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 :  T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH HOMORISEDRONATE BPH-6
 
Authors :  R. Cao, Y. -L. Liu, E. Oldfield
Date :  09 Dec 14  (Deposition) - 15 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. L. Liu, R. Cao, Y. Wang, E. Oldfield
Farnesyl Diphosphate Synthase Inhibitors With Unique Ligand-Binding Geometries.
Acs Med Chem Lett V. 6 349 2015
PubMed-ID: 25815158  |  Reference-DOI: 10.1021/ML500528X

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1HRX4Ligand/Ion[1-HYDROXY-3-(PYRIDIN-3-YL)PROPANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
2MG8Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:103 , ASP A:107 , ARG A:112 , GLN A:172 , LYS A:212 , TYR A:216 , MG A:402 , MG A:403 , MG A:404 , HRX A:405 , HOH A:577BINDING SITE FOR RESIDUE HRX A 401
02AC2SOFTWAREASP A:103 , ASP A:107 , HRX A:401 , MG A:403BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWAREASP A:103 , ASP A:107 , HRX A:401 , MG A:402BINDING SITE FOR RESIDUE MG A 403
04AC4SOFTWAREHRX A:401 , HRX A:405BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWAREPHE A:251 , GLN A:252 , ASP A:255 , LYS A:269 , HRX A:401 , MG A:404 , MG A:406BINDING SITE FOR RESIDUE HRX A 405
06AC6SOFTWAREASP A:255 , HRX A:405BINDING SITE FOR RESIDUE MG A 406
07AC7SOFTWARETYR B:99 , ASP B:103 , ASP B:107 , ARG B:112 , THR B:168 , GLN B:172 , LYS B:212 , TYR B:216 , MG B:402 , MG B:403 , MG B:404 , HRX B:405 , HOH B:522 , HOH B:548BINDING SITE FOR RESIDUE HRX B 401
08AC8SOFTWAREASP B:103 , ASP B:107 , HRX B:401 , MG B:403 , HOH B:548BINDING SITE FOR RESIDUE MG B 402
09AC9SOFTWAREASP B:103 , ASP B:107 , HRX B:401 , MG B:402 , HOH B:568BINDING SITE FOR RESIDUE MG B 403
10BC1SOFTWAREHRX B:401 , HRX B:405BINDING SITE FOR RESIDUE MG B 404
11BC2SOFTWAREPHE B:251 , GLN B:252 , ASP B:255 , LYS B:269 , HRX B:401 , MG B:404 , MG B:406 , HOH B:560BINDING SITE FOR RESIDUE HRX B 405
12BC3SOFTWAREASP B:255 , HRX B:405 , HOH B:565BINDING SITE FOR RESIDUE MG B 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RXC)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxc A   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPRLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKR 365
                                    10        20        30        40        50        60 ||     81        91       101       111       121       131       141       151       161       171       181       191||     203       213       223       233       243       253       263||     274       284       294       304       314       324       334       344       354       364 
                                                                                        62|                                                                                                                   192|                                                                  264|                                                                                                   
                                                                                         74                                                                                                                    195                                                                   266                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxc B   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKR 365
                                    10        20        30        40        50        60  ||    80        90       100       110       120       130       140       150       160       170       180       190 ||    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363  
                                                                                         63|                                                                                                                   192|                                                                                                                                                                         
                                                                                          74                                                                                                                    196
   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 4RXC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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
    HRX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
(no "Cis Peptide Bonds" information available for 4rxc)
 

(-) 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
  4rxc
    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
  Q86C09_9TRYP | Q86C09
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q86C09_9TRYP | Q86C09
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q86C09_9TRYP | Q86C09: 2ewg 2i19 2ogd 2p1c 3dyf 3dyg 3dyh 3efq 3egt 4rxd 4rxe 4ryp 5ael 5afx 5ahu

(-) Related Entries Specified in the PDB File

4rxd