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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR ACETYLHYDROLASE COVALENTLY INHIBITED BY TABUN
 
Authors :  U. Samanta, B. J. Bahnson
Date :  13 Nov 08  (Deposition) - 23 Jun 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Plasma Platelet-Activating Factor Acetylhydrolase, Secreted Protein, Alpha/Beta-Hydrolase-Fold, Ldl-Bound; Lipoprotein Associated Phospholipase A2, Lp-Pla2, Group Viia Pla2, Glycoprotein, Hydrolase, Lipid Degradation, Polymorphism, Tabun, Disease Mutation, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Samanta, S. D. Kirby, P. Srinivasan, D. M. Cerasoli, B. J. Bahnson
Crystal Structures Of Human Group-Viia Phospholipase A2 Inhibited By Organophosphorus Nerve Agents Exhibit Non-Aged Complexes.
Biochem Pharmacol V. 78 420 2009
PubMed-ID: 19394314  |  Reference-DOI: 10.1016/J.BCP.2009.04.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
    Chains: A, B, C
    EC Number: 3.1.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 47-429
    Gene: PLA2G7, PAFAH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAF ACETYLHYDROLASE, PAF 2-ACYLHYDROLASE, LDL- ASSOCIATED PHOSPHOLIPASE A2, LDL-PLA(2), 2-ACETYL-1- ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE, 1-ALKYL-2- ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 89)

Asymmetric Unit (2, 89)
No.NameCountTypeFull Name
1FMT86Ligand/IonFORMIC ACID
2NTJ3Ligand/IonR-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1FMT31Ligand/IonFORMIC ACID
2NTJ1Ligand/IonR-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
Biological Unit 2 (2, 28)
No.NameCountTypeFull Name
1FMT27Ligand/IonFORMIC ACID
2NTJ1Ligand/IonR-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
Biological Unit 3 (2, 29)
No.NameCountTypeFull Name
1FMT28Ligand/IonFORMIC ACID
2NTJ1Ligand/IonR-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE

(-) Sites  (89, 89)

Asymmetric Unit (89, 89)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:152 , LEU A:153 , SER A:273 , PHE A:274 , TRP A:298 , PHE A:322 , HIS A:351 , GLN A:352 , HOH A:1210 , HOH A:1392 , PHE C:51BINDING SITE FOR RESIDUE NTJ A 473
02AC2SOFTWAREILE A:98 , ARG A:122 , GLY A:126 , PRO C:337BINDING SITE FOR RESIDUE FMT A 503
03AC3SOFTWARETYR A:335 , ARG A:341 , LYS A:342 , MET A:343 , FMT A:522 , HOH A:1641 , ASN B:423BINDING SITE FOR RESIDUE FMT A 506
04AC4SOFTWAREASP A:374 , ILE A:375 , HOH A:1049 , HOH A:1166 , HOH A:1631BINDING SITE FOR RESIDUE FMT A 508
05AC5SOFTWAREPHE A:72 , ASP A:73 , GLY A:78 , HOH A:1288BINDING SITE FOR RESIDUE FMT A 509
06AC6SOFTWAREARG A:207 , HIS A:216 , HOH A:1323 , HOH A:1628BINDING SITE FOR RESIDUE FMT A 510
07AC7SOFTWAREALA A:390 , GLN A:393 , LYS A:394 , ASP A:403 , ASP A:406 , HOH A:1176 , HOH A:1428BINDING SITE FOR RESIDUE FMT A 511
08AC8SOFTWAREARG A:182 , LEU A:204 , TYR A:205 , HOH A:1290 , HOH A:1367 , HOH A:1713BINDING SITE FOR RESIDUE FMT A 513
09AC9SOFTWAREGLU A:320 , ARG A:347 , GLY A:348 , HOH A:1305 , HOH A:1362 , HOH A:1631 , ASP B:412BINDING SITE FOR RESIDUE FMT A 518
10BC1SOFTWAREASN A:135 , PRO A:137 , PHE A:253 , GLN A:257 , HOH A:1253BINDING SITE FOR RESIDUE FMT A 521
11BC2SOFTWARELYS A:339 , GLU A:340 , ARG A:341 , FMT A:506 , HOH A:1130 , HOH A:1641BINDING SITE FOR RESIDUE FMT A 522
12BC3SOFTWAREGLN A:88 , ARG A:139 , HOH A:1307 , HOH A:1662BINDING SITE FOR RESIDUE FMT A 524
13BC4SOFTWAREASN A:119 , HOH A:1610BINDING SITE FOR RESIDUE FMT A 527
14BC5SOFTWAREVAL A:245 , ASN A:247 , PHE A:253 , MET A:255 , HOH A:1299BINDING SITE FOR RESIDUE FMT A 528
15BC6SOFTWAREASP A:181 , ARG A:182 , ARG A:207 , FMT A:553 , HOH A:1485BINDING SITE FOR RESIDUE FMT A 531
16BC7SOFTWAREHIS A:179 , ASP A:181 , ARG A:182 , SER A:183 , ALA A:184 , THR A:187 , LEU A:204 , TYR A:205BINDING SITE FOR RESIDUE FMT A 533
17BC8SOFTWAREPHE A:322 , VAL A:350 , HIS A:351 , HOH A:1684BINDING SITE FOR RESIDUE FMT A 534
18BC9SOFTWARELYS A:386 , TRP A:405BINDING SITE FOR RESIDUE FMT A 536
19CC1SOFTWARETRP A:105 , TRP A:203 , TYR A:205 , HOH A:1074 , HOH A:1206 , HOH A:1727BINDING SITE FOR RESIDUE FMT A 538
20CC2SOFTWARELYS A:109 , GLY A:112 , THR A:113BINDING SITE FOR RESIDUE FMT A 539
21CC3SOFTWAREASP A:412 , HOH A:1271 , HOH A:1622 , ARG B:92BINDING SITE FOR RESIDUE FMT A 540
22CC4SOFTWAREASP A:240 , ASP A:260 , ASP C:240 , HIS C:241 , ASP C:260BINDING SITE FOR RESIDUE FMT A 541
23CC5SOFTWAREASP A:406 , CYS A:407 , HOH A:1622BINDING SITE FOR RESIDUE FMT A 544
24CC6SOFTWAREARG A:92 , ASP A:94 , ILE C:422 , ASN C:423 , FMT C:581 , HOH C:1749 , HOH C:1839BINDING SITE FOR RESIDUE FMT A 546
25CC7SOFTWAREHIS A:367 , ASP A:374BINDING SITE FOR RESIDUE FMT A 547
26CC8SOFTWAREASN A:100 , TYR A:188 , LYS A:201 , HOH A:1115 , HOH A:1198 , HOH A:1490 , ASP C:338BINDING SITE FOR RESIDUE FMT A 551
27CC9SOFTWAREPRO A:62 , HIS A:170 , LYS A:400 , PHE A:402 , HOH A:1726BINDING SITE FOR RESIDUE FMT A 552
28DC1SOFTWAREGLU A:220 , GLN A:221 , GLN A:224 , FMT A:531 , HOH A:1410 , HOH A:1702BINDING SITE FOR RESIDUE FMT A 553
29DC2SOFTWARETHR A:208 , LEU A:209 , GLU A:214 , ARG A:218 , HOH A:1050 , HOH A:1624 , SER C:50BINDING SITE FOR RESIDUE FMT A 554
30DC3SOFTWARELYS A:55 , PRO A:57 , ASN A:378 , FMT A:556 , HOH A:1633 , HOH A:1657 , THR C:215 , HOH C:1880BINDING SITE FOR RESIDUE FMT A 555
31DC4SOFTWARETHR A:54 , LYS A:55 , FMT A:555 , HOH A:1633 , THR C:215 , PHE C:300 , FMT C:582 , HOH C:1880 , HOH C:1909BINDING SITE FOR RESIDUE FMT A 556
32DC5SOFTWAREGLU A:265 , ARG A:290 , HIS A:395 , LEU A:396 , HOH A:1375BINDING SITE FOR RESIDUE FMT A 558
33DC6SOFTWAREPHE B:51 , GLY B:152 , LEU B:153 , SER B:273 , PHE B:274 , TRP B:298 , PHE B:322 , HIS B:351 , GLN B:352 , HOH B:1112 , HOH B:1183BINDING SITE FOR RESIDUE NTJ B 473
34DC7SOFTWAREPHE B:72 , ASP B:73 , GLY B:78 , HOH B:1656BINDING SITE FOR RESIDUE FMT B 501
35DC8SOFTWAREPHE B:322 , VAL B:350 , HIS B:351 , HOH B:1047 , HOH B:1595BINDING SITE FOR RESIDUE FMT B 502
36DC9SOFTWAREASP B:374 , ILE B:375 , FMT B:505 , HOH B:1637BINDING SITE FOR RESIDUE FMT B 504
37EC1SOFTWAREARG B:347 , ASN B:415 , FMT B:504 , FMT B:515 , HOH B:1637BINDING SITE FOR RESIDUE FMT B 505
38EC2SOFTWAREGLU B:142 , LYS B:143 , LYS B:259 , HOH B:1683BINDING SITE FOR RESIDUE FMT B 507
39EC3SOFTWAREASN A:423 , TYR B:335 , LYS B:342 , MET B:343 , GLY B:419 , HOH B:1453 , HOH B:1521BINDING SITE FOR RESIDUE FMT B 512
40EC4SOFTWARELYS B:55 , PHE B:359 , THR B:361 , LYS B:372BINDING SITE FOR RESIDUE FMT B 514
41EC5SOFTWAREASP A:412 , GLU B:320 , TYR B:321 , ARG B:347 , GLY B:348 , FMT B:505 , HOH B:1262 , HOH B:1301BINDING SITE FOR RESIDUE FMT B 515
42EC6SOFTWAREPRO B:62 , TYR B:63 , HIS B:170 , LYS B:400 , PHE B:402 , HOH B:1400BINDING SITE FOR RESIDUE FMT B 516
43EC7SOFTWAREGLU B:212 , VAL B:379 , HOH B:1111 , HOH B:1182 , HOH B:1236BINDING SITE FOR RESIDUE FMT B 517
44EC8SOFTWAREGLN B:393 , LEU B:398 , HOH B:1629BINDING SITE FOR RESIDUE FMT B 520
45EC9SOFTWARETYR B:335 , LYS B:339 , GLU B:340 , ARG B:341 , HOH B:1141 , HOH B:1536BINDING SITE FOR RESIDUE FMT B 523
46FC1SOFTWAREASN B:76 , HOH B:1533 , HOH B:1567BINDING SITE FOR RESIDUE FMT B 525
47FC2SOFTWARESER A:336 , ARG B:122 , FMT B:529 , HOH B:1325BINDING SITE FOR RESIDUE FMT B 526
48FC3SOFTWARESER A:336 , PRO A:337 , ASN B:100 , LYS B:101 , ARG B:122 , FMT B:526 , HOH B:1048 , HOH B:1325 , HOH B:1482BINDING SITE FOR RESIDUE FMT B 529
49FC4SOFTWARELYS B:55 , PRO B:57 , GLN B:211 , ASN B:378 , HOH B:1297 , HOH B:1572BINDING SITE FOR RESIDUE FMT B 530
50FC5SOFTWARETHR B:54 , LYS B:55 , MET B:128 , THR B:129 , HOH B:1132 , HOH B:1153 , HOH B:1189BINDING SITE FOR RESIDUE FMT B 532
51FC6SOFTWAREHIS B:179 , ASP B:181 , ARG B:182 , SER B:183 , ALA B:184 , THR B:187 , LEU B:204 , TYR B:205BINDING SITE FOR RESIDUE FMT B 535
52FC7SOFTWAREARG B:309 , FMT B:549 , HOH B:1480BINDING SITE FOR RESIDUE FMT B 537
53FC8SOFTWAREPRO B:57 , ASN B:60 , GLN B:211 , ASN B:378 , ILE B:381 , ASP B:382 , HOH B:1101 , HOH B:1598BINDING SITE FOR RESIDUE FMT B 542
54FC9SOFTWAREHOH B:1632 , PHE C:72 , ASP C:73BINDING SITE FOR RESIDUE FMT B 543
55GC1SOFTWAREPRO A:418 , THR B:420 , ILE B:422 , ASN B:423 , HOH B:1099 , HOH B:1663BINDING SITE FOR RESIDUE FMT B 545
56GC2SOFTWAREGLN B:257BINDING SITE FOR RESIDUE FMT B 548
57GC3SOFTWAREGLU B:305 , SER B:308 , ARG B:309 , FMT B:537 , HOH B:1157BINDING SITE FOR RESIDUE FMT B 549
58GC4SOFTWAREILE B:239 , GLY B:242 , LYS B:243 , MET B:255 , GLU B:256 , LYS B:259 , HOH B:1486BINDING SITE FOR RESIDUE FMT B 550
59GC5SOFTWAREGLU B:265 , ARG B:290 , HIS B:395 , LEU B:396BINDING SITE FOR RESIDUE FMT B 557
60GC6SOFTWAREASN B:318 , SER B:319 , GLU B:320 , GLN B:323 , THR B:345 , THR B:420 , ASN B:421 , ILE B:422BINDING SITE FOR RESIDUE FMT B 586
61GC7SOFTWAREPHE A:51 , GLY C:152 , LEU C:153 , SER C:273 , PHE C:274 , TRP C:298 , PHE C:322 , HIS C:351 , GLN C:352 , HOH C:1842 , HOH C:1926BINDING SITE FOR RESIDUE NTJ C 473
62GC8SOFTWARETHR C:54 , LYS C:55 , MET C:128 , THR C:129 , HOH C:1134 , HOH C:1195 , HOH C:1774BINDING SITE FOR RESIDUE FMT C 519
63GC9SOFTWARELYS C:386 , TRP C:405 , HOH C:2047BINDING SITE FOR RESIDUE FMT C 559
64HC1SOFTWAREARG C:182 , TYR C:205 , FMT C:561BINDING SITE FOR RESIDUE FMT C 560
65HC2SOFTWARETRP C:203 , TYR C:205 , FMT C:560 , HOH C:1938 , HOH C:2031BINDING SITE FOR RESIDUE FMT C 561
66HC3SOFTWAREGLU C:220 , GLN C:224 , HOH C:1978BINDING SITE FOR RESIDUE FMT C 562
67HC4SOFTWARELYS C:363 , LYS C:372 , ASP C:376 , SER C:377 , HOH C:1789BINDING SITE FOR RESIDUE FMT C 563
68HC5SOFTWAREASN C:135 , SER C:136 , PRO C:137 , LYS C:252 , GLN C:257 , HOH C:1822BINDING SITE FOR RESIDUE FMT C 564
69HC6SOFTWAREGLU C:320 , TYR C:321 , ARG C:347 , GLY C:348 , ASP C:412 , HOH C:2034BINDING SITE FOR RESIDUE FMT C 565
70HC7SOFTWAREARG C:223 , LYS C:227 , GLU C:285 , FMT C:573BINDING SITE FOR RESIDUE FMT C 566
71HC8SOFTWARETRP C:134 , ASN C:135 , LEU C:251 , LYS C:252BINDING SITE FOR RESIDUE FMT C 567
72HC9SOFTWARETHR C:420 , ILE C:422 , ASN C:423 , HOH C:1802 , HOH C:1897 , HOH C:2008BINDING SITE FOR RESIDUE FMT C 568
73IC1SOFTWAREASN C:415 , HOH C:1762 , HOH C:1779 , HOH C:2034BINDING SITE FOR RESIDUE FMT C 569
74IC2SOFTWARETHR C:208 , FMT C:571 , HOH C:2021BINDING SITE FOR RESIDUE FMT C 570
75IC3SOFTWARETHR C:208 , FMT C:570BINDING SITE FOR RESIDUE FMT C 571
76IC4SOFTWAREPRO C:62 , HIS C:170 , LYS C:400 , PHE C:402BINDING SITE FOR RESIDUE FMT C 572
77IC5SOFTWAREARG C:223 , GLU C:285 , FMT C:566BINDING SITE FOR RESIDUE FMT C 573
78IC6SOFTWAREASP A:91 , HOH A:1677 , TYR C:321 , PHE C:322 , VAL C:350 , HIS C:351 , HOH C:1875 , HOH C:2068BINDING SITE FOR RESIDUE FMT C 574
79IC7SOFTWAREHIS C:179 , ASP C:181 , ARG C:182 , SER C:183 , ALA C:184 , THR C:187 , LEU C:204 , TYR C:205BINDING SITE FOR RESIDUE FMT C 575
80IC8SOFTWAREASP C:181 , ARG C:182 , ARG C:207 , GLN C:221 , HOH C:1981BINDING SITE FOR RESIDUE FMT C 576
81IC9SOFTWARELYS C:266 , LEU C:396 , GLY C:397BINDING SITE FOR RESIDUE FMT C 577
82JC1SOFTWAREILE C:239 , GLY C:242 , LYS C:243 , MET C:255 , GLU C:256 , LYS C:259 , HOH C:1773BINDING SITE FOR RESIDUE FMT C 578
83JC2SOFTWAREGLN A:211 , PRO C:57 , ASN C:60 , ASN C:378 , ILE C:381 , ASP C:382 , HOH C:1817BINDING SITE FOR RESIDUE FMT C 579
84JC3SOFTWARELYS C:386 , HOH C:1456 , HOH C:1813 , HOH C:1949 , HOH C:2050BINDING SITE FOR RESIDUE FMT C 580
85JC4SOFTWAREARG A:92 , FMT A:546 , ASN C:421 , ASN C:423BINDING SITE FOR RESIDUE FMT C 581
86JC5SOFTWARELYS A:55 , FMT A:556 , PHE C:300 , LYS C:330 , HOH C:1857 , HOH C:1889 , HOH C:1909 , HOH C:1921BINDING SITE FOR RESIDUE FMT C 582
87JC6SOFTWAREARG C:309 , HOH C:1947 , HOH C:2063 , HOH C:2074BINDING SITE FOR RESIDUE FMT C 583
88JC7SOFTWARETHR A:215 , PHE A:300 , THR C:54 , LYS C:55 , HOH C:2016 , HOH C:2032BINDING SITE FOR RESIDUE FMT C 584
89JC8SOFTWAREASN C:318 , SER C:319 , GLU C:320 , GLN C:323 , THR C:345 , THR C:420 , ASN C:421 , ILE C:422BINDING SITE FOR RESIDUE FMT C 585

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F98)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:72 -Asp A:73
2Phe B:72 -Asp B:73
3Phe C:72 -Asp C:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 18)

Asymmetric Unit (6, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011583R92HPAFA_HUMANPolymorphism1805017A/B/CR92H
2UniProtVAR_047971K191NPAFA_HUMANPolymorphism45454695A/B/CK191N
3UniProtVAR_011584I198TPAFA_HUMANPolymorphism1805018A/B/CI198T
4UniProtVAR_004268V279FPAFA_HUMANDisease (PAFAD)76863441A/B/CV279F
5UniProtVAR_011585Q281RPAFA_HUMANDisease (PAFAD)201256712A/B/CQ281R
6UniProtVAR_011586V379APAFA_HUMANPolymorphism1051931A/B/CV379A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011583R92HPAFA_HUMANPolymorphism1805017AR92H
2UniProtVAR_047971K191NPAFA_HUMANPolymorphism45454695AK191N
3UniProtVAR_011584I198TPAFA_HUMANPolymorphism1805018AI198T
4UniProtVAR_004268V279FPAFA_HUMANDisease (PAFAD)76863441AV279F
5UniProtVAR_011585Q281RPAFA_HUMANDisease (PAFAD)201256712AQ281R
6UniProtVAR_011586V379APAFA_HUMANPolymorphism1051931AV379A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011583R92HPAFA_HUMANPolymorphism1805017BR92H
2UniProtVAR_047971K191NPAFA_HUMANPolymorphism45454695BK191N
3UniProtVAR_011584I198TPAFA_HUMANPolymorphism1805018BI198T
4UniProtVAR_004268V279FPAFA_HUMANDisease (PAFAD)76863441BV279F
5UniProtVAR_011585Q281RPAFA_HUMANDisease (PAFAD)201256712BQ281R
6UniProtVAR_011586V379APAFA_HUMANPolymorphism1051931BV379A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011583R92HPAFA_HUMANPolymorphism1805017CR92H
2UniProtVAR_047971K191NPAFA_HUMANPolymorphism45454695CK191N
3UniProtVAR_011584I198TPAFA_HUMANPolymorphism1805018CI198T
4UniProtVAR_004268V279FPAFA_HUMANDisease (PAFAD)76863441CV279F
5UniProtVAR_011585Q281RPAFA_HUMANDisease (PAFAD)201256712CQ281R
6UniProtVAR_011586V379APAFA_HUMANPolymorphism1051931CV379A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.PAFA_HUMAN267-276
 
 		  3A:267-276
B:267-276
C:267-276
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.PAFA_HUMAN267-276
 
 		  1A:267-276
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.PAFA_HUMAN267-276
 
 		  1-
B:267-276
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.PAFA_HUMAN267-276
 
 		  1-
-
C:267-276

(-) Exons   (0, 0)

(no "Exon" information available for 3F98)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:377
 aligned with PAFA_HUMAN | Q13093 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:377
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       
           PAFA_HUMAN    49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh..hhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeee.hhhhhhhhhhhhhh....eeeee.......hhhhhhhh...eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------H--------------------------------------------------------------------------------------------------N------T--------------------------------------------------------------------------------F-R-------------------------------------------------------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f98 A  49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       


Chain B from PDB  Type:PROTEIN  Length:377
 aligned with PAFA_HUMAN | Q13093 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:377
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       
           PAFA_HUMAN    49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh..hhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeee.hhhhhhhhhhhhhh....eeeee.......hhhhhhhh...eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------H--------------------------------------------------------------------------------------------------N------T--------------------------------------------------------------------------------F-R-------------------------------------------------------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f98 B  49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       


Chain C from PDB  Type:PROTEIN  Length:377
 aligned with PAFA_HUMAN | Q13093 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:377
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       
           PAFA_HUMAN    49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh..hhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeee.hhhhhhhhhhhhhh....eeeee.......hhhhhhhh...eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------H--------------------------------------------------------------------------------------------------N------T--------------------------------------------------------------------------------F-R-------------------------------------------------------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f98 C  49 ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTT 425
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3F98)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F98)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F98)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PAFA_HUMAN | Q13093)
molecular function
    GO:0003847    1-alkyl-2-acetylglycerophosphocholine esterase activity    Catalysis of the reaction: 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine + H2O = 1-alkyl-sn-glycero-3-phosphocholine + acetate.
    GO:0047499    calcium-independent phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. This reaction does not require Ca2+.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0034440    lipid oxidation    The removal of one or more electrons from a lipid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
    GO:0034374    low-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0034441    plasma lipoprotein oxidation    The modification of a lipoprotein by oxidation of one or more amino acids or the lipid group, occurring in the blood plasma.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0034362    low-density lipoprotein particle    A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.

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  3f98
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
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    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
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  PAFA_HUMAN | Q13093
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  3.1.1.47
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  614278
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAFA_HUMAN | Q13093: 3d59 3d5e 3f96 3f97 3f9c 5i8p 5i9i 5jad 5jah 5jal 5jan 5jao 5jap 5jar 5jas 5jat 5jau 5lp1 5lyy 5lz2 5lz4 5lz5 5lz7 5lz8 5lz9

(-) Related Entries Specified in the PDB File

3d59 THE SAME WILD TYPE PROTEIN
3d5e THE SAME PROTEIN COMPLEXED WITH PARAOXON
3f96 THE SAME PROTEIN COMPLEXED WITH SARIN
3f97 THE SAME PROTEIN COMPLEXED WITH SOMAN
3f98 THE SAME PROTEIN COMPLEXED WITH DIISOPROPYLFLUOROPHOSPHATE