Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  INHIBITORS OF THE HERBICIDAL TARGET ISPD
 
Authors :  H. W. Hoeffken
Date :  11 Mar 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Non-Mevalonate-Pathway, Herbicide, Allosteric Pocket (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Witschel, H. W. Hoeffken, M. Seet, L. Parra, T. Mietzner, F. Thater, R. Niggeweg, F. Rohl, B. Illarionov, F. Rohdich, J. Kaiser, M. Fischer, A. Bacher, F. Diederich
Inhibitors Of The Herbicidal Target Ispd: Allosteric Site Binding.
Angew. Chem. Int. Ed. Engl. V. 50 7931 2011
PubMed-ID: 21766403  |  Reference-DOI: 10.1002/ANIE.201102281
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
    Chains: A
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO113
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Variant: PREP4
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 76-302
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, ATMECT, ATMEPCT, MCT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
16BC1Ligand/Ion5-CHLORO-7-HYDROXY-6-(PHENYLMETHYL)PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2ACT2Ligand/IonACETATE ION
3CD3Ligand/IonCADMIUM ION
4CU3Ligand/IonCOPPER (II) ION
5MG1Ligand/IonMAGNESIUM ION
6NA1Ligand/IonSODIUM ION
7ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
16BC2Ligand/Ion5-CHLORO-7-HYDROXY-6-(PHENYLMETHYL)PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2ACT4Ligand/IonACETATE ION
3CD-1Ligand/IonCADMIUM ION
4CU-1Ligand/IonCOPPER (II) ION
5MG-1Ligand/IonMAGNESIUM ION
6NA-1Ligand/IonSODIUM ION
7ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:157 , GLN A:158 , ILE A:177 , ALA A:203 , GLN A:238 , VAL A:239 , VAL A:259 , ASP A:261 , ASP A:262 , VAL A:263 , SER A:264 , ILE A:265 , VAL A:266BINDING SITE FOR RESIDUE 6BC A1300
02AC2SOFTWARELYS A:123 , GLU A:141 , ASP A:147 , HOH A:2044 , HOH A:2050 , HOH A:2070BINDING SITE FOR RESIDUE CU A1301
03AC3SOFTWARELYS A:123 , GLU A:141 , ASP A:147 , HOH A:2044 , HOH A:2050 , HOH A:2070BINDING SITE FOR RESIDUE CU A1302
04AC4SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , ACT A:1307BINDING SITE FOR RESIDUE MG A1303
05AC5SOFTWAREGLU A:167 , HOH A:2065 , HOH A:2066BINDING SITE FOR RESIDUE CD A1304
06AC6SOFTWAREASP A:290 , HOH A:2156 , HOH A:2158BINDING SITE FOR RESIDUE CU A1305
07AC7SOFTWARELEU A:292 , GLU A:295 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE ACT A1306
08AC8SOFTWAREPRO A:120 , GLU A:121 , GLU A:191 , LEU A:244 , HIS A:271 , MG A:1303 , ZN A:1310 , HOH A:2084 , HOH A:2161 , HOH A:2162BINDING SITE FOR RESIDUE ACT A1307
09AC9SOFTWARELYS A:214 , ASP A:261 , GLU A:267 , HOH A:2120 , HOH A:2138BINDING SITE FOR RESIDUE CD A1308
10BC1SOFTWAREASP A:135BINDING SITE FOR RESIDUE NA A1309
11BC2SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , ACT A:1307BINDING SITE FOR RESIDUE ZN A1310
12BC3SOFTWAREGLU A:138 , GLU A:141 , ASP A:169 , ASN A:171 , HOH A:2036 , HOH A:2045BINDING SITE FOR RESIDUE CD A1311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YC5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YC5)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_ARATH175-182  1A:175-182
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_ARATH175-182  2A:175-182

(-) Exons   (0, 0)

(no "Exon" information available for 2YC5)

(-) 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:217
 aligned with ISPD_ARATH | P69834 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:225
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
           ISPD_ARATH    75 KEKSVSVILLAGGQGKRMKMSMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILS 299
               SCOP domains d2yc5a_ A: 4        -diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..--------..hhhh.ee..eehhhhhhhhhhhh..eeeeeee.hhhhhhhhhh.......eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee.......................eeeeeeeeehhhhhhhhhhhhhhhh......hhhhhh.....eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------ISPD    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc5 A  75 MEKSVSVILLAG--------SMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILS 299
                                    84 |       -|      104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
                                      86       95
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YC5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPD_ARATH | P69834)
molecular function
    GO:0050518    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 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
    6BC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:236 - Pro A:237   [ 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
  2yc5
    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
  ISPD_ARATH | P69834
    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)
  2.7.7.60
    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
  ISPD_ARATH | P69834
    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
        ISPD_ARATH | P69834: 1w77 2yc3 2ycm 4nai 4nak 4nal 4nan

(-) Related Entries Specified in the PDB File

1w77 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE (ISPD) FROM ARABIDOPSIS THALIANA
2yc3 INHIBITORS OF THE HERBICIDAL TARGET ISPD
2ycm INHIBITORS OF HERBICIDAL TARGET ISPD