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 :  STRUCTURE OF THE REDUCED PENTAERYTHRITOL TETRANITRATE REDUCTASE
 
Authors :  T. M. Barna, P. C. E. Moody
Date :  04 Jun 01  (Deposition) - 05 Jul 01  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavoenzyme, Reduced Flavoenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Barna, H. Khan, N. C. Bruce, I. Barsukov, N. S. Scrutton, P. C. Moody
Crystal Structure Of Pentaerythritol Tetranitrate Reductase: "Flipped" Binding Geometries For Steroid Substrates In Different Redox States Of The Enzyme
J. Mol. Biol. V. 310 433 2001
PubMed-ID: 11428899  |  Reference-DOI: 10.1006/JMBI.2001.4779

(-) Compounds

Molecule 1 - PENTAERYTHRITOL TETRANITRATE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PONR1
    Expression System Strain: K12
    Expression System Taxid: 83333
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550
    Other Details: NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE
    Strain: PB2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:23 , PRO A:24 , LEU A:25 , THR A:26 , ALA A:58 , GLN A:100 , HIS A:181 , HIS A:184 , ARG A:233 , LEU A:275 , ALA A:302 , GLY A:323 , ARG A:324 , TYR A:351 , HOH A:2520 , HOH A:2582 , HOH A:2583 , HOH A:2584 , HOH A:2585BINDING SITE FOR RESIDUE FMN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H63)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:32 -Pro A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H63)

(-) Exons   (0, 0)

(no "Exon" information available for 1H63)

(-) 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:364
 aligned with P71278_ENTCL | P71278 from UniProtKB/TrEMBL  Length:365

    Alignment length:364
                                    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    
         P71278_ENTCL     2 SAEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 365
               SCOP domains d1h63a_ A: Pentaerythritol tetranirate reductase                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1h63A00 A:1-364 Aldolase class I                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee...eee...............hhhhhhhhhhh....eeeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh..ee........eeeee.....eeeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.eeeee....ee..ee...hhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h63 A   1 SAEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 364
                                    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
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H63)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P71278_ENTCL | P71278)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
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
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:32 - Pro A:33   [ 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
  1h63
    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
  P71278_ENTCL | P71278
    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
  P71278_ENTCL | P71278
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P71278_ENTCL | P71278: 1gvo 1gvq 1gvr 1gvs 1h50 1h51 1h60 1h61 1h62 1vyp 1vyr 1vys 2aba 2abb 3f03 3kft 3p62 3p67 3p74 3p7y 3p80 3p81 3p82 3p84 3p8i 3p8j 5lgx 5lgz

(-) Related Entries Specified in the PDB File

1h50 STUCTURE OF PENTAERYTHRITOL TETRANIRATE REDUCTASE AND COMPLEXES
1h51 OXIDISED PENTAERYTHRITOL TETRANIRATE REDUCTASE ( SCN COMPLEX)
1h60 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH PROGESTERONE
1h61 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH PREDNISONE
1h62 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE IN COMPLEX WITH 1,4-ANDROSTADIEN- 3,17-DIONE