Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  PSEUDOMONAS AERUGINOSA PHBH R220Q FREE OF P-OHB
 
Authors :  J. Wang, M. Ortiz-Maldonado, B. Entsch, D. Ballou, D. L. Gatti
Date :  19 Sep 01  (Deposition) - 27 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Phbh, Fad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang, M. Ortiz-Maldonado, B. Entsch, V. Massey, D. Ballou, D. L. Gatti
Protein And Ligand Dynamics In 4-Hydroxybenzoate Hydroxylase.
Proc. Natl. Acad. Sci. Usa V. 99 608 2002
PubMed-ID: 11805318  |  Reference-DOI: 10.1073/PNAS.022640199

(-) Compounds

Molecule 1 - P-HYDROXYBENZOATE HYDROXYLASE
    Chains: A
    EC Number: 1.14.13.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO32Ligand/IonSULFITE ION
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO34Ligand/IonSULFITE ION
3SO416Ligand/IonSULFATE ION
Biological Unit 2 (3, 22)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO34Ligand/IonSULFITE ION
3SO416Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:81 , PRO A:248 , SER A:249 , GLU A:250 , HOH A:610BINDING SITE FOR RESIDUE SO4 A 701
02AC2SOFTWAREARG A:327 , ALA A:330 , ARG A:334 , HOH A:597BINDING SITE FOR RESIDUE SO4 A 702
03AC3SOFTWARELYS A:175 , ARG A:362BINDING SITE FOR RESIDUE SO4 A 703
04AC4SOFTWAREARG A:352 , PRO A:354 , ASP A:355 , HOH A:525BINDING SITE FOR RESIDUE SO4 A 704
05AC5SOFTWAREARG A:33 , GLU A:126 , ARG A:128 , HOH A:432BINDING SITE FOR RESIDUE SO4 A 705
06AC6SOFTWAREARG A:42 , ARG A:44 , HOH A:502BINDING SITE FOR RESIDUE SO4 A 706
07AC7SOFTWAREARG A:206BINDING SITE FOR RESIDUE SO4 A 707
08AC8SOFTWAREARG A:128 , HIS A:162BINDING SITE FOR RESIDUE SO4 A 708
09AC9SOFTWAREASP A:131 , GLN A:133 , GLY A:134 , HOH A:515BINDING SITE FOR RESIDUE SO3 A 709
10BC1SOFTWAREARG A:33BINDING SITE FOR RESIDUE SO3 A 710
11BC2SOFTWAREILE A:8 , GLY A:9 , GLY A:11 , PRO A:12 , SER A:13 , LEU A:31 , GLU A:32 , ARG A:33 , GLN A:34 , ARG A:42 , ARG A:44 , ALA A:45 , GLN A:102 , VAL A:127 , CYS A:158 , ASP A:159 , GLY A:160 , GLY A:163 , ILE A:164 , GLY A:285 , ASP A:286 , ALA A:296 , GLY A:298 , LEU A:299 , HOH A:401 , HOH A:403 , HOH A:404 , HOH A:407 , HOH A:416 , HOH A:418 , HOH A:432 , HOH A:441 , HOH A:471 , HOH A:479 , HOH A:508 , HOH A:526 , HOH A:547BINDING SITE FOR RESIDUE FAD A 395

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K0L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:274 -Pro A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K0L)

(-) Exons   (0, 0)

(no "Exon" information available for 1K0L)

(-) 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:394
 aligned with PHHY_PSEAE | P20586 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390    
           PHHY_PSEAE     1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE 394
               SCOP domains d1k0la1 A:1-173,A:276-394 p-Hydroxybenzoate hydroxylase, PHBH                                                                                                                d1k0la2 A:174-275 p-Hydroxybenzoate hydroxylase (PHBH)                                                d1k0la1 A:1-173,A:276-394 p-Hydroxybenzoate hydroxylase, PHBH                                                           SCOP domains
               CATH domains 1k0lA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]   1k0lA02                1k0lA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]                1k0lA02 A:73-95,A:181-268,A:352-388 D-Amino Acid Oxidase, subunit A, domain 2           1k0lA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]              1k0lA02 A:73-95,A:181-268,A:352-388  ------ CATH domains
               Pfam domains -FAD_binding_3-1k0lA01 A:2-343                                                                                                                                                                                                                                                                                                                         --------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee...hhhhhhh.....eehhhhhhhhhhh..hhhhhhhheee..eeeee..eeeeehhhhhhh...eee.hhhhhhhhhhhhhhhhh.eee...eeeeee.......eeeeee..eeeeee..eeee.......hhhhhhhhhheeeeeeeeeeeeeeee.........eee......eeeee.....eeeeeee....hhhhhhhhhhhhhhhhh.hhhhhhhh......eeeeeeeeeeeee..ee..eee.hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k0l A   1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSQYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE 394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHHY_PSEAE | P20586)
molecular function
    GO:0018659    4-hydroxybenzoate 3-monooxygenase activity    Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O.
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0043639    benzoate catabolic process    The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.
    GO:0043640    benzoate catabolic process via hydroxylation    The chemical reactions and pathways resulting in the breakdown of benzoate, by its hydroxylation to cis-1,2-dihydroxybenzoate followed by dehydrogenation to catechol.
    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.
    GO:0044550    secondary metabolite biosynthetic process    The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon.

 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO3  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:274 - Pro A:275   [ 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
  1k0l
    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
  PHHY_PSEAE | P20586
    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)
  1.14.13.2
    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
  PHHY_PSEAE | P20586
    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
        PHHY_PSEAE | P20586: 1d7l 1dob 1doc 1dod 1doe 1ius 1iut 1iuu 1iuv 1iuw 1iux 1k0i 1k0j 1pxa 1pxb 1pxc 1ykj

(-) Related Entries Specified in the PDB File

1iuw 1k0i 1k0j