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 :  CRYSTAL STRUCTURE OF RUBREDOXIN REDUCTASE FROM PSEUDOMONAS AERUGINOSA.
 
Authors :  G. Hagelueken, L. Wiehlmann, T. M. Adams, H. Kolmar, D. W. Heinz, B. Tuem W. -D. Schubert
Date :  14 Jun 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Alkane Degradation, Nadh Oxidoreductase, Rubredoxin Reductase, Fad, Nad, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hagelueken, L. Wiehlmann, T. M. Adams, H. Kolmar, D. W. Heinz, B. Tuemmler, W. -D. Schubert
Crystal Structure Of The Electron Transfer Complex Rubredoxin - Rubredoxin Reductase From Pseudomonas Aeruginosa.
Proc. Natl. Acad. Sci. Usa V. 104 12276 2007
PubMed-ID: 17636129  |  Reference-DOI: 10.1073/PNAS.0702919104

(-) Compounds

Molecule 1 - RUBREDOXIN REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3PEG6Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:184 , VAL A:317 , HOH A:2218 , HOH A:2219BINDING SITE FOR RESIDUE PEG A1385
2AC2SOFTWAREMET A:290 , PRO A:314 , ASN A:376BINDING SITE FOR RESIDUE PEG A1386
3AC3SOFTWAREGLY A:183 , LEU A:184 , LEU A:185 , HIS A:186 , TRP A:339BINDING SITE FOR RESIDUE PEG A1387
4AC4SOFTWARESER A:264 , ARG A:266 , PRO A:307 , GLN A:309 , HOH A:2220BINDING SITE FOR RESIDUE PEG A1388
5AC5SOFTWAREARG A:82 , ARG A:244BINDING SITE FOR RESIDUE PEG A1389
6AC6SOFTWAREARG A:82 , VAL A:83 , ARG A:115 , PRO A:117 , GLU A:246 , LEU A:247 , HOH A:2221BINDING SITE FOR RESIDUE PEG A1390
7AC7SOFTWARELEU A:155 , ILE A:156 , HOH A:2130BINDING SITE FOR RESIDUE CL A1391
8AC8SOFTWAREARG A:242 , THR A:245 , GLU A:246 , ARG A:257BINDING SITE FOR RESIDUE CL A1392
9AC9SOFTWAREILE A:10 , GLY A:11 , THR A:12 , GLY A:13 , LEU A:14 , ALA A:15 , THR A:36 , ALA A:37 , ASP A:38 , LYS A:45 , PRO A:46 , THR A:81 , ARG A:82 , VAL A:83 , ALA A:108 , TRP A:109 , GLY A:110 , ILE A:156 , GLU A:159 , PHE A:160 , GLY A:276 , ASP A:277 , LEU A:287 , TYR A:288 , VAL A:289 , LEU A:292 , LYS A:320 , HOH A:2022 , HOH A:2091 , HOH A:2156 , HOH A:2222 , HOH A:2223 , HOH A:2224 , HOH A:2226 , HOH A:2227 , HOH A:2228 , HOH A:2229 , HOH A:2230 , HOH A:2231BINDING SITE FOR RESIDUE FAD A1393

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V3A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V3A)

(-) Exons   (0, 0)

(no "Exon" information available for 2V3A)

(-) 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:381
 aligned with RURE_PSEAE | Q9HTK9 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:381
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 
           RURE_PSEAE     4 RAPLVIIGTGLAGYNLAREWRKLDGETPLLMITADDGRSYSKPMLSTGFSKNKDADGLAMAEPGAMAEQLNARILTHTRVTGIDPGHQRIWIGEEEVRYRDLVLAWGAEPIRVPVEGDAQDALYPINDLEDYARFRQAAAGKRRVLLLGAGLIGCEFANDLSSGGYQLDVVAPCEQVMPGLLHPAAAKAVQAGLEGLGVRFHLGPVLASLKKAGEGLEAHLSDGEVIPCDLVVSAVGLRPRTELAFAAGLAVNRGIVVDRSLRTSHANIYALGDCAEVDGLNLLYVMPLMACARALAQTLAGNPSQVAYGPMPVTVKTPACPLVVSPPPRGMDGQWLVEGSGTDLKVLCRDTAGRVIGYALTGAAVNEKLALNKELPGLMA 384
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhh......eeee......ee.hhhhhhh.....hhhhheeehhhhhhhhh..eee......eeehhh.eeee..eeee..eeee...eee............eee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhh...eeee...eeeeeee..eeeeee....eeee.eeee...eee.hhhhhhh.......eee..........eee....eee......hhhhhhhhhhhhhhhhh............eee......eeee........eeeeeee..eeeeeee.....eeeeeee.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3a A   4 RAPLVIIGTGLAGYNLAREWRKLDGETPLLMITADDGRSYSKPMLSTGFSKNKDADGLAMAEPGAMAEQLNARILTHTRVTGIDPGHQRIWIGEEEVRYRDLVLAWGAEPIRVPVEGDAQDALYPINDLEDYARFRQAAAGKRRVLLLGAGLIGCEFANDLSSGGYQLDVVAPCEQVMPGLLHPAAAKAVQAGLEGLGVRFHLGPVLASLKKAGEGLEAHLSDGEVIPCDLVVSAVGLRPRTELAFAAGLAVNRGIVVDRSLRTSHANIYALGDCAEVDGLNLLYVMPLMACARALAQTLAGNPSQVAYGPMPVTVKTPACPLVVSPPPRGMDGQWLVEGSGTDLKVLCRDTAGRVIGYALTGAAVNEKLALNKELPGLMA 384
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383
   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 2V3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V3A)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RURE_PSEAE | Q9HTK9)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0015044    rubredoxin-NAD+ reductase activity    Catalysis of the reaction: reduced rubredoxin + NAD+ = oxidized rubredoxin + NADH + H+.
    GO:0015046    rubredoxin-NADP reductase activity    Catalysis of the reaction: reduced rubredoxin + NADP+ = oxidized rubredoxin + NADPH + H+.
biological process
    GO:0043448    alkane catabolic process    The chemical reactions and pathways resulting in the breakdown of an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v3a)
 

(-) 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
  2v3a
    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
  RURE_PSEAE | Q9HTK9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  RURE_PSEAE | Q9HTK9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RURE_PSEAE | Q9HTK9: 2v3b

(-) Related Entries Specified in the PDB File

2v3b CRYSTAL STRUCTURE OF THE ELECTRON TRANSFER COMPLEX RUBREDOXIN - RUBREDOXIN REDUCTASE FROM PSEUDOMONAS AERUGINOSA.