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(-) Description

Title :  HUMAN PHOSPODIESTERASE 4B IN COMPLEX WITH PYRIDYLOXY-BENZOXABOROLE BASED INHIBITOR
 
Authors :  F. L. Rock, Y. Zhou, D. Sullivan
Date :  24 May 16  (Deposition) - 31 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, K. Jarnagin
To Be Published
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B
    Chains: A
    EC Number: 3.1.4.53
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 101-423
    Gene: PDE4B, DPDE4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DPDE4,PDE32

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
16QQ1Ligand/Ion6-[[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1(6),2,4-TRIEN-3-YL]OXY]-5-CHLORANYL-2-(4-OXIDANYLIDENEPENTOXY)PYRIDINE-3-CARBONITRILE
2EDO17Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , 6QQ A:503binding site for residue ZN A 501
02AC2SOFTWAREASP A:275 , 6QQ A:503 , HOH A:603 , HOH A:639 , HOH A:662binding site for residue MG A 502
03AC3SOFTWAREHIS A:234 , HIS A:238 , HIS A:274 , ASP A:275 , MET A:347 , ASP A:392 , LEU A:393 , ASN A:395 , PRO A:396 , ILE A:410 , MET A:431 , GLN A:443 , PHE A:446 , ZN A:501 , MG A:502 , HOH A:639 , HOH A:666binding site for residue 6QQ A 503
04AC4SOFTWARETHR A:208 , PHE A:209 , ASN A:325 , LEU A:326 , THR A:327 , GLN A:330 , EDO A:520 , HOH A:621binding site for residue EDO A 504
05AC5SOFTWARETHR A:215 , HIS A:319 , CYS A:320 , ASP A:321 , MET A:324 , HOH A:674binding site for residue EDO A 505
06AC6SOFTWAREHIS A:226 , EDO A:507 , HOH A:605 , HOH A:608binding site for residue EDO A 506
07AC7SOFTWAREHIS A:226 , LYS A:313 , EDO A:506 , HOH A:605binding site for residue EDO A 507
08AC8SOFTWARESER A:251 , ASP A:256binding site for residue EDO A 508
09AC9SOFTWARELEU A:249 , THR A:252 , TRP A:458 , ASP A:465 , ILE A:469binding site for residue EDO A 509
10AD1SOFTWAREALA A:167 , GLU A:171 , HOH A:619binding site for residue EDO A 510
11AD2SOFTWARESER A:429 , PRO A:430 , MET A:431binding site for residue EDO A 511
12AD3SOFTWAREARG A:477 , ASN A:478binding site for residue EDO A 512
13AD4SOFTWAREPRO A:253 , ASP A:465binding site for residue EDO A 513
14AD5SOFTWARELYS A:168binding site for residue EDO A 514
15AD6SOFTWAREARG A:331 , ARG A:335 , HOH A:613binding site for residue EDO A 515
16AD7SOFTWAREASN A:174 , GLU A:202 , SER A:251binding site for residue EDO A 516
17AD8SOFTWARESER A:282 , PRO A:430 , CYS A:432 , HOH A:620binding site for residue EDO A 517
18AD9SOFTWARELEU A:255 , ALA A:257 , VAL A:258 , PHE A:259binding site for residue EDO A 518
19AE1SOFTWAREARG A:203 , ASP A:204 , LEU A:205 , THR A:208 , ASP A:261 , ILE A:264 , HOH A:601binding site for residue EDO A 519
20AE2SOFTWARETHR A:208 , ASP A:261 , GLN A:330 , EDO A:504binding site for residue EDO A 520

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K6J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:463 -Pro A:464

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6J)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6J)

(-) 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:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k6j A 162 NEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMI 484
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 5K6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6J)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:463 - Pro A:464   [ RasMol ]  
 

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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 4wzi 4x0f

(-) Related Entries Specified in the PDB File

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