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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH SELAGINPULVILINS K
 
Authors :  Y. Huang, T. Zhang, X. Zheng, S. Yin, H. B. Luo
Date :  24 Nov 16  (Deposition) - 22 Feb 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Natural Pde4 Inhibtor, Hydrolase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Huang, X. Liu, D. Wu, G. Tang, Z. Lai, X. Zheng, S. Yin, H. B. Luo
The Discovery, Complex Crystal Structure, And Recognition Mechanism Of A Novel Natural Pde4 Inhibitor From Selaginell Pulvinata
Biochem. Pharmacol. V. 130 51 2017
PubMed-ID: 28159622  |  Reference-DOI: 10.1016/J.BCP.2017.01.016

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
    Chains: A, B
    EC Number: 3.1.4.53
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 381-714
    Gene: PDE4D, DPDE3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE3,PDE43

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1J202Ligand/Ion1-[2-(4-HYDROXYPHENYL)ETHYNYL]-9,9-BIS(4-METHOXYPHENYL)-7-OXIDANYL-FLUORENE-2-CARBALDEHYDE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1J201Ligand/Ion1-[2-(4-HYDROXYPHENYL)ETHYNYL]-9,9-BIS(4-METHOXYPHENYL)-7-OXIDANYL-FLUORENE-2-CARBALDEHYDE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1J201Ligand/Ion1-[2-(4-HYDROXYPHENYL)ETHYNYL]-9,9-BIS(4-METHOXYPHENYL)-7-OXIDANYL-FLUORENE-2-CARBALDEHYDE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:160 , SER A:208 , MET A:273 , HIS A:276 , PHE A:340 , GLN A:343 , PRO A:356 , MET A:357 , CYS A:358 , GLN A:369 , PHE A:372 , ILE A:376 , HOH A:620 , HOH A:628binding site for residue J20 A 501
2AC2SOFTWAREHIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:620 , HOH A:638binding site for residue ZN A 502
3AC3SOFTWAREASP A:201 , HOH A:628 , HOH A:638 , HOH A:641 , HOH A:648 , HOH A:668binding site for residue MG A 503
4AC4SOFTWAREHIS B:160 , SER B:208 , MET B:273 , HIS B:276 , PHE B:340 , GLN B:343 , PRO B:356 , MET B:357 , CYS B:358 , GLN B:369 , PHE B:372 , ILE B:376 , HOH B:610 , HOH B:628binding site for residue J20 B 501
5AC5SOFTWAREASP B:201 , HOH B:609 , HOH B:614 , HOH B:628 , HOH B:634 , HOH B:647binding site for residue MG B 502
6AC6SOFTWAREHIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , HOH B:610 , HOH B:634binding site for residue ZN B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:389 -Pro A:390
2His B:389 -Pro B:390

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WQA)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wqa A  79 IPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 412
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408    


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wqa B  79 IPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ 412
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408
   Legend:   → Mismatch (orange background)
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    → 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 5WQA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (52, 52)

Asymmetric Unit(hide GO term definitions)

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  PDE4D_HUMAN | Q08499
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 Related Entries

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UniProtKB/Swiss-Prot
        PDE4D_HUMAN | Q08499: 1e9k 1mkd 1oyn 1ptw 1q9m 1tb7 1tbb 1xom 1xon 1xoq 1xor 1y2b 1y2c 1y2d 1y2e 1y2k 1zkn 2fm0 2fm5 2pw3 2qyn 3g4g 3g4i 3g4k 3g4l 3g58 3iad 3iak 3k4s 3sl3 3sl4 3sl5 3sl6 3sl8 3v9b 4ogb 4w1o 4wcu 5k1i 5k32 5tkb

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