Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

3SL3

Crystal structure of the apo form of the catalytic domain of PDE4D2

Functional Information from GO Data
ChainGOidnamespacecontents
A0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
A0007165biological_processsignal transduction
A0008081molecular_functionphosphoric diester hydrolase activity
B0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
B0007165biological_processsignal transduction
B0008081molecular_functionphosphoric diester hydrolase activity
C0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
C0007165biological_processsignal transduction
C0008081molecular_functionphosphoric diester hydrolase activity
D0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
D0007165biological_processsignal transduction
D0008081molecular_functionphosphoric diester hydrolase activity
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 1
ChainResidue
ALYS262
AASP266
AHOH550
AHOH588
BHOH531

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 2
ChainResidue
DDMS6
DGLU182
AEDO20
ALEU188
ALYS255
AGLN256

site_idAC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 3
ChainResidue
AEDO9
AASN115
AARG116
AGLU150
AASP151
ATYR153
AASN162
AHOH545

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 4
ChainResidue
APHE238
AARG257
AHOH590
AHOH602

site_idAC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 5
ChainResidue
AEDO12
AASP156
AALA158
APRO205
AARG342
AARG346
AHOH599

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 6
ChainResidue
AEDO7
APHE135
AGLN256
AHOH511
DDMS6

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 7
ChainResidue
AEDO6
ATHR134
ALYS136
DEDO9
DPRO179
DASP391

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 8
ChainResidue
AGLN250
AASN251
AHOH548
AHOH577
DHOH556

site_idAC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 9
ChainResidue
AEDO3
AASP151
ATYR153
AHIS154
AALA155
AHOH545
CASP156
CHOH483

site_idBC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 10
ChainResidue
ATHR178
AASP391

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 11
ChainResidue
APO416
AGLU230
ATHR271
AASP272
AMET273
AHOH567
AHOH574

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 12
ChainResidue
AEDO5
AHIS154
AASP156
AVAL157
APRO205
CHOH474

site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PEG A 13
ChainResidue
ALEU132
ALYS136
AILE137

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 14
ChainResidue
APO416
AASP201
AHOH528
AHOH529
AHOH573
AHOH574

site_idBC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 15
ChainResidue
APO416
AHIS164
AHIS200
AASP201
AASP318
AHOH573

site_idBC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 A 16
ChainResidue
AEDO11
AZN14
AZN15
AHIS160
AHIS164
AASP201
AASP318
AHOH509
AHOH530
AHOH573

site_idBC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO A 17
ChainResidue
ALYS275

site_idBC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 18
ChainResidue
APHE340
AGLN343
AHIS204
AGLY206
AVAL207
AGLU339

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 19
ChainResidue
ATHR148
AHIS152
AGLU243
AHOH555
CSER217
CARG350

site_idCC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 20
ChainResidue
AEDO2
ATHR186
ALEU188
ASER259
AMET263
AHOH580

site_idCC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 21
ChainResidue
ALYS239
AGLN242
AGLU243
CEDO18
CASN216
CSER217
CGLU218
DGLN242

site_idCC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 1
ChainResidue
BDMS15
BGLN210
BHOH511
BHOH531

site_idCC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO B 2
ChainResidue
BALA183
BVAL184

site_idCC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 3
ChainResidue
BTHR289
BLYS291
BLEU298
BLEU299

site_idCC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 4
ChainResidue
BASN115
BALA155
BASN161
BASN162
BARG335

site_idCC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 5
ChainResidue
BLEU175
BTHR178
BTRP384
BASP391

site_idCC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 6
ChainResidue
BASP374
BHIS378
BHOH541

site_idDC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO B 7
ChainResidue
BDMS14
BHIS204
BGLY206
BVAL207
BGLU339
BPHE340
BGLN343
BHOH517

site_idDC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN B 8
ChainResidue
BPO410
BASP201
BHOH524
BHOH525
BHOH526
BHOH569

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN B 9
ChainResidue
BPO410
BHIS164
BHIS200
BASP201
BASP318
BHOH569

site_idDC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 B 10
ChainResidue
BZN8
BZN9
BHIS160
BHIS164
BASP201
BASP318
BHOH567
BHOH569
BHOH574

site_idDC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 11
ChainResidue
BGLU218
DHIS152
DLYS239
DHOH594

site_idDC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 12
ChainResidue
BILE354
BSER355
BMET357
BCYS358
BASP359
BASN362

site_idDC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 13
ChainResidue
BASP334
BMET337
BGLU338
BPHE341

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS B 14
ChainResidue
BEDO7
BSER208
BGLN343
BPRO356
BCYS358
BHOH565

site_idDC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS B 15
ChainResidue
BEDO1
BGLN210
BSER274
BHOH577
BHOH584

site_idEC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 16
ChainResidue
BTHR186
BASP187
BHOH582

site_idEC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PEG B 17
ChainResidue
BHIS152
BGLU243
BHOH519
DTHR215
DSER217
DGLU218
DLEU219
DARG350

site_idEC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO C 1
ChainResidue
AARG350
CHIS152
CGLU243

site_idEC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 7
ChainResidue
AGLU244
CASN214
CARG350
CMET352
CHOH506
DLYS254

site_idEC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO C 2
ChainResidue
AGLU218
CTYR223
CHIS232
CALA235
CHOH463

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 3
ChainResidue
AASP156
CEDO13
CGLU150
CASP151
CTYR153
CASN162

site_idEC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EPE C 4
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331

site_idEC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE DMS C 5
ChainResidue
CARG257
CARG261

site_idEC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO C 6
ChainResidue
CLYS262
CASP266
DASN224

site_idFC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO C 12
ChainResidue
CLYS275
CHOH465

site_idFC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO C 8
ChainResidue
BHIS389
BPRO390
CTHR134
CPHE135
CLYS136
CASN251
CGLN256

site_idFC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO C 9
ChainResidue
CASP203
CLEU219

site_idFC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO C 10
ChainResidue
CASP156
CVAL157
CPRO205
CARG342
CARG346
CHOH468
CHOH502

site_idFC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO C 11
ChainResidue
CHIS160
CHIS204
CGLY206
CVAL207
CGLU339
CPHE340
CGLN343

site_idFC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 13
ChainResidue
CEDO3
CASN115
CALA155
CASN161
CASN162
CILE163

site_idFC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN C 14
ChainResidue
CPO416
CASP201
CHOH456
CHOH457
CHOH458
CHOH459

site_idFC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN C 15
ChainResidue
CPO416
CHIS164
CHIS200
CASP201
CASP318
CHOH458

site_idFC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PO4 C 16
ChainResidue
CZN14
CZN15
CHOH58
CHIS160
CHIS164
CASP201
CASP318
CHOH458

site_idGC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 18
ChainResidue
AEDO21
AGLU243
AHOH555
CGLU218

site_idGC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO D 4
ChainResidue
DASP266
DGLN311

site_idGC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS D 6
ChainResidue
AEDO2
AEDO6
DSER177
DPRO179
DGLU182
DHOH553

site_idGC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 1
ChainResidue
BSER217
BHOH502
DEDO23
DTHR148
DHIS152
DGLU243

site_idGC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 9
ChainResidue
AEDO7
ATHR134
APHE135
AASN251
AGLN256
DPRO179
DASP391

site_idGC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 2
ChainResidue
DEDO5
DLEU175
DTHR178
DVAL388
DASP391
DHOH541

site_idGC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 3
ChainResidue
DLEU181
DALA183
DVAL184
DPHE185
DHOH553

site_idGC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DMS D 25
ChainResidue
DGLU150
DASP151
DTYR153
DASN162

site_idGC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 5
ChainResidue
DEDO2
DASN100
DLYS101
DTRP102
DHOH550

site_idHC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 27
ChainResidue
DASN100
DGLU128
DHIS173
DSER177

site_idHC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO D 7
ChainResidue
DHIS123

site_idHC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG D 8
ChainResidue
CASP225
CHOH461
DGLN258
DLYS262
DASP266

site_idHC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D 10
ChainResidue
DASN302
DTYR303
DSER304

site_idHC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PEG D 11
ChainResidue
DTHR186
DLEU188
DGLU189
DSER259
DMET263
DHOH523

site_idHC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D 12
ChainResidue
DASP247
DPHE249
DARG257

site_idHC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 13
ChainResidue
DASP156
DVAL157
DALA158
DGLU338
DGLU339
DHOH605

site_idHC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 14
ChainResidue
DPRO325
DLEU326
DGLN327
DHOH582

site_idHC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 15
ChainResidue
DGLU244
DASN245
DSER294
DGLY296
DHOH520

site_idIC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 16
ChainResidue
DTHR134
DLYS136
DASN251
DGLN256

site_idIC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ZN D 17
ChainResidue
DPO419
DASP201
DHOH535
DHOH536
DHOH537

site_idIC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ZN D 18
ChainResidue
DPO419
DHIS164
DHIS200
DASP201
DASP318

site_idIC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PO4 D 19
ChainResidue
DZN17
DZN18
DHIS160
DHIS164
DASP201
DASP318
DHOH574

site_idIC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D 20
ChainResidue
DMET286
DTHR289
DASP305

site_idIC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO D 21
ChainResidue
DGLN127
DHOH507

site_idIC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D 22
ChainResidue
DASP98
DLYS101
DTRP102

site_idIC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO D 23
ChainResidue
BTHR215
BARG350
DEDO1
DTHR148
DGLU243
DGLU244
DCYS246
DHOH554

site_idIC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 24
ChainResidue
DASN321
DTHR333
DILE336
DGLN369
DHOH529

site_idJC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO D 26
ChainResidue
DASP266
DGLN311

Functional Information from PROSITE/UniProt
site_idPS00126
Number of Residues12
DetailsPDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF
ChainResidueDetails
AHIS200-PHE211

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343
ChainResidueDetails
AHIS160
BHIS160
CHIS160
DHIS160

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7
ChainResidueDetails
AHIS160
DHIS160
DASN321
DGLN369
AASN321
AGLN369
BHIS160
BASN321
BGLN369
CHIS160
CASN321
CGLN369

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:2PW3
ChainResidueDetails
AHIS164
BHIS164
CHIS164
DHIS164

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:1XOR, ECO:0007744|PDB:2PW3
ChainResidueDetails
AHIS200
AASP318
BHIS200
BASP318
CHIS200
CASP318
DHIS200
DASP318

site_idSWS_FT_FI5
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW
ChainResidueDetails
AASP201
APHE372
BASP201
BPHE372
CASP201
CPHE372
DASP201
DPHE372

site_idSWS_FT_FI6
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
ChainResidueDetails
ALYS85
BLYS85
CLYS85
DLYS85

222926

PDB entries from 2024-07-24

PDB statisticsPDBj update infoContact PDBjnumon