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3SL4

Crystal structure of the catalytic domain of PDE4D2 with compound 10D

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 Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 1
ChainResidue
APO420
AHIS164
AHIS200
AASP201
AASP318
AHOH486

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 2
ChainResidue
AHOH486
AHOH490
AHOH529
APO420
AHOH54
AASP201

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 4
ChainResidue
ALYS262
AILE265
AASP266
BHOH500
BHOH535

site_idAC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 5
ChainResidue
AGLU218
CLYS239

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE DMS A 6
ChainResidue
APRO138
AASP140
ATHR141

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 7
ChainResidue
AARG350
CEDO8
CTHR148
CASP151

site_idAC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 9
ChainResidue
AASP156
AALA158
APRO205
AGLU339
AARG342
AARG346
AHOH482

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 10
ChainResidue
ALEU175
ATHR178
ATRP384
AVAL388
AILE395

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 11
ChainResidue
ALEU132
ALYS136
AILE137
AVAL139
AHOH471
AHOH478

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG A 440
ChainResidue
AASN115
AARG116
AGLU150
AASP151
ATYR153
AASN162
AHOH542

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 13
ChainResidue
AEDO18
ALEU188
ALYS255
AGLN256
ASER259
DDMS8
DGLU182

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 14
ChainResidue
APHE238
APHE249
AARG257
AARG261
AHOH536
AHOH539

site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 15
ChainResidue
AASP266
AGLN311

site_idBC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 16
ChainResidue
AGLU218
CHIS152
CLYS239
CHOH479

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 17
ChainResidue
AASN115
AALA155
AASN162
AILE163

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 18
ChainResidue
AEDO13
ATHR186
ALEU188
ASER259
AMET263

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 19
ChainResidue
AARG330
AGLU366
ATHR409
AHOH463
BPRO411
BGLN412

site_idBC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 A 20
ChainResidue
AZN1
AZN2
AJN423
AHIS160
AHIS164
AASP201
AASP318
AHOH452
AHOH485
AHOH486

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 21
ChainResidue
DLYS239
DGLN242
ALYS239
AGLN242
AHOH547
CASN216

site_idCC2
Number of Residues14
DetailsBINDING SITE FOR RESIDUE JN4 A 23
ChainResidue
APO420
ATYR159
ALEU319
AASN321
APRO322
ATYR329
ATHR333
AILE336
AMET337
AMET357
AGLN369
APHE372
AHOH444
AHOH485

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 441
ChainResidue
AGLN258
BEDO9
BGLN210
BASN214

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS A 442
ChainResidue
AHIS105
AVAL106
APHE107
AARG108
AGLN331

site_idCC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 443
ChainResidue
ATHR148
AHIS152
AGLU243
AHOH462
CHOH73
CPHE211
CTHR215
CARG350

site_idCC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN B 1
ChainResidue
BPO420
BHIS164
BHIS200
BASP201
BASP318
BHOH489

site_idCC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN B 2
ChainResidue
BPO420
BHOH47
BHOH57
BASP201
BHOH484
BHOH489

site_idCC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 4
ChainResidue
BSER208
BPHE340
BPRO356
BCYS358
BHOH482

site_idCC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EPE B 6
ChainResidue
BEDO18
BASP140
BLYS290
BVAL292
CTHR253
CLYS254
CHOH485

site_idDC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS B 7
ChainResidue
BEDO13
BGLU150
BASP151
BTYR153
BASN162

site_idDC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO B 8
ChainResidue
BGLU218

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 9
ChainResidue
AGLN258
AEDO441
BASN214
BHOH515
DSER294
DSER295

site_idDC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO B 10
ChainResidue
BHOH71
BGLU218

site_idDC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 11
ChainResidue
BHOH58
BGLN210
BHOH454
BHOH509

site_idDC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 13
ChainResidue
BDMS7
BASN115
BALA155
BASN162
BILE163
BARG335

site_idDC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 15
ChainResidue
BPHE211
BASN214
BGLU347
BMET352
BGLU353
BSER355

site_idDC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 16
ChainResidue
BLEU176
BSER177
BTHR178
BLEU181
BGLU182
BHOH459
BHOH486

site_idDC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO B 17
ChainResidue
BALA183
BPHE185

site_idEC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO B 18
ChainResidue
BEPE6
BEDO19
BLYS290
BLEU387
BVAL388
BHIS389
BHOH527
CHOH485

site_idEC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO B 19
ChainResidue
BEDO18
BPRO179
BALA180
BHIS389
BPRO390
BASP391
CEDO6
CTHR253
CLYS255

site_idEC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 B 20
ChainResidue
BZN1
BZN2
BJN421
BHIS160
BHIS164
BASP201
BASP318
BHOH451
BHOH489
BHOH510

site_idEC4
Number of Residues14
DetailsBINDING SITE FOR RESIDUE JN4 B 21
ChainResidue
BPO420
BTYR159
BMET273
BLEU319
BASN321
BTRP332
BTHR333
BILE336
BMET337
BMET357
BGLN369
BPHE372
BHOH510
BHOH526

site_idEC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO C 8
ChainResidue
AEDO7
CHIS152
CGLU243

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN C 1
ChainResidue
CPO417
CHIS164
CHIS200
CASP201
CASP318
CHOH487

site_idEC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN C 2
ChainResidue
CPO417
CASP201
CHOH481
CHOH487
CHOH491
CHOH516

site_idEC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO C 4
ChainResidue
CASN115
CALA155
CASN161
CASN162
CILE163

site_idEC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO C 5
ChainResidue
BHIS389
BPRO390
CTHR134
CPHE135
CLYS136
CASN251
CGLN256

site_idFC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 6
ChainResidue
BEDO19
CLEU188
CLYS255
CSER259

site_idFC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EPE C 7
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331

site_idFC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 440
ChainResidue
CLEU175
CTHR178
CTRP384
CASP391

site_idFC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE DMS C 10
ChainResidue
CARG257
CARG261
CHOH489

site_idFC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 11
ChainResidue
CLYS262
CASP266
DASN224
DASP225

site_idFC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 12
ChainResidue
CASP266
CALA270
CLYS275
CGLN311

site_idFC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 13
ChainResidue
CASP156
CVAL157
CALA158
CGLU339
CARG342
CHOH507

site_idFC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 14
ChainResidue
AASP156
CGLU150
CASP151
CTYR153

site_idFC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 15
ChainResidue
CHIS154
CASP203
CPRO205
CLEU219

site_idGC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 C 17
ChainResidue
CZN1
CZN2
CJN418
CHIS160
CHIS164
CASP201
CASP318
CHOH484
CHOH487
CHOH503

site_idGC2
Number of Residues14
DetailsBINDING SITE FOR RESIDUE JN4 C 18
ChainResidue
CPO417
CTYR159
CMET273
CLEU319
CASN321
CPRO322
CTHR333
CILE336
CMET337
CMET357
CGLN369
CPHE372
CHOH482
CHOH484

site_idGC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 5
ChainResidue
BTHR215
BARG350
BHOH528
DTHR148
DHIS152
DGLU243
DHOH495

site_idGC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG D 12
ChainResidue
DEDO7
DASN100
DLYS101
DTRP102
DVAL174
DHOH447
DHOH534

site_idGC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN D 1
ChainResidue
DPO424
DHIS164
DHIS200
DASP201
DASP318
DHOH482

site_idGC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN D 2
ChainResidue
DPO424
DHOH76
DASP201
DHOH482
DHOH546
DHOH557

site_idGC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 4
ChainResidue
ATHR134
AASN251
AGLN256
AHOH460
DPRO179
DASP391

site_idGC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 440
ChainResidue
DLEU181
DALA183
DVAL184
DPHE185
DHOH449

site_idGC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO D 6
ChainResidue
DASN115

site_idHC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 7
ChainResidue
DPEG12
DLEU175
DTHR178
DASP391
DHOH473

site_idHC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS D 8
ChainResidue
AEDO13
AHOH477
DSER177
DTHR178
DPRO179
DGLU182

site_idHC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DMS D 9
ChainResidue
BGLU349
BARG350
DASP140
DTHR144

site_idHC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO D 10
ChainResidue
DHIS123

site_idHC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D 11
ChainResidue
DEDO14
DASP266
DGLN311

site_idHC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG D 441
ChainResidue
CASP225
CHOH464
DGLN258
DLYS262
DASP266

site_idHC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS D 13
ChainResidue
DEDO17
DASN115
DGLU150
DASP151
DTYR153
DASN162

site_idHC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 14
ChainResidue
DEDO11
DASP266
DLYS275
DGLN311

site_idHC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 15
ChainResidue
DMET286
DTHR289
DLYS291
DLEU299

site_idIC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PEG D 16
ChainResidue
DPRO325
DLEU326
DASP401
DASN402

site_idIC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 17
ChainResidue
DDMS13
DASN115
DALA155
DASN161
DASN162

site_idIC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D 18
ChainResidue
DASN100
DGLU128
DHIS173
DSER177
DHOH472

site_idIC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG D 19
ChainResidue
DASP156
DVAL157
DALA158
DPRO205
DGLU339
DARG346
DHOH476

site_idIC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 20
ChainResidue
CASN231
CLEU234
CPHE238
CARG261
DLEU221
DASN224
DHOH488

site_idIC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO D 21
ChainResidue
CASN231
DEDO22
DMET222
DTYR223
DASN224
DSER226
DASN231
DHOH452
DHOH468

site_idIC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 22
ChainResidue
DEDO21
DSER226
DASN231
DHOH468

site_idIC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE DMS D 23
ChainResidue
DHIS105
DVAL106
DPHE107
DARG108
DGLN327
DLEU328
DGLN331

site_idIC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 D 24
ChainResidue
DZN1
DZN2
DHIS160
DHIS164
DASP201
DASP318
DJN4442
DHOH482
DHOH483
DHOH518

site_idJC1
Number of Residues17
DetailsBINDING SITE FOR RESIDUE JN4 D 442
ChainResidue
DPO424
DTYR159
DMET273
DLEU319
DASN321
DPRO322
DTYR329
DTHR333
DILE336
DMET337
DMET357
DSER368
DGLN369
DPHE372
DHOH483
DHOH554
DHOH559

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

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PDB entries from 2024-07-10

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