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(-) Description

Title :  THE STRUCTURE OF HUMAN PDE12 RESIDUES 161-609 IN COMPLEX WITH GSK3036342A
 
Authors :  R. T. Nolte, B. Wisely, L. Wang, E. R. Wood
Date :  29 Mar 15  (Deposition) - 17 Jun 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Pde12 2'-5'A Eep Nuclease Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Wood, R. Bledsoe, J. Chai, P. Daka, H. Deng, Y. Ding, S. Harris-Gurley, L. H. Kryn, E. Nartey, J. Nichols, R. T. Nolte, N. Prabhu, C. Rise, T. Sheahan, J. B. Shotwell, D. Smith, V. Tai, J. D. Taylor, G. Tomberlin, L. Wang, B. Wisely, S. You, B. Xia, H. Dickso
The Role Of Phosphodiesterase 12 (Pde12) As A Negative Regulator Of The Innate Immune Response And The Discovery O Antiviral Inhibitors.
J. Biol. Chem. V. 290 19681 2015
PubMed-ID: 26055709  |  Reference-DOI: 10.1074/JBC.M115.653113

(-) Compounds

Molecule 1 - 2',5'-PHOSPHODIESTERASE 12
    Chains: A
    EC Number: 3.1.4.-, 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 469008
    Expression System Variant: DE3
    Fragment: UNP RESIDUES 155-609
    Gene: PDE12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: TEV CLONING TAG ON N-TERMINUS
    Synonym: 2-PDE,MITOCHONDRIAL DEADENYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
14LC1Ligand/Ion3-(6-{[(2S,3S)-3-(HYDROXYMETHYL)-2-PHENYLMORPHOLIN-4-YL]CARBONYL}-1-METHYL-1H-BENZIMIDAZOL-2-YL)-1H-INDOLE-6-CARBONITRILE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:207 , LYS A:377 , ARG A:431 , SER A:432 , TYR A:458 , EDO A:702 , HOH A:822 , HOH A:843 , HOH A:893binding site for residue SO4 A 701
2AC2SOFTWARELYS A:377 , SER A:433 , HIS A:456 , LEU A:457 , TYR A:458 , TRP A:459 , SO4 A:701binding site for residue EDO A 702
3AC3SOFTWAREPHE A:177 , PRO A:274 , GLY A:275 , CYS A:277 , ASP A:280 , LYS A:337binding site for residue EDO A 703
4AC4SOFTWAREHIS A:281 , LYS A:412 , GLU A:416 , SER A:580 , GLU A:583 , HOH A:818 , HOH A:857 , HOH A:936 , HOH A:1037binding site for residue TRS A 704
5AC5SOFTWAREPRO A:208 , GLU A:209 , TYR A:307 , THR A:310 , SER A:313 , GLU A:351 , TRP A:459 , PRO A:461 , ASN A:498 , SER A:499 , THR A:500 , THR A:503 , PHE A:556 , MG A:706 , HOH A:842 , HOH A:844 , HOH A:920 , HOH A:973 , HOH A:1098binding site for residue 4LC A 705
6AC6SOFTWAREGLU A:351 , ASP A:598 , 4LC A:705 , HOH A:828 , HOH A:847 , HOH A:1038binding site for residue MG A 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z2B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:590 -Pro A:591

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z2B)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z2B)

(-) 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:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....ee.......eeeee..hhhhheeeeeee............hhhhh.......eee..........hhhhh...eeeeee..........eeee....ee......hhhhhhh.........eeeeeeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhh.eeeeeee....eeeeeee...eeeeee..eehhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhee...hhhhhh..........ee....eee........ee....ee..eeeeee...eeeeee....hhhhhh................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z2b A 161 PPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAEPEVGVPSSLSPSSPSSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGHSRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVINGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCLDYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK 609
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   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 4Z2B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z2B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z2B)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:590 - Pro A:591   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE12_HUMAN | Q6L8Q7: 4z0v 4zkf

(-) Related Entries Specified in the PDB File

4z0v RELATED UNLIGANDED PROTEIN STRUCTURE