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(-) Description

Title :  CRYSTAL STRUCTURE OF LP_PLA2 IN COMPLEX WITH DARAPLADIB
 
Authors :  Q. F. Liu, Y. C. Xu
Date :  20 Feb 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lp_pla2 Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. F. Liu, X. D. Chen, W. Y. Chen, X. J. Yuan, H. X. Su, J. H. Shen, Y. C. Xu
Structural And Thermodynamic Characterization Of Protein-Ligand Interactions Formed Between Lipoprotein-Associated Phospholipase A2 And Inhibitors
J. Med. Chem. V. 59 5115 2016
PubMed-ID: 27078579  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00282

(-) Compounds

Molecule 1 - PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
    Chains: A, B
    EC Number: 3.1.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: ROSETTA2 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 47-429
    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

  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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15HV2Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-2-{2-[(4-FLUOROBENZYL)SULFANYL]-4-OXO-4,5,6,7-TETRAHYDRO-1H-CYCLOPENTA[D]PYRIMIDIN-1-YL}-N-{[4'-(TRIFLUOROMETHYL)BIPHENYL-4-YL]METHYL}ACETAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15HV1Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-2-{2-[(4-FLUOROBENZYL)SULFANYL]-4-OXO-4,5,6,7-TETRAHYDRO-1H-CYCLOPENTA[D]PYRIMIDIN-1-YL}-N-{[4'-(TRIFLUOROMETHYL)BIPHENYL-4-YL]METHYL}ACETAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
15HV1Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-2-{2-[(4-FLUOROBENZYL)SULFANYL]-4-OXO-4,5,6,7-TETRAHYDRO-1H-CYCLOPENTA[D]PYRIMIDIN-1-YL}-N-{[4'-(TRIFLUOROMETHYL)BIPHENYL-4-YL]METHYL}ACETAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:107 , PHE A:110 , LEU A:111 , LEU A:121 , GLY A:152 , LEU A:153 , GLY A:154 , LEU A:159 , TYR A:160 , SER A:273 , PHE A:274 , TRP A:298 , HIS A:351 , GLN A:352 , PHE A:357 , LEU A:369 , LEU A:371binding site for residue 5HV A 501
2AC2SOFTWARELEU B:107 , PHE B:110 , LEU B:111 , LEU B:121 , GLY B:152 , LEU B:153 , GLY B:154 , ALA B:155 , LEU B:159 , SER B:273 , PHE B:274 , TRP B:298 , HIS B:351 , GLN B:352 , PHE B:357 , LEU B:369binding site for residue 5HV B 501
3AC3SOFTWAREGLN A:88 , ASP A:89 , ASN A:90 , ASN B:100 , LYS B:101 , ARG B:122binding site for residue SO4 B 502
4AC4SOFTWAREARG B:207binding site for residue SO4 B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I9I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:72 -Asp A:73
2Phe B:72 -Asp B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I9I)

(-) Exons   (0, 0)

(no "Exon" information available for 5I9I)

(-) 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:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh..hhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhh...eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee..........hhhhh...eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9i A  54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINT 424
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 


Chain B from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee......eeeeeeeee..ee...hhhhhhhhhhhhh.hhhhhhhhhhhhh..ee..ee.........eeeeeee.....hhhhhhhhhhhhhh...eeeee........eeee..hhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee..................eeeeee....hhhhhhhhhh......eeeeee...hhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9i B  55 KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNIN 423
                                    64        74        84   ||   99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       340       350       360       370       380       390       400       410       420   
                                                            88|                                                                                                                                                                                                                                                337|                                                                                    
                                                             94                                                                                                                                                                                                                                                 339
   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 5I9I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I9I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I9I)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5i8p