Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  3-OXO-DELTA5-STEROID ISOMERASE, NMR, 20 STRUCTURES
 
Authors :  Z. R. Wu, S. Ebrahimian, M. E. Zawrotny, L. D. Thornburg, G. C. Perez- Alvarado, P. Brothers, R. M. Pollack, M. F. Summers
Date :  12 Mar 97  (Deposition) - 12 Nov 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Isomerase, Ksi, 3-Ketosteroid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. R. Wu, S. Ebrahimian, M. E. Zawrotny, L. D. Thornburg, G. C. Perez-Alvarado, P. Brothers, R. M. Pollack, M. F. Summers
Solution Structure Of 3-Oxo-Delta5-Steroid Isomerase.
Science V. 276 415 1997
PubMed-ID: 9103200  |  Reference-DOI: 10.1126/SCIENCE.276.5311.415
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-OXO-DELTA5-STEROID ISOMERASE
    Atcc: 11996
    Chains: A, B
    EC Number: 5.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKC2
    Expression System Strain: NCM533
    Expression System Taxid: 562
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 285
    Synonym: KSI, 3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ISK)

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1SIAUNKNOWNTYR A:14 , ASP A:38 , ASP A:99 , PHE A:101TYR A14 AND ASP A99 BOTH STABILIZE THE INTERMEDIATE BY FORMING HYDROGEN-BOND TO IT. ASP A38 TRANSFERS PROTON FROM C-4B TO C-6B.
2SIBUNKNOWNTYR B:14 , ASP B:38 , ASP B:99 , PHE B:101TYR B14 AND ASP B99 BOTH STABILIZE THE INTERMEDIATE BY FORMING HYDROGEN-BOND TO IT. ASP B38 TRANSFERS PROTON FROM C-4B TO C-6B.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asp A:38 -Pro A:39
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asp B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ISK)

(-) Sequences/Alignments

NMR Structure
   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:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1iska_ A: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1iskA00 A:1-125  [code=3.10.450.50, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee.......eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1isk A   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1iskb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1iskB00 B:1-125  [code=3.10.450.50, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee.......eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1isk B   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 2)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A,B   (SDIS_COMTE | P00947)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004769    steroid delta-isomerase activity    Catalysis of the reaction: a 3-oxo-delta(5)-steroid = a 3-oxo-delta(4)-steroid.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 1isk)
 
  Sites
    SIA  [ RasMol ]  +environment [ RasMol ]
    SIB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:38 - Pro A:39   [ RasMol ]  
    Asp B:38 - Pro B:39   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  1isk
    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
  SDIS_COMTE | P00947
    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)
  5.3.3.1
    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
  SDIS_COMTE | P00947
    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
        SDIS_COMTE | P00947: 1buq 1ocv 1ogz 1ohp 1ohs 1qjg 3m8c 3mhe 3mki 3myt 3nbr 3nhx 3nm2 3nuv 3nxj 3ov4 3t8u 3unl 4l7k 5dre 8cho

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ISK)