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

(-) Description

Title :  CRYSTAL STRUCTURE OF UPPS IN COMPLEX WITH FPP AND AN ALLOSTERIC INHIBITOR
 
Authors :  S. Liu, X. Qiu
Date :  01 May 14  (Deposition) - 15 Oct 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Undecaprenyl Diphosphate Synthase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Danley, E. T. Baima, M. Mansour, K. F. Fennell, B. A. Chrunyk, J. P. Mueller, S. Liu, X. Qiu
Discovery And Structural Characterization Of An Allosteric Inhibitor Of Bacterial Cis-Prenyltransferase.
Protein Sci. V. 24 20 2015
PubMed-ID: 25287857  |  Reference-DOI: 10.1002/PRO.2579

(-) Compounds

Molecule 1 - ISOPRENYL TRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, SPR0240
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: ATCC BAA-255 / R6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
12ZW2Ligand/Ion3-(2-CHLOROPHENYL)-5-METHYL-N-[4-(PROPAN-2-YL)PHENYL]-1,2-OXAZOLE-4-CARBOXAMIDE
2CD15Ligand/IonCADMIUM ION
3FPP2Ligand/IonFARNESYL DIPHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:49 , GLN A:53 , ALA A:71 , ILE A:87 , PRO A:91 , TYR A:98 , VAL A:99 , LEU A:102 , ALA A:129 , PHE A:143 , FPP A:302BINDING SITE FOR RESIDUE 2ZW A 301
02AC2SOFTWAREMET A:27 , ASP A:28 , GLY A:29 , ASN A:30 , GLY A:31 , ARG A:32 , ARG A:41 , HIS A:45 , LEU A:52 , ALA A:71 , ARG A:79 , ILE A:87 , 2ZW A:301 , CD A:303 , HOH A:494BINDING SITE FOR RESIDUE FPP A 302
03AC3SOFTWAREASP A:28 , FPP A:302 , HOH A:404 , HOH A:419 , HOH A:433BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWAREGLU A:114 , ASP A:116 , HOH A:403 , ASP B:81BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWAREGLU A:176 , HOH A:406 , HOH A:408 , HOH B:404BINDING SITE FOR RESIDUE CD A 305
06AC6SOFTWAREASP A:191 , HOH A:451 , HOH A:459 , HOH A:478BINDING SITE FOR RESIDUE CD A 306
07AC7SOFTWAREASP A:96 , HOH A:588 , HOH A:596 , HOH A:599BINDING SITE FOR RESIDUE CD A 307
08AC8SOFTWAREGLU A:50BINDING SITE FOR RESIDUE CD A 308
09AC9SOFTWAREGLU A:204 , HOH A:552BINDING SITE FOR RESIDUE CD A 309
10BC1SOFTWAREGLU A:101BINDING SITE FOR RESIDUE CD A 310
11BC2SOFTWAREASP A:163 , HOH A:541 , HOH A:561BINDING SITE FOR RESIDUE CD A 311
12BC3SOFTWAREMET B:49 , GLN B:53 , ALA B:71 , ILE B:87 , PRO B:91 , TYR B:98 , VAL B:99 , LEU B:102 , ALA B:129 , PHE B:143 , FPP B:302BINDING SITE FOR RESIDUE 2ZW B 301
13BC4SOFTWAREMET B:27 , ASP B:28 , GLY B:29 , ASN B:30 , GLY B:31 , ARG B:32 , ARG B:41 , HIS B:45 , ALA B:71 , ARG B:79 , ILE B:87 , 2ZW B:301 , CD B:303 , HOH B:439 , HOH B:507BINDING SITE FOR RESIDUE FPP B 302
14BC5SOFTWAREASP B:28 , FPP B:302 , HOH B:420 , HOH B:436 , HOH B:439BINDING SITE FOR RESIDUE CD B 303
15BC6SOFTWAREASP B:191 , HOH B:409 , HOH B:412 , HOH B:606BINDING SITE FOR RESIDUE CD B 304
16BC7SOFTWAREGLU B:75 , HOH B:407 , HOH B:421 , HOH B:490BINDING SITE FOR RESIDUE CD B 305
17BC8SOFTWAREHOH A:401 , GLU B:176 , HOH B:581BINDING SITE FOR RESIDUE CD B 306
18BC9SOFTWAREHIS A:246 , GLU B:204 , HOH B:479 , HOH B:531BINDING SITE FOR RESIDUE CD B 307
19CC1SOFTWAREASP B:163 , HOH B:518 , HOH B:534 , HOH B:538BINDING SITE FOR RESIDUE CD B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q9M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q9M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q9M)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q9M)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..................eeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q9m A  17 TQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENWTRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRH 246
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..................eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q9m B  18 QVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENWTRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRR 245
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237
   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  (0, 0)

(no "SCOP Domain" information available for 4Q9M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q9M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q9M)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    2ZW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FPP  [ 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 ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4q9m)
 

(-) 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
  4q9m
    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
  ISPT_STRR6 | Q8DRB3
    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)
  2.5.1.-
    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
  ISPT_STRR6 | Q8DRB3
    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
        ISPT_STRR6 | Q8DRB3: 4q9o

(-) Related Entries Specified in the PDB File

4q9o