PDB entry 5xkm

View 5xkm on RCSB PDB site
Description: Crystal structure of human phosphodiesterase 2A in complex with 6-methyl-N-(1-(4-(trifluoromethoxy)phenyl)propyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide
Class: hydrolase
Keywords: Hydrolase, Hydrolase Inhibitor, PDE2A
Deposited on 2017-05-08, released 2017-08-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-12-06, with a file datestamp of 2017-12-01.
Experiment type: XRAY
Resolution: 2.16 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5xkma_
  • Chain 'B':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed):
    • Uniprot O00408 (3-344)
      • expression tag (0-2)
    Domains in SCOPe 2.07: d5xkmb1, d5xkmb2
  • Chain 'C':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed):
    • Uniprot O00408 (3-End)
      • expression tag (0-2)
    Domains in SCOPe 2.07: d5xkmc1, d5xkmc2
  • Chain 'D':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5xkmd_
  • Chain 'E':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5xkme_
  • Chain 'F':
    Compound: cGMP-dependent 3',5'-cyclic phosphodiesterase
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE2A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5xkmf_
  • Heterogens: MG, ZN, 87R, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5xkmA (A:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5xkmA (A:)
    ddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnykidcpt
    larfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdl
    dhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdyqrml
    dlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtkgwkt
    trkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykllqdlf
    pkaaelyervasnrehwtkvshkftirglpsnnsldflde
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5xkmB (B:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5xkmC (C:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5xkmC (C:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfld
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5xkmD (D:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5xkmD (D:)
    eytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnykidcptla
    rfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdldh
    rgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdyqrmldl
    mrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtkgwkttr
    kiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykllqdlfpk
    aaelyervasnrehwtkvshkftirglpsnnsldfld
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5xkmE (E:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5xkmE (E:)
    iqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnykidcptlarfclmvkkg
    yrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdldhrgtnnsfqv
    assegsvmerhhfaqaiailnthgcnifdhfsrkdyqrmldlmrdiilatdlahhlrifk
    dlqkmaevgydrnnkqhhrlllcllmtscdlsdqtkgwkttrkiaeliykeffsqgdlek
    amgnrpmemmdrekayipelqisfmehiampiykllqdlfpkaaelyervasnrehwtkv
    shkftirglpsnnsldfld
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5xkmF (F:)
    ghasddeytkllhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnyki
    dcptlarfclmvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscm
    chdldhrgtnnsfqvasksvlaalyssegsvmerhhfaqaiailnthgcnifdhfsrkdy
    qrmldlmrdiilatdlahhlrifkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtk
    gwkttrkiaeliykeffsqgdlekamgnrpmemmdrekayipelqisfmehiampiykll
    qdlfpkaaelyervasnrehwtkvshkftirglpsnnsldfldee
    

    Sequence, based on observed residues (ATOM records): (download)
    >5xkmF (F:)
    llhdgiqpvaaidsnfasftytprslpeddtsmailsmlqdmnfinnykidcptlarfcl
    mvkkgyrdppyhnwmhafsvshfcyllyknleltnyledieifalfiscmchdldhrgtn
    nsfqsegsvmerhhfaqaiailnthgcnifdhfsrkdyqrmldlmrdiilatdlahhlri
    fkdlqkmaevgydrnnkqhhrlllcllmtscdlsdqtkgwkttrkiaeliykeffsqgdl
    ekamgnrpmemmdrekayipelqisfmehiampiykllqdlfpkaaelyervasnrehwt
    kvshkftirglpsnnsldfld