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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE HUMAN LIPOCALIN PGDS IN COMPLEX WITH SUBSTRATE ANALOG U44069
 
Authors :  S. M. Lim, D. Chen, H. Teo, A. Roos, T. Nyman, L. Tresaugues, K. Pervushin P. Nordlund
Date :  03 Jan 13  (Deposition) - 20 Mar 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Isomerase, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Lim, D. Chen, H. Teo, A. Roos, A. E. Jansson, T. Nyman, L. Tresaugues, K. Pervushin, P. Nordlund
Structural And Dynamic Insights Into Substrate Binding And Catalysis Of Human Lipocalin Prostaglandin D Synthase.
J. Lipid Res. V. 54 1630 2013
PubMed-ID: 23526831  |  Reference-DOI: 10.1194/JLR.M035410

(-) Compounds

Molecule 1 - LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE
    Chains: A
    EC Number: 5.3.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH4
    Expression System Strain: ROSETTA BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDS, PTGDS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-TRACE PROTEIN, CEREBRIN-28, GLUTATHIONE-INDEPENDENT PGD SYNTHASE, PROSTAGLANDIN-H2 D-ISOMERASE, PROSTAGLANDIN-D2 SYNTHASE, PGD2 SYNTHASE, PGDS, PGDS2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PWZ2Ligand/Ion(5E)-7-{(1R,4S,5S,6R)-5-[(1E,3S)-3-HYDROXYOCT-1-EN-1-YL]-2-OXABICYCLO[2.2.1]HEPT-6-YL}HEPT-5-ENOIC ACID
2SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:42 , TRP A:54 , LYS A:66 , VAL A:68 , THR A:80 , TRP A:112 , TYR A:116 , PRO A:139 , GLY A:140 , PHE A:143BINDING SITE FOR RESIDUE PWZ A 201
2AC2SOFTWARESER A:45 , SER A:67 , SER A:81 , TYR A:107 , SER A:109 , TRP A:112 , TYR A:149 , SCN A:203 , HOH A:317 , HOH A:327 , HOH A:382BINDING SITE FOR RESIDUE PWZ A 202
3AC3SOFTWAREGLN A:36 , ASP A:37 , ARG A:85 , PWZ A:202BINDING SITE FOR RESIDUE SCN A 203
4AC4SOFTWAREPRO A:32 , TYR A:128 , LEU A:159 , LYS A:162 , HOH A:350BINDING SITE FOR RESIDUE SCN A 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMO)

(-) 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    
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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:155
                                                                                                                                                                                           
               SCOP domains d4imoa_ A: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhheeeeeeeeee.hhhhhhh......eeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeeeee....eeeeeeeeee....eeeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhh..hhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imo A  28 VSVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVAPATDGGLNLTSTFLRKNQCETRTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPGEDFRMATLYSRTQTPRAELKEKFTAFCKAQGFTEDTIVFLPQ 182
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  PTGDS_HUMAN | P41222
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTGDS_HUMAN | P41222: 2wwp 3o19 3o22 3o2y 4imn 4orr 4ors 4oru 4orw 4orx 4ory 4os0 4os3 4os8 5wy9

(-) Related Entries Specified in the PDB File

4imn CRYSTAL STRUCTURE OF WILD TYPE HUMAN LIPOCALIN PGDS BOUND WITH PEG