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3F98

Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by tabun

Functional Information from GO Data
ChainGOidnamespacecontents
A0003847molecular_function1-alkyl-2-acetylglycerophosphocholine esterase activity
A0005515molecular_functionprotein binding
A0005543molecular_functionphospholipid binding
A0005576cellular_componentextracellular region
A0009395biological_processphospholipid catabolic process
A0016486biological_processpeptide hormone processing
A0016787molecular_functionhydrolase activity
A0016788molecular_functionhydrolase activity, acting on ester bonds
A0034362cellular_componentlow-density lipoprotein particle
A0034364cellular_componenthigh-density lipoprotein particle
A0034374biological_processlow-density lipoprotein particle remodeling
A0034440biological_processlipid oxidation
A0034441biological_processplasma lipoprotein particle oxidation
A0034638biological_processphosphatidylcholine catabolic process
A0046469biological_processplatelet activating factor metabolic process
A0047499molecular_functioncalcium-independent phospholipase A2 activity
A0050729biological_processpositive regulation of inflammatory response
A0062234biological_processplatelet activating factor catabolic process
A0090026biological_processpositive regulation of monocyte chemotaxis
B0003847molecular_function1-alkyl-2-acetylglycerophosphocholine esterase activity
B0005515molecular_functionprotein binding
B0005543molecular_functionphospholipid binding
B0005576cellular_componentextracellular region
B0009395biological_processphospholipid catabolic process
B0016486biological_processpeptide hormone processing
B0016787molecular_functionhydrolase activity
B0016788molecular_functionhydrolase activity, acting on ester bonds
B0034362cellular_componentlow-density lipoprotein particle
B0034364cellular_componenthigh-density lipoprotein particle
B0034374biological_processlow-density lipoprotein particle remodeling
B0034440biological_processlipid oxidation
B0034441biological_processplasma lipoprotein particle oxidation
B0034638biological_processphosphatidylcholine catabolic process
B0046469biological_processplatelet activating factor metabolic process
B0047499molecular_functioncalcium-independent phospholipase A2 activity
B0050729biological_processpositive regulation of inflammatory response
B0062234biological_processplatelet activating factor catabolic process
B0090026biological_processpositive regulation of monocyte chemotaxis
C0003847molecular_function1-alkyl-2-acetylglycerophosphocholine esterase activity
C0005515molecular_functionprotein binding
C0005543molecular_functionphospholipid binding
C0005576cellular_componentextracellular region
C0009395biological_processphospholipid catabolic process
C0016486biological_processpeptide hormone processing
C0016787molecular_functionhydrolase activity
C0016788molecular_functionhydrolase activity, acting on ester bonds
C0034362cellular_componentlow-density lipoprotein particle
C0034364cellular_componenthigh-density lipoprotein particle
C0034374biological_processlow-density lipoprotein particle remodeling
C0034440biological_processlipid oxidation
C0034441biological_processplasma lipoprotein particle oxidation
C0034638biological_processphosphatidylcholine catabolic process
C0046469biological_processplatelet activating factor metabolic process
C0047499molecular_functioncalcium-independent phospholipase A2 activity
C0050729biological_processpositive regulation of inflammatory response
C0062234biological_processplatelet activating factor catabolic process
C0090026biological_processpositive regulation of monocyte chemotaxis
Functional Information from PDB Data
site_idAC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE NTJ A 473
ChainResidue
AGLY152
AHOH1392
CPHE51
ALEU153
ASER273
APHE274
ATRP298
APHE322
AHIS351
AGLN352
AHOH1210

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 503
ChainResidue
AILE98
AARG122
AGLY126
CPRO337

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 506
ChainResidue
ATYR335
AARG341
ALYS342
AMET343
AFMT522
AHOH1641
BASN423

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 508
ChainResidue
AASP374
AILE375
AHOH1049
AHOH1166
AHOH1631

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 509
ChainResidue
APHE72
AASP73
AGLY78
AHOH1288

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 510
ChainResidue
AARG207
AHIS216
AHOH1323
AHOH1628

site_idAC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 511
ChainResidue
AALA390
AGLN393
ALYS394
AASP403
AASP406
AHOH1176
AHOH1428

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 513
ChainResidue
AARG182
ALEU204
ATYR205
AHOH1290
AHOH1367
AHOH1713

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 518
ChainResidue
AGLU320
AARG347
AGLY348
AHOH1305
AHOH1362
AHOH1631
BASP412

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 521
ChainResidue
AASN135
APRO137
APHE253
AGLN257
AHOH1253

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 522
ChainResidue
ALYS339
AGLU340
AARG341
AFMT506
AHOH1130
AHOH1641

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 524
ChainResidue
AGLN88
AARG139
AHOH1307
AHOH1662

site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 527
ChainResidue
AASN119
AHOH1610

site_idBC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 528
ChainResidue
AVAL245
AASN247
APHE253
AMET255
AHOH1299

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 531
ChainResidue
AASP181
AARG182
AARG207
AFMT553
AHOH1485

site_idBC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT A 533
ChainResidue
AHIS179
AASP181
AARG182
ASER183
AALA184
ATHR187
ALEU204
ATYR205

site_idBC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 534
ChainResidue
APHE322
AVAL350
AHIS351
AHOH1684

site_idBC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 536
ChainResidue
ALYS386
ATRP405

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 538
ChainResidue
AHOH1074
AHOH1206
AHOH1727
ATRP105
ATRP203
ATYR205

site_idCC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT A 539
ChainResidue
ALYS109
AGLY112
ATHR113

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 540
ChainResidue
AASP412
AHOH1271
AHOH1622
BARG92

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 541
ChainResidue
AASP240
AASP260
CASP240
CHIS241
CASP260

site_idCC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT A 544
ChainResidue
AASP406
ACYS407
AHOH1622

site_idCC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 546
ChainResidue
AARG92
AASP94
CILE422
CASN423
CFMT581
CHOH1749
CHOH1839

site_idCC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 547
ChainResidue
AHIS367
AASP374

site_idCC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 551
ChainResidue
AASN100
ATYR188
ALYS201
AHOH1115
AHOH1198
AHOH1490
CASP338

site_idCC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 552
ChainResidue
APRO62
AHIS170
ALYS400
APHE402
AHOH1726

site_idDC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 553
ChainResidue
AGLU220
AGLN221
AGLN224
AFMT531
AHOH1410
AHOH1702

site_idDC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT A 554
ChainResidue
ATHR208
ALEU209
AGLU214
AARG218
AHOH1050
AHOH1624
CSER50

site_idDC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT A 555
ChainResidue
ALYS55
APRO57
AASN378
AFMT556
AHOH1633
AHOH1657
CTHR215
CHOH1880

site_idDC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FMT A 556
ChainResidue
ATHR54
ALYS55
AFMT555
AHOH1633
CTHR215
CPHE300
CFMT582
CHOH1880
CHOH1909

site_idDC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 558
ChainResidue
AGLU265
AARG290
AHIS395
ALEU396
AHOH1375

site_idDC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE NTJ B 473
ChainResidue
BPHE51
BGLY152
BLEU153
BSER273
BPHE274
BTRP298
BPHE322
BHIS351
BGLN352
BHOH1112
BHOH1183

site_idDC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 501
ChainResidue
BPHE72
BASP73
BGLY78
BHOH1656

site_idDC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT B 502
ChainResidue
BPHE322
BVAL350
BHIS351
BHOH1047
BHOH1595

site_idDC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 504
ChainResidue
BASP374
BILE375
BFMT505
BHOH1637

site_idEC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT B 505
ChainResidue
BARG347
BASN415
BFMT504
BFMT515
BHOH1637

site_idEC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 507
ChainResidue
BGLU142
BLYS143
BLYS259
BHOH1683

site_idEC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT B 512
ChainResidue
AASN423
BTYR335
BLYS342
BMET343
BGLY419
BHOH1453
BHOH1521

site_idEC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 514
ChainResidue
BLYS55
BPHE359
BTHR361
BLYS372

site_idEC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT B 515
ChainResidue
AASP412
BGLU320
BTYR321
BARG347
BGLY348
BFMT505
BHOH1262
BHOH1301

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT B 516
ChainResidue
BPRO62
BTYR63
BHIS170
BLYS400
BPHE402
BHOH1400

site_idEC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT B 517
ChainResidue
BGLU212
BVAL379
BHOH1111
BHOH1182
BHOH1236

site_idEC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT B 520
ChainResidue
BGLN393
BLEU398
BHOH1629

site_idEC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT B 523
ChainResidue
BTYR335
BLYS339
BGLU340
BARG341
BHOH1141
BHOH1536

site_idFC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT B 525
ChainResidue
BASN76
BHOH1533
BHOH1567

site_idFC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 526
ChainResidue
ASER336
BARG122
BFMT529
BHOH1325

site_idFC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE FMT B 529
ChainResidue
ASER336
APRO337
BASN100
BLYS101
BARG122
BFMT526
BHOH1048
BHOH1325
BHOH1482

site_idFC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT B 530
ChainResidue
BLYS55
BPRO57
BGLN211
BASN378
BHOH1297
BHOH1572

site_idFC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT B 532
ChainResidue
BTHR54
BLYS55
BMET128
BTHR129
BHOH1132
BHOH1153
BHOH1189

site_idFC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT B 535
ChainResidue
BHIS179
BASP181
BARG182
BSER183
BALA184
BTHR187
BLEU204
BTYR205

site_idFC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT B 537
ChainResidue
BARG309
BFMT549
BHOH1480

site_idFC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT B 542
ChainResidue
BPRO57
BASN60
BGLN211
BASN378
BILE381
BASP382
BHOH1101
BHOH1598

site_idFC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT B 543
ChainResidue
BHOH1632
CPHE72
CASP73

site_idGC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT B 545
ChainResidue
APRO418
BTHR420
BILE422
BASN423
BHOH1099
BHOH1663

site_idGC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE FMT B 548
ChainResidue
BGLN257

site_idGC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT B 549
ChainResidue
BGLU305
BSER308
BARG309
BFMT537
BHOH1157

site_idGC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT B 550
ChainResidue
BILE239
BGLY242
BLYS243
BMET255
BGLU256
BLYS259
BHOH1486

site_idGC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT B 557
ChainResidue
BGLU265
BARG290
BHIS395
BLEU396

site_idGC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT B 586
ChainResidue
BASN318
BSER319
BGLU320
BGLN323
BTHR345
BTHR420
BASN421
BILE422

site_idGC7
Number of Residues11
DetailsBINDING SITE FOR RESIDUE NTJ C 473
ChainResidue
APHE51
CGLY152
CLEU153
CSER273
CPHE274
CTRP298
CPHE322
CHIS351
CGLN352
CHOH1842
CHOH1926

site_idGC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT C 519
ChainResidue
CTHR54
CLYS55
CMET128
CTHR129
CHOH1134
CHOH1195
CHOH1774

site_idGC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 559
ChainResidue
CLYS386
CTRP405
CHOH2047

site_idHC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 560
ChainResidue
CARG182
CTYR205
CFMT561

site_idHC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT C 561
ChainResidue
CTRP203
CTYR205
CFMT560
CHOH1938
CHOH2031

site_idHC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 562
ChainResidue
CGLU220
CGLN224
CHOH1978

site_idHC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT C 563
ChainResidue
CLYS363
CLYS372
CASP376
CSER377
CHOH1789

site_idHC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT C 564
ChainResidue
CASN135
CSER136
CPRO137
CLYS252
CGLN257
CHOH1822

site_idHC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT C 565
ChainResidue
CGLU320
CTYR321
CARG347
CGLY348
CASP412
CHOH2034

site_idHC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 566
ChainResidue
CARG223
CLYS227
CGLU285
CFMT573

site_idHC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 567
ChainResidue
CTRP134
CASN135
CLEU251
CLYS252

site_idHC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT C 568
ChainResidue
CTHR420
CILE422
CASN423
CHOH1802
CHOH1897
CHOH2008

site_idIC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 569
ChainResidue
CASN415
CHOH1762
CHOH1779
CHOH2034

site_idIC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 570
ChainResidue
CTHR208
CFMT571
CHOH2021

site_idIC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT C 571
ChainResidue
CTHR208
CFMT570

site_idIC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 572
ChainResidue
CPRO62
CHIS170
CLYS400
CPHE402

site_idIC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 573
ChainResidue
CARG223
CGLU285
CFMT566

site_idIC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT C 574
ChainResidue
AASP91
AHOH1677
CTYR321
CPHE322
CVAL350
CHIS351
CHOH1875
CHOH2068

site_idIC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT C 575
ChainResidue
CHIS179
CASP181
CARG182
CSER183
CALA184
CTHR187
CLEU204
CTYR205

site_idIC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT C 576
ChainResidue
CASP181
CARG182
CARG207
CGLN221
CHOH1981

site_idIC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 577
ChainResidue
CLYS266
CLEU396
CGLY397

site_idJC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT C 578
ChainResidue
CILE239
CGLY242
CLYS243
CMET255
CGLU256
CLYS259
CHOH1773

site_idJC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FMT C 579
ChainResidue
AGLN211
CPRO57
CASN60
CASN378
CILE381
CASP382
CHOH1817

site_idJC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT C 580
ChainResidue
CLYS386
CHOH1456
CHOH1813
CHOH1949
CHOH2050

site_idJC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 581
ChainResidue
AARG92
AFMT546
CASN421
CASN423

site_idJC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT C 582
ChainResidue
ALYS55
AFMT556
CPHE300
CLYS330
CHOH1857
CHOH1889
CHOH1909
CHOH1921

site_idJC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 583
ChainResidue
CARG309
CHOH1947
CHOH2063
CHOH2074

site_idJC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT C 584
ChainResidue
ATHR215
APHE300
CTHR54
CLYS55
CHOH2016
CHOH2032

site_idJC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT C 585
ChainResidue
CASN318
CSER319
CGLU320
CGLN323
CTHR345
CTHR420
CASN421
CILE422

Functional Information from PROSITE/UniProt
site_idPS00120
Number of Residues10
DetailsLIPASE_SER Lipases, serine active site. IAVIGHSFGG
ChainResidueDetails
AILE267-GLY276

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsACT_SITE: Nucleophile => ECO:0000269|PubMed:18784071
ChainResidueDetails
ASER273
BSER273
CSER273

site_idSWS_FT_FI2
Number of Residues6
DetailsACT_SITE: Charge relay system => ECO:0000255|PROSITE-ProRule:PRU10037, ECO:0000269|PubMed:18784071
ChainResidueDetails
AASP296
AHIS351
BASP296
BHIS351
CASP296
CHIS351

site_idSWS_FT_FI3
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255
ChainResidueDetails
AASN423
BASN423
CASN423

224931

PDB entries from 2024-09-11

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