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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF APO PROSTAGLANDIN F SYNTHASE FROM LEISHMANIA MAJOR FRIEDLIN
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 May 12  (Deposition) - 13 Jun 12  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. O. Moen, J. W. Fairman, S. R. Barnes, A. Sullivan, S. Nakazawa-Hewitt, W. C. Van Voorhis, B. L. Staker, D. D. Lorimer, P. J. Myler, T. E. Edwards
Structures Of Prostaglandin F Synthase From The Protozoa Leishmania Major And Trypanosoma Cruzi With Nadp.
Acta Crystallogr F Struct V. 71 609 2015 Biol Commun
PubMed-ID: 25945716  |  Reference-DOI: 10.1107/S2053230X15006883

(-) Compounds

Molecule 1 - PROSTAGLANDIN F2-ALPHA SYNTHASE/D-ARABINOSE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.188
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PGFS, LMJF_31_2150
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: FRIEDLIN
    Synonym: PROSTAGLANDIN F SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2CL1Ligand/IonCHLORIDE ION
3EDO18Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:14 , LYS A:16 , TRP A:25 , GLN A:26 , EDO A:303 , EDO A:305 , EDO A:308 , HOH A:414 , HOH A:449 , HOH A:476 , HOH A:492 , HOH A:596 , HOH A:620BINDING SITE FOR RESIDUE CIT A 301
02AC2SOFTWAREPRO A:18 , GLU A:72 , ASP A:73 , HOH A:450 , HOH A:526 , HOH A:698BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREGLY A:14 , LYS A:16 , TRP A:25 , PRO A:277 , CIT A:301 , HOH A:492 , HOH A:630BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREASP A:118 , CYS A:163 , THR A:164 , THR A:166 , GLN A:283 , HOH A:677BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREASN A:13 , GLY A:14 , VAL A:15 , TRP A:81 , PHE A:284 , CIT A:301 , HOH A:492 , HOH A:568BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREHIS A:154 , GLU A:157 , ASP A:158 , HOH A:446 , HOH A:474BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREALA A:52 , TRP A:81 , GLU A:84 , HOH A:438 , HOH A:506BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWARETRP A:25 , TYR A:54 , HIS A:112 , ASN A:150 , TRP A:197 , CIT A:301 , HOH A:473BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWARETYR A:138 , LYS A:141 , HOH A:523 , HOH A:534 , HOH A:559 , HOH A:588 , HOH A:629BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARESER A:198 , PRO A:199 , LEU A:200 , GLY A:201 , PRO A:239 , LYS A:240BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREALA A:260 , GLU A:261 , HOH A:462BINDING SITE FOR RESIDUE CL A 311
12BC3SOFTWAREGLY B:14 , LYS B:16 , TRP B:25 , GLN B:26 , EDO B:302 , EDO B:307 , HOH B:422 , HOH B:442 , HOH B:478 , HOH B:499 , HOH B:669 , HOH B:698BINDING SITE FOR RESIDUE CIT B 301
13BC4SOFTWAREGLY B:14 , LYS B:16 , TRP B:25 , PRO B:277 , CIT B:301 , HOH B:601 , HOH B:698BINDING SITE FOR RESIDUE EDO B 302
14BC5SOFTWAREGLU B:72 , HOH B:446 , HOH B:525 , HOH B:568 , HOH B:694BINDING SITE FOR RESIDUE EDO B 303
15BC6SOFTWAREASN B:13 , GLY B:14 , TRP B:81 , PHE B:284 , HOH B:517 , HOH B:636 , HOH B:698 , HOH B:720BINDING SITE FOR RESIDUE EDO B 304
16BC7SOFTWARETYR B:138 , HOH B:475 , HOH B:479 , HOH B:490 , HOH B:560 , HOH B:585BINDING SITE FOR RESIDUE EDO B 305
17BC8SOFTWARELYS B:240 , SER B:241 , VAL B:242 , HIS B:243BINDING SITE FOR RESIDUE EDO B 306
18BC9SOFTWARETRP B:25 , TYR B:54 , HIS B:112 , ASN B:150 , TRP B:197 , CIT B:301 , HOH B:465BINDING SITE FOR RESIDUE EDO B 307
19CC1SOFTWARETHR B:271 , SER B:273 , HOH B:489 , HOH B:686BINDING SITE FOR RESIDUE EDO B 308
20CC2SOFTWAREARG B:228 , PHE B:254BINDING SITE FOR RESIDUE EDO B 309
21CC3SOFTWAREALA B:52 , TRP B:81 , GLU B:84 , HOH B:421BINDING SITE FOR RESIDUE EDO B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F40)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F40)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F40)

(-) Exons   (0, 0)

(no "Exon" information available for 4F40)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4f40a_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....eee...ee......hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.......eeeee......hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f40 A   3 GVDKAMVTLSNGVKMPQFGLGVWQSPAGEVTENAVKWALCAGYRHIDTAAIYKNEESVGAGLRASGVPREDVFITTKLWNTEQGYESTLAAFEESRQKLGVDYIDLYLIHWPRGKDILSKEGKKYLDSWRAFEQLYKEKKVRAIGVSNFHIHHLEDVLAMCTVTPMVNQVELHPLNNQADLRAFCDAKQIKVEAWSPLGKLLSNPILSAIGAKYNKTAAQVILRWNIQKNLITIPKSVHRERIEENADIFDFELGAEDVMSIDALNTNSRYGPDPDEAQF 284
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       204       214       224       234       244       254       264       274       284
                                                                                                                                                                                                                                201|                                                                                
                                                                                                                                                                                                                                 204                                                                                


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4f40b_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....eee...ee......hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.......eeeee......hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f40 B   3 GVDKAMVTLSNGVKMPQFGLGVWQSPAGEVTENAVKWALCAGYRHIDTAAIYKNEESVGAGLRASGVPREDVFITTKLWNTEQGYESTLAAFEESRQKLGVDYIDLYLIHWPRGKDILSKEGKKYLDSWRAFEQLYKEKKVRAIGVSNFHIHHLEDVLAMCTVTPMVNQVELHPLNNQADLRAFCDAKQIKVEAWSPLGKLLSNPILSAIGAKYNKTAAQVILRWNIQKNLITIPKSVHRERIEENADIFDFELGAEDVMSIDALNTNSRYGPDPDEAQF 284
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       204       214       224       234       244       254       264       274       284
                                                                                                                                                                                                                                201|                                                                                
                                                                                                                                                                                                                                 204
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F40)

(-) Gene Ontology  (11, 11)

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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4f40)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4f40
    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
  PGFS_LEIMA | P22045
    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)
  1.1.1.188
    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
  PGFS_LEIMA | P22045
    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
        PGFS_LEIMA | P22045: 4g5d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4F40)