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(-) Description

Title :  CRYSTAL STRUCTURE OF CROSSLINK STABILIZED LONG-FORM PDE4B
 
Authors :  P. Cedervall, J. Pandit
Date :  19 Nov 14  (Deposition) - 11 Mar 15  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Cedervall, A. Aulabaugh, K. F. Geoghegan, T. J. Mclellan, J. Pandit
Engineered Stabilization And Structural Analysis Of The Autoinhibited Conformation Of Pde4.
Proc. Natl. Acad. Sci. Usa V. 112 E1414 2015
PubMed-ID: 25775568  |  Reference-DOI: 10.1073/PNAS.1419906112

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    Chains: A, B
    EC Number: 3.1.4.53
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 122-736
    Gene: PDE4B, DPDE4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE4,PDE32

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION
2MG2Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:410 , HIS A:446 , ASP A:447 , ASP A:564 , HOH A:1089binding site for residue ZN A 801
2AC2SOFTWAREHIS A:491 , ASP A:605 , HIS A:607 , HOH A:906binding site for residue ZN A 802
3AC3SOFTWAREASP A:397 , TYR A:399 , SER A:401 , HOH A:952 , HOH A:1052binding site for residue NA A 803
4AC4SOFTWAREASP A:447 , HOH A:950 , HOH A:956 , HOH A:1089 , HOH A:1090binding site for residue MG A 804
5AC5SOFTWAREARG A:503binding site for residue IOD A 805
6AC6SOFTWAREHIS B:410 , HIS B:446 , ASP B:447 , ASP B:564 , HOH B:1039binding site for residue ZN B 801
7AC7SOFTWAREASP B:397 , TYR B:399 , SER B:401 , HOH B:941 , HOH B:993binding site for residue NA B 802
8AC8SOFTWAREASP B:447 , HOH B:918 , HOH B:937 , HOH B:1039 , HOH B:1040 , HOH B:1041binding site for residue MG B 803
9AC9SOFTWAREARG B:503binding site for residue IOD B 804

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:267 -B:610
2A:610 -B:267

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:635 -Pro A:636
2Ser B:541 -Gly B:542
3Gln B:635 -Pro B:636

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WZI)

(-) 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:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wzi A 166 VTPFAQVLASLRSVRNNFTIQKLAMETLEELDWALDQLETIQTYRSVSEMASNKFKRMLNRELTHLSEMSRCGNQVSEYISNTFLDKENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTAIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHADIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHAADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMADKHTACVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQAMIP 657
                                   175       185|      225       235       245       255       265       275      |335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655  
                                             185|                                                               282|                                                                                                                                                                                                                                                                                                                                    
                                              216                                                                333                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wzi B 166 VTPFAQVLASLRSVRNNFTILTQEESYQKLAMETLEELDWALDQLETIQTYRSVSEMASNKFKRMLNRELTHLSEMSRCGNQVSEYISNTFLDKFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTAIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHADIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHAADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMADKHTACVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQAMIP 657
                                   175       185 ||    218       228       238       248       258       268       278   ||  333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653    
                                               187|                                                                    282|                                                                                                                                                                                                                                                                                                                                         
                                                211                                                                     328
   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 4WZI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:635 - Pro A:636   [ RasMol ]  
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  PDE4B_HUMAN | Q07343
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4B_HUMAN | Q07343: 1f0j 1jp1 1jp2 1ro6 1ro9 1ror 1tb5 1xlx 1xlz 1xm4 1xm6 1xmu 1xmy 1xn0 1xos 1xot 1y2h 1y2j 2chm 2qyl 3d3p 3frg 3g45 3gwt 3hc8 3hdz 3hmv 3kkt 3ly2 3o0j 3o56 3o57 3w5e 3wd9 4kp6 4myq 4nw7 4x0f 5k6j

(-) Related Entries Specified in the PDB File

4x0f