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 LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM, IPP AND CA2+
 
Authors :  S. Aripirala, S. Gabelli, L. M. Amzel
Date :  03 Apr 13  (Deposition) - 05 Mar 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Geranyl Transferase, Fpps, Farnesyl Pyrophosphate Synthase, Farnesyl Diphosphate Synthase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Aripirala, D. Gonzalez-Pacanowska, E. Oldfield, M. Kaiser, L. M. Amzel, S. B. Gabelli
Structural And Thermodynamic Basis Of The Inhibition Of Leishmania Major Farnesyl Diphosphate Synthase By Nitrogen-Containing Bisphosphonates.
Acta Crystallogr. , Sect. D V. 70 802 2014
PubMed-ID: 24598749  |  Reference-DOI: 10.1107/S1399004713033221

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.1, 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FPPS, LMJF_22_1360
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
14762Ligand/Ion3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM
2CA6Ligand/IonCALCIUM ION
3FME2Mod. Amino AcidN-FORMYLMETHIONINE
4IPE2Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:47 , LYS A:48 , ARG A:51 , GLN A:91 , ARG A:108 , THR A:208 , TYR A:211 , PHE A:246 , GLN A:247 , ASP A:250 , 476 A:402 , HOH A:509 , HOH A:513 , HOH A:533 , HOH A:551 , HOH A:553 , HOH A:573 , HOH A:597BINDING SITE FOR RESIDUE IPE A 401
02AC2SOFTWAREPHE A:94 , ASP A:98 , ASP A:102 , ARG A:107 , THR A:163 , GLN A:167 , LYS A:207 , THR A:208 , ASP A:250 , LYS A:264 , IPE A:401 , CA A:403 , CA A:404 , CA A:405 , HOH A:504 , HOH A:534 , HOH A:562 , ASN B:126BINDING SITE FOR RESIDUE 476 A 402
03AC3SOFTWAREASP A:98 , ASP A:102 , 476 A:402 , CA A:405 , HOH A:501 , HOH A:504 , HOH A:543BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREASP A:250 , 476 A:402 , HOH A:505 , HOH A:506 , HOH A:545BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREASP A:98 , ASP A:102 , 476 A:402 , CA A:403 , HOH A:502 , HOH A:503BINDING SITE FOR RESIDUE CA A 405
06AC6SOFTWAREGLY B:47 , LYS B:48 , ARG B:51 , GLN B:91 , ARG B:108 , THR B:208 , TYR B:211 , PHE B:246 , GLN B:247 , ASP B:250 , 476 B:402 , HOH B:509 , HOH B:512 , HOH B:528 , HOH B:539 , HOH B:560 , HOH B:563 , HOH B:584BINDING SITE FOR RESIDUE IPE B 401
07AC7SOFTWAREASN A:126 , PHE B:94 , ASP B:98 , ASP B:102 , ARG B:107 , GLN B:167 , LYS B:207 , THR B:208 , ASP B:250 , LYS B:264 , IPE B:401 , CA B:403 , CA B:404 , CA B:405 , HOH B:504 , HOH B:595 , HOH B:608BINDING SITE FOR RESIDUE 476 B 402
08AC8SOFTWAREASP B:98 , ASP B:102 , 476 B:402 , CA B:405 , HOH B:502 , HOH B:504 , HOH B:527BINDING SITE FOR RESIDUE CA B 403
09AC9SOFTWAREASP B:250 , 476 B:402 , HOH B:505 , HOH B:506 , HOH B:525BINDING SITE FOR RESIDUE CA B 404
10BC1SOFTWAREASP B:98 , ASP B:102 , 476 B:402 , CA B:403 , HOH B:503 , HOH B:790BINDING SITE FOR RESIDUE CA B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZX)

(-) 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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4jzxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzx A   1 mAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKLGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTYKRQK 362
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  
                            |                                                                                                                                                                                                                                                                                                                                                                         
                            1-FME                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4jzxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzx B   1 mAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKLGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTYKRQK 362
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  
                            1-FME
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    476  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jzx)
 

(-) 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
  4jzx
    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
  Q4QBL1_LEIMA | Q4QBL1
    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)
  2.5.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.5.1.10
    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
  Q4QBL1_LEIMA | Q4QBL1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4QBL1_LEIMA | Q4QBL1: 4jzb 4k10

(-) Related Entries Specified in the PDB File

4jzb LMFPPS IN COMPLEX WITH 30OB, IPP AND CA2+
4k10