Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-VINYLGLYCINE FE COMPLEX)
 
Authors :  J. M. Elkins, P. J. Rutledge, N. I. Burzlaff, I. J. Clifton, R. M. Adlingt P. L. Roach, J. E. Baldwin
Date :  19 Feb 03  (Deposition) - 19 Jun 03  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Antibiotic Biosynthesis, B-Lactam Antibiotic, Oxygenase, Penicillin Biosynthesis, Oxidoreductase, Iron (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Elkins, P. J. Rutledge, N. I. Burzlaff, I. J. Clifton, R. M. Adlington, P. L. Roach, J. E. Baldwin
Crystallographic Studies On The Reaction Of Isopenicillin N Synthase With An Unsaturated Substrate Analogue
Org. Biomol. Chem. V. 1 1455 2003
PubMed-ID: 12926272  |  Reference-DOI: 10.1039/B212270G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOPENICILLIN N SYNTHASE
    Chains: A
    EC Number: 1.21.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJB703
    Expression System Strain: NM554
    Expression System Taxid: 562
    Organism Scientific: EMERICELLA NIDULANS
    Organism Taxid: 162425
    Synonym: ISOPENICILLIN N SYNTHASE, IPNS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ASV1Ligand/IonDELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-VINYLGLYCINE
2FE21Ligand/IonFE (II) ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:53 , ASP A:140 , PHE A:141 , HOH A:2324 , HOH A:2336 , HOH A:2578 , HOH A:2579 , HOH A:2580 , HOH A:2581 , HOH A:2582 , HOH A:2583BINDING SITE FOR RESIDUE SO4 A1333
2AC2SOFTWAREASN A:262 , ASN A:263 , ARG A:300 , HOH A:2584BINDING SITE FOR RESIDUE SO4 A1334
3AC3SOFTWAREARG A:76 , GLN A:83 , HOH A:2203 , HOH A:2586BINDING SITE FOR RESIDUE SO4 A1335
4AC4SOFTWAREHIS A:214 , ASP A:216 , HIS A:270 , ASV A:1332 , HOH A:2427 , HOH A:2434BINDING SITE FOR RESIDUE FE2 A1336
5AC5SOFTWAREARG A:87 , TYR A:91 , SER A:183 , ILE A:187 , TYR A:189 , PHE A:211 , HIS A:214 , ASP A:216 , GLN A:225 , SER A:281 , PRO A:283 , PHE A:285 , FE2 A:1336 , HOH A:2434 , HOH A:2571 , HOH A:2572 , HOH A:2573 , HOH A:2574 , HOH A:2575 , HOH A:2576 , HOH A:2577BINDING SITE FOR RESIDUE ASV A1332

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:193 -Pro A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IPNS_1PS00185 Isopenicillin N synthase signature 1.IPNS_EMENI97-106  1A:97-106
2FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.IPNS_EMENI176-288  1A:176-288
3IPNS_2PS00186 Isopenicillin N synthase signature 2.IPNS_EMENI250-263  1A:250-263

(-) Exons   (0, 0)

(no "Exon" information available for 1ODM)

(-) 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:329
 aligned with IPNS_EMENI | P05326 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:329
                                    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       272       282       292       302       312       322         
           IPNS_EMENI     3 SVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
               SCOP domains d1odma_ A: Isopenicillin N synthase                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1odmA00 A:3-331 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------DIOX_N-1odmA02 A:9-132                                                                                                      ------------------------------------------------2OG-FeII_Oxy-1odmA01 A:181-288                                                                              ------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhh.hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..............eee.........eeeee........hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.......eeeeeee......hhhhhee.....eeeeeee.....eeeeee.....eeeee..eeee.......eeeeehhhhhhhh........eeee.....eeeeeeee.........................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------IPNS_1    ---------------------------------------------------------------------FE2OG_OXY  PDB: A:176-288 UniProt: 176-288                                                                       ------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IPNS_2        -------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1odm A   3 SVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
                                    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       272       282       292       302       312       322
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)
(-)
Clan: no clan defined [family: DIOX_N] (24)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IPNS_EMENI | P05326)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0016216    isopenicillin-N synthase activity    Catalysis of the reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O(2) = 2 H(2)O + isopenicillin N.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0042318    penicillin biosynthetic process    The chemical reactions and pathways resulting in the formation of any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

 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
    ASV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:193 - Pro A:194   [ 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
  1odm
    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
  IPNS_EMENI | P05326
    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)
  1.21.3.1
    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
  IPNS_EMENI | P05326
    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
        IPNS_EMENI | P05326: 1bk0 1blz 1hb1 1hb2 1hb3 1hb4 1ips 1obn 1oc1 1odn 1qiq 1qje 1qjf 1uzw 1w03 1w04 1w05 1w06 1w3v 1w3x 2bjs 2bu9 2ivi 2ivj 2jb4 2vau 2vbb 2vbd 2vbp 2vcm 2ve1 2wo7 2y60 2y6f 3zku 3zky 3zoi 4bb3

(-) Related Entries Specified in the PDB File

1bk0 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX)
1blz ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE-NO COMPLEX)
1hb1 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC ACOV FE COMPLEX)
1hb2 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1hb3 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1hb4 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1ips ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX)
1obn ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -AMINOBUTYRATE-FE- NO COMPLEX
1oc1 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -AMINOBUTYRATE-FE COMPLEX
1qiq ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACMC FE COMPLEX)
1qje ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (IPN - FE COMPLEX)
1qjf ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MONOCYCLIC SULFOXIDE - FE COMPLEX)