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

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE NADPH:QUINONE OXIDOREDUCTASE (YP_296108.1) FROM RALSTONIA EUTROPHA JMP134 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  31 Aug 09  (Deposition) - 15 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_296108. 1, Putative Nadph:Quinone Oxidoreductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Nadph:Quinone Oxidoreductase (Yp_296108. 1) From Ralstonia Eutropha Jmp134 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REUT_A1899, YP_296108.1
    Organism Common: ALCALIGENES EUTROPHUS
    Organism Scientific: RALSTONIA EUTROPHA
    Organism Taxid: 264198
    Strain: JMP134

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 42)

Asymmetric/Biological Unit (4, 42)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3MSE28Mod. Amino AcidSELENOMETHIONINE
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:45 , VAL A:154 , ASN A:155 , THR A:158 , SER A:181 , ASN A:182 , LEU A:183 , ARG A:203 , LYS A:204 , GLN A:207 , THR A:247 , TYR A:285 , LEU A:288 , TRP A:308 , LEU A:309 , LEU A:310 , ARG A:362 , ALA A:363 , THR A:364 , LYS A:367 , ACT A:382 , HOH A:411 , HOH A:492 , HOH A:502 , HOH A:535 , HOH A:545 , HOH A:554 , HOH A:579 , HOH A:633 , HOH A:645 , HOH A:651 , HOH A:701BINDING SITE FOR RESIDUE NDP A 401
02AC2SOFTWAREGLN A:185 , GLN A:189 , GLN A:214 , HOH A:529 , HOH A:564 , HOH A:595 , HOH A:660BINDING SITE FOR RESIDUE EDO A 379
03AC3SOFTWARETRP A:308 , LEU A:309 , PHE A:313 , HOH A:500BINDING SITE FOR RESIDUE EDO A 380
04AC4SOFTWARESER A:3 , SER A:23 , ASP A:25 , TYR A:271 , GLY B:85BINDING SITE FOR RESIDUE EDO A 381
05AC5SOFTWARESER A:46 , NDP A:401 , HOH A:553 , HOH A:599 , TYR B:274BINDING SITE FOR RESIDUE ACT A 382
06AC6SOFTWARELEU A:160 , VAL A:163 , GLU A:164 , ARG A:167 , ARG A:321 , LEU A:325 , ACT A:384 , HOH A:549 , HOH A:601BINDING SITE FOR RESIDUE ACT A 383
07AC7SOFTWAREARG A:167 , ASP A:194 , ACT A:383BINDING SITE FOR RESIDUE ACT A 384
08AC8SOFTWAREPRO B:45 , VAL B:154 , ASN B:155 , THR B:158 , ALA B:178 , SER B:181 , ASN B:182 , LEU B:183 , ARG B:203 , LYS B:204 , GLN B:207 , ALA B:246 , THR B:247 , TYR B:285 , LEU B:288 , TRP B:308 , LEU B:309 , LEU B:310 , ARG B:362 , THR B:364 , LYS B:367 , EDO B:379 , HOH B:484 , HOH B:527 , HOH B:551 , HOH B:565 , HOH B:568 , HOH B:590 , HOH B:600 , HOH B:602 , HOH B:676BINDING SITE FOR RESIDUE NDP B 401
09AC9SOFTWARETYR A:274 , SER B:46 , ASN B:95 , LEU B:309 , NDP B:401 , HOH B:468BINDING SITE FOR RESIDUE EDO B 379
10BC1SOFTWAREGLN B:189 , GLN B:214 , HIS B:340 , HOH B:435 , HOH B:508BINDING SITE FOR RESIDUE EDO B 380
11BC2SOFTWARELYS B:251 , GLU B:294 , ASN B:296 , EDO B:382BINDING SITE FOR RESIDUE EDO B 381
12BC3SOFTWARETHR B:258 , PHE B:295 , ASN B:296 , EDO B:381 , HOH B:405BINDING SITE FOR RESIDUE EDO B 382
13BC4SOFTWAREARG B:319 , GLU B:320BINDING SITE FOR RESIDUE EDO B 383
14BC5SOFTWAREASP B:135 , PHE B:153 , LYS B:326BINDING SITE FOR RESIDUE EDO B 384

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IUP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IUP)

(-) 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:376
 aligned with Q470B9_CUPNJ | Q470B9 from UniProtKB/TrEMBL  Length:378

    Alignment length:376
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      
         Q470B9_CUPNJ     2 HSALQLRSRIKSSGELELSLDSIDTPHPGPDEVLIRIEASPLNPSDLGLLFGAADMSTAKASGTAERPIVTARVPEGAMRSMAGRLDASMPVGNEGAGVVVEAGSSPAAQALMGKTVAAIGGAMYSQYRCIPADQCLVLPEGATPADGASSFVNPLTALGMVETMRLEGHSALVHTAAASNLGQMLNQICLKDGIKLVNIVRKQEQADLLKAQGAVHVCNAASPTFMQDLTEALVSTGATIAFDATGGGKLGGQILTCMEAALNKSAREYSRYGSTTHKQVYLYGGLDTSPTEFNRNFGMAWGMGGWLLFPFLQKIGRERANALKQRVVAELKTTFASHYSKEISLAEVLDLDMIAVYNKRATGEKYLINPNKGLA 377
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeeee.......eeeeeeeeee.hhhhhhhhhh..eeeeeeeee....eeeeee.hhhhhhhhhhhh.eeee....eeeeeeee..hhhhhh....eeee........eeeee...eee.....hhhhhh..hhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....eee....hhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhhhh.............eeeee....eeeeeee.......eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhh.......eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iup A   2 HSALQLRSRIKSSGELELSLDSIDTPHPGPDEVLIRIEASPLNPSDLGLLFGAADmSTAKASGTAERPIVTARVPEGAmRSmAGRLDASmPVGNEGAGVVVEAGSSPAAQALmGKTVAAIGGAmYSQYRCIPADQCLVLPEGATPADGASSFVNPLTALGmVETmRLEGHSALVHTAAASNLGQmLNQICLKDGIKLVNIVRKQEQADLLKAQGAVHVCNAASPTFmQDLTEALVSTGATIAFDATGGGKLGGQILTCmEAALNKSAREYSRYGSTTHKQVYLYGGLDTSPTEFNRNFGmAWGmGGWLLFPFLQKIGRERANALKQRVVAELKTTFASHYSKEISLAEVLDLDmIAVYNKRATGEKYLINPNKGLA 377
                                    11        21        31        41        51     |  61        71        81 |      91       101       111  |    121   |   131       141       151       161|   |  171       181    |  191       201       211       221      |231       241       251       261       271       281       291       301   |   311       321       331       341       351   |   361       371      
                                                                                  57-MSE                 80-MSE     91-MSE                114-MSE    125-MSE                              162-MSE                 186-MSE                                   228-MSE                         260-MSE                                  301-MSE                                               355-MSE                  
                                                                                                            83-MSE                                                                            166-MSE                                                                                                                                    305-MSE                                                                    


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with Q470B9_CUPNJ | Q470B9 from UniProtKB/TrEMBL  Length:378

    Alignment length:375
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371     
         Q470B9_CUPNJ     2 HSALQLRSRIKSSGELELSLDSIDTPHPGPDEVLIRIEASPLNPSDLGLLFGAADMSTAKASGTAERPIVTARVPEGAMRSMAGRLDASMPVGNEGAGVVVEAGSSPAAQALMGKTVAAIGGAMYSQYRCIPADQCLVLPEGATPADGASSFVNPLTALGMVETMRLEGHSALVHTAAASNLGQMLNQICLKDGIKLVNIVRKQEQADLLKAQGAVHVCNAASPTFMQDLTEALVSTGATIAFDATGGGKLGGQILTCMEAALNKSAREYSRYGSTTHKQVYLYGGLDTSPTEFNRNFGMAWGMGGWLLFPFLQKIGRERANALKQRVVAELKTTFASHYSKEISLAEVLDLDMIAVYNKRATGEKYLINPNKGL 376
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeeee.......eeeeeeeeee.hhhhhhhhhh..eeeeeeeee....eeeeee.hhhhhhhhhhhh..eee....eeeeeeee..hhhhhh....eeee........eeeee...eee.....hhhhhh..hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhhhhh............eeeee....eeeeeee.......eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..........eeehhhhhhhhhhhhhhh.......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iup B   2 HSALQLRSRIKSSGELELSLDSIDTPHPGPDEVLIRIEASPLNPSDLGLLFGAADmSTAKASGTAERPIVTARVPEGAmRSmAGRLDASmPVGNEGAGVVVEAGSSPAAQALmGKTVAAIGGAmYSQYRCIPADQCLVLPEGATPADGASSFVNPLTALGmVETmRLEGHSALVHTAAASNLGQmLNQICLKDGIKLVNIVRKQEQADLLKAQGAVHVCNAASPTFmQDLTEALVSTGATIAFDATGGGKLGGQILTCmEAALNKSAREYSRYGSTTHKQVYLYGGLDTSPTEFNRNFGmAWGmGGWLLFPFLQKIGRERANALKQRVVAELKTTFASHYSKEISLAEVLDLDmIAVYNKRATGEKYLINPNKGL 376
                                    11        21        31        41        51     |  61        71        81 |      91       101       111  |    121   |   131       141       151       161|   |  171       181    |  191       201       211       221      |231       241       251       261       271       281       291       301   |   311       321       331       341       351   |   361       371     
                                                                                  57-MSE                 80-MSE     91-MSE                114-MSE    125-MSE                              162-MSE                 186-MSE                                   228-MSE                         260-MSE                                  301-MSE                                               355-MSE                 
                                                                                                            83-MSE                                                                            166-MSE                                                                                                                                    305-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 3IUP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q470B9_CUPNJ | Q470B9)
molecular function
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3iup)
 

(-) 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
  3iup
    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
  Q470B9_CUPNJ | Q470B9
    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
  Q470B9_CUPNJ | Q470B9
    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 3IUP)

(-) Related Entries Specified in the PDB File

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