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 :  NADPH BOUND STRUCTURE OF THE SHORT CHAIN OXIDOREDUCTASE Q9HYA2 FROM PSEUDOMONAS AERUGINOSA PAO1 CONTAINING AN ATYPICAL CATALYTIC CENTER
 
Authors :  R. Huether, T. C. Umland, W. L. Duax
Date :  15 Jan 10  (Deposition) - 14 Apr 10  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sdr, Scor, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Huether, Q. Mao, W. L. Duax, T. C. Umland
The Short-Chain Oxidoreductase Q9Hya2 From Pseudomonas Aeruginosa Pao1 Contains An Atypical Catalytic Center.
Protein Sci. V. 19 1097 2010
PubMed-ID: 20340135  |  Reference-DOI: 10.1002/PRO.384

(-) Compounds

Molecule 1 - SHORT CHAIN OXIDOREDUCTASE Q9HYA2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETSUMO
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA3507
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , SER A:17 , SER A:18 , ALA A:39 , ARG A:40 , ASP A:41 , ARG A:44 , CYS A:66 , ASP A:67 , VAL A:68 , ALA A:95 , GLY A:96BINDING SITE FOR RESIDUE NDP A 301
2AC2SOFTWARELEU A:148 , MET A:156 , ARG A:163BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWAREGLY B:15 , ALA B:39 , ARG B:40 , ARG B:44 , HOH B:443 , HOH B:454 , HOH B:475BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWARESER B:18 , GLY B:19 , SER B:194 , GLY B:195 , HOH B:496 , HOH B:523BINDING SITE FOR RESIDUE GOL B 302
5AC5SOFTWAREGLY C:15 , SER C:17 , SER C:18 , ALA C:39 , ARG C:40 , ASP C:41 , CYS C:66 , ASP C:67 , VAL C:68 , ALA C:95 , GLY C:96 , GLN C:97 , HOH C:448 , HOH C:466BINDING SITE FOR RESIDUE NDP C 301
6AC6SOFTWARELEU C:148 , THR C:159 , ARG C:163BINDING SITE FOR RESIDUE CL C 302
7AC7SOFTWAREGLY D:15 , ALA D:39 , ARG D:40 , HOH D:440 , HOH D:459BINDING SITE FOR RESIDUE SO4 D 301
8AC8SOFTWARESER D:18 , GLY D:19 , ARG D:44 , GLY D:195 , ARG D:198BINDING SITE FOR RESIDUE GOL D 302
9AC9SOFTWARESER D:146 , LEU D:148 , ARG D:163BINDING SITE FOR RESIDUE CL D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LF2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu C:205 -Glu C:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LF2)

(-) Exons   (0, 0)

(no "Exon" information available for 3LF2)

(-) 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:257
 aligned with Q9HYA2_PSEAE | Q9HYA2 from UniProtKB/TrEMBL  Length:265

    Alignment length:263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   
         Q9HYA2_PSEAE     3 PYDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
               SCOP domains d3lf2a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh.------hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf2 A   3 PYDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEA------DWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202|      212       222       232       242       252       262   
                                                                                                                                                                                                                                  203    210                                                       


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q9HYA2_PSEAE | Q9HYA2 from UniProtKB/TrEMBL  Length:265

    Alignment length:263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   
         Q9HYA2_PSEAE     3 PYDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
               SCOP domains d3lf2b_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf2 B   3 PYDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   


Chain C from PDB  Type:PROTEIN  Length:261
 aligned with Q9HYA2_PSEAE | Q9HYA2 from UniProtKB/TrEMBL  Length:265

    Alignment length:261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
         Q9HYA2_PSEAE     5 DLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
               SCOP domains d3lf2c_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf2 C   5 DLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 


Chain D from PDB  Type:PROTEIN  Length:262
 aligned with Q9HYA2_PSEAE | Q9HYA2 from UniProtKB/TrEMBL  Length:265

    Alignment length:262
                                    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  
         Q9HYA2_PSEAE     4 YDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
               SCOP domains d3lf2d_ D: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----adh_short-3lf2D01 D:9-178                                                                                                                                                 --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----adh_short-3lf2D02 D:9-178                                                                                                                                                 --------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----adh_short-3lf2D03 D:9-178                                                                                                                                                 --------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----adh_short-3lf2D04 D:9-178                                                                                                                                                 --------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lf2 D   4 YDLSEAVAVVTGGSSGIGLATVELLLEAGAAVAFCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLGCASILVNNAGQGRVSTFAETTDEAWSEELQLKFFSVIHPVRAFLPQLESRADAAIVCVNSLLASQPEPHMVATSAARAGVKNLVRSMAFEFAPKGVRVNGILIGLVESGQWRRRFEAREERELDWAQWTAQLARNKQIPLGRLGKPIEAARAILFLASPLSAYTTGSHIDVSGGLSRHA 265
                                    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
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LF2)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9HYA2_PSEAE | Q9HYA2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
    Glu C:205 - Glu C:206   [ 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
  3lf2
    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
  Q9HYA2_PSEAE | Q9HYA2
    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
  Q9HYA2_PSEAE | Q9HYA2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9HYA2_PSEAE | Q9HYA2: 3lf1

(-) Related Entries Specified in the PDB File

3lf1 THE APO STRUCTURE OF THIS PROTEIN