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 :  ARABIDOPSIS THALIANA ISPD IN COMPLEX WITH TRIBROMODICHLORO-PSEUDILIN
 
Authors :  A. Kunfermann, M. Witschel, B. Illarionov, R. Martin, M. Rottmann, H. W M. Seet, W. Eisenreich, H. -J. Knolker, M. Fischer, A. Bacher, M. Groll F. Diederich
Date :  22 Oct 13  (Deposition) - 29 Jan 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Herbicide, Anti-Infectives, Pseudilin, Natural Product, Drug Discovery, Allosteric Inhibition, Rossmann Fold, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kunfermann, M. Witschel, B. Illarionov, R. Martin, M. Rottmann, H. W. Hoffken, M. Seet, W. Eisenreich, H. J. Knolker, M. Fischer, A. Bacher, M. Groll, F. Diederich
Pseudilins: Halogenated, Allosteric Inhibitors Of The Non-Mevalonate Pathway Enzyme Ispd.
Angew. Chem. Int. Ed. Engl. V. 53 2235 2014
PubMed-ID: 24446431  |  Reference-DOI: 10.1002/ANIE.201309557

(-) 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: 1007065
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 76-302
    Gene: AT2G02500, ISPD, MCT, MECT, MEPCT, T8K22.20
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS, THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, ATMECT, ATMEPCT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CD5Ligand/IonCADMIUM ION
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3H701Ligand/Ion2,4-DICHLORO-6-(3,4,5-TRIBROMO-1H-PYRROL-2-YL)PHENOL
4K7Ligand/IonPOTASSIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3H702Ligand/Ion2,4-DICHLORO-6-(3,4,5-TRIBROMO-1H-PYRROL-2-YL)PHENOL
4K-1Ligand/IonPOTASSIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:203 , LYS A:214 , GLN A:238 , VAL A:239 , LEU A:245 , SER A:264 , ILE A:265 , VAL A:266 , CD A:403 , HOH A:516 , HOH A:555BINDING SITE FOR RESIDUE H70 A 401
02AC2SOFTWARELYS A:195 , ASP A:196 , ALA A:199 , VAL A:200 , TYR A:274 , K A:409BINDING SITE FOR RESIDUE DTT A 402
03AC3SOFTWAREGLN A:238 , H70 A:401 , HOH A:552BINDING SITE FOR RESIDUE CD A 403
04AC4SOFTWAREGLU A:167 , HOH A:510 , HOH A:548BINDING SITE FOR RESIDUE CD A 404
05AC5SOFTWAREASP A:261 , HOH A:511 , HOH A:517 , HOH A:519 , HOH A:551 , HOH A:552BINDING SITE FOR RESIDUE CD A 405
06AC6SOFTWARELYS A:123 , GLU A:138 , GLU A:141 , ASP A:169 , HOH A:546BINDING SITE FOR RESIDUE CD A 406
07AC7SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:502BINDING SITE FOR RESIDUE CD A 407
08AC8SOFTWAREASP A:290BINDING SITE FOR RESIDUE K A 408
09AC9SOFTWAREDTT A:402 , HOH A:549BINDING SITE FOR RESIDUE K A 409
10BC1SOFTWAREARG A:182 , PRO A:183 , LEU A:184 , ASN A:282 , ILE A:283BINDING SITE FOR RESIDUE K A 410
11BC2SOFTWAREILE A:108 , ALA A:109 , SER A:112 , SER A:180 , PRO A:183BINDING SITE FOR RESIDUE K A 411
12BC3SOFTWARELYS A:77 , SER A:117 , MET A:119 , VAL A:122 , ASP A:145 , VAL A:146BINDING SITE FOR RESIDUE K A 412
13BC4SOFTWAREASN A:186 , ASP A:189 , HOH A:501 , HOH A:509BINDING SITE FOR RESIDUE K A 413
14BC5SOFTWAREGLU A:141 , ASP A:147 , HOH A:507BINDING SITE FOR RESIDUE K A 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NAL)

(-) 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 4NAL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NAL)

(-) Exons   (0, 0)

(no "Exon" information available for 4NAL)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d4nala_ 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..ee.hhhhhhhhhh...eeeeeee.hhhhhhhhhh.......eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee...................eeeeeeeeehhhhhhhhhhhhhhhh.......hhhhhh....eeee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nal A  75 MEKSVSVILLAGGPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
                                    84  ||   103       113       123       133       143       153       163       173       183       193       203       213       223 ||    237       247       257       267       277       287       297   
                                       87|                                                                                                                             225|                                                                      
                                        97                                                                                                                              230
   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 4NAL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NAL)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H70  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ 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 ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ 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
  4nal
    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 2yc5 2ycm 4nai 4nak 4nan

(-) Related Entries Specified in the PDB File

1ini STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRITOL SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOPRENOID BIOSYNTHESIS.
1w77 THE CRYSTAL STRUCTURE OF A PLANT 2C-METHYL-D-ERYTHRITOL 4- PHOSPHATE CYTIDYLYLTRANSFERASE EXHIBITS A DISTINCT QUATERNARY STRUCTURE COMPARED TO BACTERIAL HOMOLOGUES AND A POSSIBLE ROLE IN FEEDBACK REGULATION FOR CYTIDINE MONOPHOSPHATE.
2yc5 INHIBITORS OF THE HERBICIDAL TARGET ISPD: ALLOSTERIC SITE BINDING.
4nai 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
4nak
4nan