeeeeee........ee..eee.......hhhhhhhhhhhhhhh......eeeeeeee........eeeeeeeee............eeeeeeeehhhhh......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gz8 C   0 HMTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLTQ 155
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      


Chain D from PDB  Type:PROTEIN  Length:154
 aligned with Q8EFJ3_SHEON | Q8EFJ3 from UniProtKB/TrEMBL  Length:237

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
         Q8EFJ3_SHEON     1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhh...eeeeeeeeeeee..eeeeeeeee........ee..eee.......hhhhhhhhhhhhhhh......eeeeeeee........eeeeeeeeee...........eeeeeeeehhhhh......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz8 D   1 MTEAEYLANYDPKAFKAQLLTVDAVLFTYHDQQLKVLLVQRSNHPFLGLWGLPGGFIDETCDESLEQTVLRKLAEKTAVVPPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQIQIASVSDVKWWPLADVLQMPLAFDHLQLIEQARERLT 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 3GZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GZ8)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8EFJ3_SHEON | Q8EFJ3)
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.

 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
    APR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:44 - Pro A:45   [ RasMol ]  
    His B:44 - Pro B:45   [ RasMol ]  
    His C:44 - Pro C:45   [ RasMol ]  
    His D:44 - Pro D:45   [ 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
  3gz8
    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
  Q8EFJ3_SHEON | Q8EFJ3
    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
  Q8EFJ3_SHEON | Q8EFJ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8EFJ3_SHEON | Q8EFJ3: 3gz5 3gz6

(-) Related Entries Specified in the PDB File

3gz5 3gz6