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 :  CRYSTAL STRUCTURE OF LP_PLA2 IN COMPLEX WITH NOVEL INHIBITOR
 
Authors :  Q. F. Liu, Y. C. Xu
Date :  19 Feb 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1VQ72Ligand/Ion6-[1,1-BIS(OXIDANYLIDENE)-1,4-THIAZINAN-4-YL]-4-[[4-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENOXY]-3,5-BIS(FLUORANYL)PHENYL]METHOXY]-1-METHYL-PYRIMIDIN-2-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1VQ71Ligand/Ion6-[1,1-BIS(OXIDANYLIDENE)-1,4-THIAZINAN-4-YL]-4-[[4-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENOXY]-3,5-BIS(FLUORANYL)PHENYL]METHOXY]-1-METHYL-PYRIMIDIN-2-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1VQ71Ligand/Ion6-[1,1-BIS(OXIDANYLIDENE)-1,4-THIAZINAN-4-YL]-4-[[4-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENOXY]-3,5-BIS(FLUORANYL)PHENYL]METHOXY]-1-METHYL-PYRIMIDIN-2-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:107 , PHE A:110 , 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 , PHE A:322 , HIS A:351 , GLN A:352 , ALA A:355 , PHE A:357 , LEU A:371binding site for residue VQ7 A 501
2AC2SOFTWARELEU B:107 , PHE B:110 , LEU B:111 , LEU B:121 , GLY B:152 , LEU B:153 , GLY B:154 , TYR B:160 , SER B:273 , PHE B:274 , TRP B:298 , PHE B:322 , HIS B:351 , GLN B:352 , ALA B:355 , PHE B:357 , LEU B:371binding site for residue VQ7 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I8P)

(-) 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 5I8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I8P)

(-) Exons   (0, 0)

(no "Exon" information available for 5I8P)

(-) 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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh.hhhhhhhhhhhhh..ee..ee.........eeeeeee.....hhhhhhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee..........hhhhh...eeeeee....hhhhhhhhhhh......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i8p A  54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNI 422
                                    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         


Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeee......eeeeeeee....ee...hhhhhhhhhhhhh..hhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhh...eeeee........eeee..hhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeee.hhhhhhhhhhhhh....eeeee..................eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i8p B  55 KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQLDTLWIPNKEYFWGLSKFLGTWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
                                    64        74        84   ||   98       108    || 119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419      
                                                            88|                 113|                                                                                                                                                                                                                                                                                                                      
                                                             93                  115
   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 5I8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I8P)

(-) Gene Ontology  (16, 16)

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
    VQ7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:72 - Asp A:73   [ RasMol ]  
    Phe B:72 - Asp B:73   [ RasMol ]  
 
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
  5i8p
    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
  PAFA_HUMAN | Q13093
    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)
  3.1.1.47
    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
  PAFA_HUMAN | Q13093
    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
        PAFA_HUMAN | Q13093: 3d59 3d5e 3f96 3f97 3f98 3f9c 5i9i 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

5i9i