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(-) Description

Title :  EXPLOITATION OF A NOVEL BINDING POCKET IN HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 (LP-PLA2) DISCOVERED THROUGH X-RAY FRAGMENT SCREENING
 
Authors :  P. J. Day
Date :  12 Apr 16  (Deposition) - 25 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipase, Lipid Metabolism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Woolford, J. E. Pero, S. Aravapalli, V. Berdini, J. E. Coyle, P. J. Day, A. M. Dodson, P. Grondin, F. P. Holding, L. Y. Lee, P. Li, E. S. Manas, J. Marino, A. C. Martin, B. W. Mccleland, R. L. Mcmenamin, C. W. Murray, C. E. Neipp, L. W. Page, V. K. Patel, F. Potvain, S. Rich, R. A. Rivero, K. Smith, D. O. Somers, L. Trottet, R. Velagaleti, G. Williams, R. Xie
Exploitation Of A Novel Binding Pocket In Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovere Through X-Ray Fragment Screening.
J. Med. Chem. V. 59 5356 2016
PubMed-ID: 27167608  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00212

(-) Compounds

Molecule 1 - PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
    Chains: A
    EC Number: 3.1.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PLA2G7, PAFAH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAF ACETYLHYDROLASE,1-ALKYL-2-ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE,2-ACETYL-1-ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE,GROUP-VIIA PHOSPHOLIPASE A2,GVIIA-PLA2,LDL-ASSOCIATED PHOSPHOLIPASE A2,LDL- PLA(2),PAF 2-ACYLHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
16HP1Ligand/Ion1,3-DIMETHYL-6-(2-METHYLPROPOXY)PYRIMIDINE-2,4(1H,3H)-DIONE
2CA1Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:351binding site for residue CL A 501
2AC2SOFTWAREARG A:92 , LEU A:93 , PRO A:325 , ALA A:326binding site for residue CL A 502
3AC3SOFTWAREGLU A:285 , HOH A:678 , HOH A:719binding site for residue CA A 503
4AC4SOFTWAREASP A:89 , LEU A:153 , GLU A:214 , SER A:273 , TRP A:298 , PHE A:322 , HOH A:626binding site for residue 6HP A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JAN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:72 -Asp A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JAN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JAN)

(-) Exons   (0, 0)

(no "Exon" information available for 5JAN)

(-) 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:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee......eeeeeeeee......eee...hhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee.......hhhhh......eeeeee....hhhhhhhhhhh......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jan A  55 KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JAN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JAN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JAN)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Phe A:72 - Asp A:73   [ RasMol ]  
 

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  5jan
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  PAFA_HUMAN | Q13093
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAFA_HUMAN | Q13093: 3d59 3d5e 3f96 3f97 3f98 3f9c 5i8p 5i9i 5jad 5jah 5jal 5jao 5jap 5jar 5jas 5jat 5jau 5lp1 5lyy 5lz2 5lz4 5lz5 5lz7 5lz8 5lz9

(-) Related Entries Specified in the PDB File

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