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4Y8C

Crystal structure of phosphodiesterase 9 in complex with (S)-C33

Functional Information from GO Data
ChainGOidnamespacecontents
A0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
A0004115molecular_function3',5'-cyclic-AMP phosphodiesterase activity
A0005515molecular_functionprotein binding
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005783cellular_componentendoplasmic reticulum
A0005794cellular_componentGolgi apparatus
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0007165biological_processsignal transduction
A0008081molecular_functionphosphoric diester hydrolase activity
A0010613biological_processpositive regulation of cardiac muscle hypertrophy
A0016787molecular_functionhydrolase activity
A0019933biological_processcAMP-mediated signaling
A0032587cellular_componentruffle membrane
A0042383cellular_componentsarcolemma
A0042995cellular_componentcell projection
A0043204cellular_componentperikaryon
A0046068biological_processcGMP metabolic process
A0046069biological_processcGMP catabolic process
A0046872molecular_functionmetal ion binding
A0047555molecular_function3',5'-cyclic-GMP phosphodiesterase activity
A0048471cellular_componentperinuclear region of cytoplasm
A1900273biological_processpositive regulation of long-term synaptic potentiation
A2000178biological_processnegative regulation of neural precursor cell proliferation
B0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
B0004115molecular_function3',5'-cyclic-AMP phosphodiesterase activity
B0005515molecular_functionprotein binding
B0005654cellular_componentnucleoplasm
B0005737cellular_componentcytoplasm
B0005783cellular_componentendoplasmic reticulum
B0005794cellular_componentGolgi apparatus
B0005829cellular_componentcytosol
B0005886cellular_componentplasma membrane
B0007165biological_processsignal transduction
B0008081molecular_functionphosphoric diester hydrolase activity
B0010613biological_processpositive regulation of cardiac muscle hypertrophy
B0016787molecular_functionhydrolase activity
B0019933biological_processcAMP-mediated signaling
B0032587cellular_componentruffle membrane
B0042383cellular_componentsarcolemma
B0042995cellular_componentcell projection
B0043204cellular_componentperikaryon
B0046068biological_processcGMP metabolic process
B0046069biological_processcGMP catabolic process
B0046872molecular_functionmetal ion binding
B0047555molecular_function3',5'-cyclic-GMP phosphodiesterase activity
B0048471cellular_componentperinuclear region of cytoplasm
B1900273biological_processpositive regulation of long-term synaptic potentiation
B2000178biological_processnegative regulation of neural precursor cell proliferation
Functional Information from PDB Data
site_idAC1
Number of Residues8
Detailsbinding site for residue 49D A 601
ChainResidue
AMET365
ALEU420
ALEU421
ATYR424
APHE441
AALA452
AGLN453
APHE456

site_idAC2
Number of Residues6
Detailsbinding site for residue ZN A 602
ChainResidue
AHIS292
AASP293
AASP402
AHOH701
AHOH702
AHIS256

site_idAC3
Number of Residues6
Detailsbinding site for residue MG A 603
ChainResidue
AASP293
AHOH702
AHOH703
AHOH704
AHOH705
AHOH706

site_idAC4
Number of Residues9
Detailsbinding site for residue 49D B 601
ChainResidue
BMET365
BLEU420
BLEU421
BTYR424
BPHE441
BALA452
BGLN453
BPHE456
BHOH702

site_idAC5
Number of Residues6
Detailsbinding site for residue ZN B 602
ChainResidue
BHIS256
BHIS292
BASP293
BASP402
BMG603
BHOH701

site_idAC6
Number of Residues7
Detailsbinding site for residue MG B 603
ChainResidue
BASP293
BZN602
BHOH701
BHOH703
BHOH704
BHOH705
BHOH706

Functional Information from PROSITE/UniProt
site_idPS00126
Number of Residues12
DetailsPDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDLdHpGynNtY
ChainResidueDetails
AHIS292-TYR303

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor => ECO:0000269|PubMed:18757755
ChainResidueDetails
AALA312
BALA312

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:18757755
ChainResidueDetails
AALA312
ATRP484
ASER512
BALA312
BTRP484
BSER512

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:18757755, ECO:0000269|PubMed:19919087, ECO:0000269|PubMed:20121115, ECO:0000269|PubMed:21483814, ECO:0000269|PubMed:22985069, ECO:0000269|PubMed:23025719, ECO:0007744|PDB:2HD1, ECO:0007744|PDB:2YY2, ECO:0007744|PDB:3DYN, ECO:0007744|PDB:3JSI, ECO:0007744|PDB:3JSW, ECO:0007744|PDB:3K3E, ECO:0007744|PDB:3K3H, ECO:0007744|PDB:3N3Z, ECO:0007744|PDB:4E90, ECO:0007744|PDB:4G2J, ECO:0007744|PDB:4G2L, ECO:0007744|PDB:4GH6
ChainResidueDetails
AASN316
AILE352
AARG353
AILE462
BASN316
BILE352
BARG353
BILE462

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q8QZV1
ChainResidueDetails
AMET379
BMET379

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PDB entries from 2024-07-17

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