Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - 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)

(-) Description

Title :  STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH A CDP DERIVED FLUORESCENT INHIBITOR
 
Authors :  C. M. Crane, J. Kaiser, N. L. Ramsden, S. Lauw, F. Rohdich, E. Wolfgang, W. N. Hunter, A. Bacher, F. Diederich
Date :  11 May 06  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Isoprenoid, Lyase, Isoprene Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Crane, J. Kaiser, N. L. Ramsden, S. Lauw, F. Rohdich, W. Eisenreich, W. N. Hunter, A. Bacher, F. Diederich
Fluorescent Inhibitors For Ispf, An Enzyme In The Non-Mevalonate Pathway For Isoprenoid Biosynthesis And A Potential Target For Antimalarial Therapy.
Angew. Chem. Int. Ed. Engl. V. 45 1069 2006
PubMed-ID: 16392111  |  Reference-DOI: 10.1002/ANIE.200503003

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ISPF, MECS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
12AA1Ligand/Ion5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT
2GPP1Ligand/IonGERANYL DIPHOSPHATE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
12AA3Ligand/Ion5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT
2GPP3Ligand/IonGERANYL DIPHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , HIS A:42 , 2AA A:901BINDING SITE FOR RESIDUE ZN A 900
2AC2SOFTWAREASP A:8 , HIS A:10 , SER A:35 , ASP A:56 , GLY A:58 , PHE A:61 , ALA A:71 , ASP A:72 , SER A:73 , GLU A:75 , LEU A:76 , ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , ZN A:900 , HOH A:908 , HOH A:934BINDING SITE FOR RESIDUE 2AA A 901
3AC3SOFTWAREPHE A:7 , THR A:134 , GLY A:138 , PHE A:139 , THR A:140 , ARG A:142 , GLU A:149BINDING SITE FOR RESIDUE GPP A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GZL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:16 -Pro A:17
2Ala A:102 -Pro A:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GZL)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ECOLI35-50  1A:35-50
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ECOLI35-50  3A:35-50

(-) Exons   (0, 0)

(no "Exon" information available for 2GZL)

(-) 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:159
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                              1                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148         
           ISPF_ECOLI     - --MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKA 157
               SCOP domains d2gzla_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                            SCOP domains
               CATH domains 2gzlA00 A:-1-157  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee......eee..eee............hhhhhhhhhhhhhhh...hhhhhh..hhhhh...hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gzl A  -1 LEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKA 157
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GZL)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPF_ECOLI | P62617)
molecular function
    GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
    GO:0006744    ubiquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

 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
    2AA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GPP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:102 - Pro A:103   [ RasMol ]  
    Gly A:16 - Pro A:17   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  2gzl
    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
  ISPF_ECOLI | P62617
    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)
  4.6.1.12
    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
  ISPF_ECOLI | P62617
    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
        ISPF_ECOLI | P62617: 1gx1 1h47 1h48 1jy8 1knj 1knk 1u3l 1u3p 1u40 1u43 1yqn 2amt 3elc 3eor 3ern 3esj 3fba

(-) Related Entries Specified in the PDB File

1gx1 THE SAME PROTEIN COMPLEXED WITH CDP
1knj THE SAME PROTEIN COMPLEXED WITH C5P AND CDI
1u3p THE SAME PROTEIN BUT NATIVE
2amt THE SAME PROTEIN COMPLEXED WITH A CDP DERIVED FLUORESCENT INHIBITOR