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3F98
Biol. Unit 1
Info
Asym.Unit (227 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (77 KB)
Biol.Unit 3 (77 KB)
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(1)
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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 32)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1aa: FORMIC ACID (FMTaa)
1ab: FORMIC ACID (FMTab)
1ac: FORMIC ACID (FMTac)
1ad: FORMIC ACID (FMTad)
1ae: FORMIC ACID (FMTae)
1af: FORMIC ACID (FMTaf)
1ag: FORMIC ACID (FMTag)
1ah: FORMIC ACID (FMTah)
1ai: FORMIC ACID (FMTai)
1aj: FORMIC ACID (FMTaj)
1ak: FORMIC ACID (FMTak)
1al: FORMIC ACID (FMTal)
1am: FORMIC ACID (FMTam)
1an: FORMIC ACID (FMTan)
1ao: FORMIC ACID (FMTao)
1ap: FORMIC ACID (FMTap)
1aq: FORMIC ACID (FMTaq)
1ar: FORMIC ACID (FMTar)
1as: FORMIC ACID (FMTas)
1at: FORMIC ACID (FMTat)
1au: FORMIC ACID (FMTau)
1av: FORMIC ACID (FMTav)
1aw: FORMIC ACID (FMTaw)
1ax: FORMIC ACID (FMTax)
1ay: FORMIC ACID (FMTay)
1az: FORMIC ACID (FMTaz)
1b: FORMIC ACID (FMTb)
1ba: FORMIC ACID (FMTba)
1bb: FORMIC ACID (FMTbb)
1bc: FORMIC ACID (FMTbc)
1bd: FORMIC ACID (FMTbd)
1be: FORMIC ACID (FMTbe)
1bf: FORMIC ACID (FMTbf)
1bg: FORMIC ACID (FMTbg)
1bh: FORMIC ACID (FMTbh)
1bi: FORMIC ACID (FMTbi)
1bj: FORMIC ACID (FMTbj)
1bk: FORMIC ACID (FMTbk)
1bl: FORMIC ACID (FMTbl)
1bm: FORMIC ACID (FMTbm)
1bn: FORMIC ACID (FMTbn)
1bo: FORMIC ACID (FMTbo)
1bp: FORMIC ACID (FMTbp)
1bq: FORMIC ACID (FMTbq)
1br: FORMIC ACID (FMTbr)
1bs: FORMIC ACID (FMTbs)
1bt: FORMIC ACID (FMTbt)
1bu: FORMIC ACID (FMTbu)
1bv: FORMIC ACID (FMTbv)
1bw: FORMIC ACID (FMTbw)
1bx: FORMIC ACID (FMTbx)
1by: FORMIC ACID (FMTby)
1bz: FORMIC ACID (FMTbz)
1c: FORMIC ACID (FMTc)
1ca: FORMIC ACID (FMTca)
1cb: FORMIC ACID (FMTcb)
1cc: FORMIC ACID (FMTcc)
1cd: FORMIC ACID (FMTcd)
1ce: FORMIC ACID (FMTce)
1cf: FORMIC ACID (FMTcf)
1cg: FORMIC ACID (FMTcg)
1ch: FORMIC ACID (FMTch)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
1f: FORMIC ACID (FMTf)
1g: FORMIC ACID (FMTg)
1h: FORMIC ACID (FMTh)
1i: FORMIC ACID (FMTi)
1j: FORMIC ACID (FMTj)
1k: FORMIC ACID (FMTk)
1l: FORMIC ACID (FMTl)
1m: FORMIC ACID (FMTm)
1n: FORMIC ACID (FMTn)
1o: FORMIC ACID (FMTo)
1p: FORMIC ACID (FMTp)
1q: FORMIC ACID (FMTq)
1r: FORMIC ACID (FMTr)
1s: FORMIC ACID (FMTs)
1t: FORMIC ACID (FMTt)
1u: FORMIC ACID (FMTu)
1v: FORMIC ACID (FMTv)
1w: FORMIC ACID (FMTw)
1x: FORMIC ACID (FMTx)
1y: FORMIC ACID (FMTy)
1z: FORMIC ACID (FMTz)
2a: R-ETHYL N,N-DIMETHYLPHOSPHONAMIDAT... (NTJa)
2b: R-ETHYL N,N-DIMETHYLPHOSPHONAMIDAT... (NTJb)
2c: R-ETHYL N,N-DIMETHYLPHOSPHONAMIDAT... (NTJc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
31
Ligand/Ion
FORMIC ACID
2
NTJ
1
Ligand/Ion
R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
[
close Hetero Component info
]
Sites
(43, 43)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: EC3 (SOFTWARE)
34: EC5 (SOFTWARE)
35: FC2 (SOFTWARE)
36: FC3 (SOFTWARE)
37: GC1 (SOFTWARE)
38: GC7 (SOFTWARE)
39: IC6 (SOFTWARE)
40: JC2 (SOFTWARE)
41: JC4 (SOFTWARE)
42: JC5 (SOFTWARE)
43: JC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY 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:51
BINDING SITE FOR RESIDUE NTJ A 473
02
AC2
SOFTWARE
ILE A:98 , ARG A:122 , GLY A:126 , PRO C:337
BINDING SITE FOR RESIDUE FMT A 503
03
AC3
SOFTWARE
TYR A:335 , ARG A:341 , LYS A:342 , MET A:343 , FMT A:522 , HOH A:1641 , ASN B:423
BINDING SITE FOR RESIDUE FMT A 506
04
AC4
SOFTWARE
ASP A:374 , ILE A:375 , HOH A:1049 , HOH A:1166 , HOH A:1631
BINDING SITE FOR RESIDUE FMT A 508
05
AC5
SOFTWARE
PHE A:72 , ASP A:73 , GLY A:78 , HOH A:1288
BINDING SITE FOR RESIDUE FMT A 509
06
AC6
SOFTWARE
ARG A:207 , HIS A:216 , HOH A:1323 , HOH A:1628
BINDING SITE FOR RESIDUE FMT A 510
07
AC7
SOFTWARE
ALA A:390 , GLN A:393 , LYS A:394 , ASP A:403 , ASP A:406 , HOH A:1176 , HOH A:1428
BINDING SITE FOR RESIDUE FMT A 511
08
AC8
SOFTWARE
ARG A:182 , LEU A:204 , TYR A:205 , HOH A:1290 , HOH A:1367 , HOH A:1713
BINDING SITE FOR RESIDUE FMT A 513
09
AC9
SOFTWARE
GLU A:320 , ARG A:347 , GLY A:348 , HOH A:1305 , HOH A:1362 , HOH A:1631 , ASP B:412
BINDING SITE FOR RESIDUE FMT A 518
10
BC1
SOFTWARE
ASN A:135 , PRO A:137 , PHE A:253 , GLN A:257 , HOH A:1253
BINDING SITE FOR RESIDUE FMT A 521
11
BC2
SOFTWARE
LYS A:339 , GLU A:340 , ARG A:341 , FMT A:506 , HOH A:1130 , HOH A:1641
BINDING SITE FOR RESIDUE FMT A 522
12
BC3
SOFTWARE
GLN A:88 , ARG A:139 , HOH A:1307 , HOH A:1662
BINDING SITE FOR RESIDUE FMT A 524
13
BC4
SOFTWARE
ASN A:119 , HOH A:1610
BINDING SITE FOR RESIDUE FMT A 527
14
BC5
SOFTWARE
VAL A:245 , ASN A:247 , PHE A:253 , MET A:255 , HOH A:1299
BINDING SITE FOR RESIDUE FMT A 528
15
BC6
SOFTWARE
ASP A:181 , ARG A:182 , ARG A:207 , FMT A:553 , HOH A:1485
BINDING SITE FOR RESIDUE FMT A 531
16
BC7
SOFTWARE
HIS A:179 , ASP A:181 , ARG A:182 , SER A:183 , ALA A:184 , THR A:187 , LEU A:204 , TYR A:205
BINDING SITE FOR RESIDUE FMT A 533
17
BC8
SOFTWARE
PHE A:322 , VAL A:350 , HIS A:351 , HOH A:1684
BINDING SITE FOR RESIDUE FMT A 534
18
BC9
SOFTWARE
LYS A:386 , TRP A:405
BINDING SITE FOR RESIDUE FMT A 536
19
CC1
SOFTWARE
TRP A:105 , TRP A:203 , TYR A:205 , HOH A:1074 , HOH A:1206 , HOH A:1727
BINDING SITE FOR RESIDUE FMT A 538
20
CC2
SOFTWARE
LYS A:109 , GLY A:112 , THR A:113
BINDING SITE FOR RESIDUE FMT A 539
21
CC3
SOFTWARE
ASP A:412 , HOH A:1271 , HOH A:1622 , ARG B:92
BINDING SITE FOR RESIDUE FMT A 540
22
CC4
SOFTWARE
ASP A:240 , ASP A:260 , ASP C:240 , HIS C:241 , ASP C:260
BINDING SITE FOR RESIDUE FMT A 541
23
CC5
SOFTWARE
ASP A:406 , CYS A:407 , HOH A:1622
BINDING SITE FOR RESIDUE FMT A 544
24
CC6
SOFTWARE
ARG A:92 , ASP A:94 , ILE C:422 , ASN C:423 , FMT C:581 , HOH C:1749 , HOH C:1839
BINDING SITE FOR RESIDUE FMT A 546
25
CC7
SOFTWARE
HIS A:367 , ASP A:374
BINDING SITE FOR RESIDUE FMT A 547
26
CC8
SOFTWARE
ASN A:100 , TYR A:188 , LYS A:201 , HOH A:1115 , HOH A:1198 , HOH A:1490 , ASP C:338
BINDING SITE FOR RESIDUE FMT A 551
27
CC9
SOFTWARE
PRO A:62 , HIS A:170 , LYS A:400 , PHE A:402 , HOH A:1726
BINDING SITE FOR RESIDUE FMT A 552
28
DC1
SOFTWARE
GLU A:220 , GLN A:221 , GLN A:224 , FMT A:531 , HOH A:1410 , HOH A:1702
BINDING SITE FOR RESIDUE FMT A 553
29
DC2
SOFTWARE
THR A:208 , LEU A:209 , GLU A:214 , ARG A:218 , HOH A:1050 , HOH A:1624 , SER C:50
BINDING SITE FOR RESIDUE FMT A 554
30
DC3
SOFTWARE
LYS A:55 , PRO A:57 , ASN A:378 , FMT A:556 , HOH A:1633 , HOH A:1657 , THR C:215 , HOH C:1880
BINDING SITE FOR RESIDUE FMT A 555
31
DC4
SOFTWARE
THR 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:1909
BINDING SITE FOR RESIDUE FMT A 556
32
DC5
SOFTWARE
GLU A:265 , ARG A:290 , HIS A:395 , LEU A:396 , HOH A:1375
BINDING SITE FOR RESIDUE FMT A 558
33
EC3
SOFTWARE
ASN A:423 , TYR B:335 , LYS B:342 , MET B:343 , GLY B:419 , HOH B:1453 , HOH B:1521
BINDING SITE FOR RESIDUE FMT B 512
34
EC5
SOFTWARE
ASP A:412 , GLU B:320 , TYR B:321 , ARG B:347 , GLY B:348 , FMT B:505 , HOH B:1262 , HOH B:1301
BINDING SITE FOR RESIDUE FMT B 515
35
FC2
SOFTWARE
SER A:336 , ARG B:122 , FMT B:529 , HOH B:1325
BINDING SITE FOR RESIDUE FMT B 526
36
FC3
SOFTWARE
SER 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:1482
BINDING SITE FOR RESIDUE FMT B 529
37
GC1
SOFTWARE
PRO A:418 , THR B:420 , ILE B:422 , ASN B:423 , HOH B:1099 , HOH B:1663
BINDING SITE FOR RESIDUE FMT B 545
38
GC7
SOFTWARE
PHE 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:1926
BINDING SITE FOR RESIDUE NTJ C 473
39
IC6
SOFTWARE
ASP A:91 , HOH A:1677 , TYR C:321 , PHE C:322 , VAL C:350 , HIS C:351 , HOH C:1875 , HOH C:2068
BINDING SITE FOR RESIDUE FMT C 574
40
JC2
SOFTWARE
GLN A:211 , PRO C:57 , ASN C:60 , ASN C:378 , ILE C:381 , ASP C:382 , HOH C:1817
BINDING SITE FOR RESIDUE FMT C 579
41
JC4
SOFTWARE
ARG A:92 , FMT A:546 , ASN C:421 , ASN C:423
BINDING SITE FOR RESIDUE FMT C 581
42
JC5
SOFTWARE
LYS A:55 , FMT A:556 , PHE C:300 , LYS C:330 , HOH C:1857 , HOH C:1889 , HOH C:1909 , HOH C:1921
BINDING SITE FOR RESIDUE FMT C 582
43
JC7
SOFTWARE
THR A:215 , PHE A:300 , THR C:54 , LYS C:55 , HOH C:2016 , HOH C:2032
BINDING SITE FOR RESIDUE FMT C 584
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_011583 (R92H, chain A, )
2: VAR_047971 (K191N, chain A, )
3: VAR_011584 (I198T, chain A, )
4: VAR_004268 (V279F, chain A, )
5: VAR_011585 (Q281R, chain A, )
6: VAR_011586 (V379A, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011583
R
92
H
PAFA_HUMAN
Polymorphism
1805017
A
R
92
H
2
UniProt
VAR_047971
K
191
N
PAFA_HUMAN
Polymorphism
45454695
A
K
191
N
3
UniProt
VAR_011584
I
198
T
PAFA_HUMAN
Polymorphism
1805018
A
I
198
T
4
UniProt
VAR_004268
V
279
F
PAFA_HUMAN
Disease (PAFAD)
16874954
A
V
279
F
5
UniProt
VAR_011585
Q
281
R
PAFA_HUMAN
Disease (PAFAD)
---
A
Q
281
R
6
UniProt
VAR_011586
V
379
A
PAFA_HUMAN
Polymorphism
1051931
A
V
379
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: LIPASE_SER (A:267-276)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LIPASE_SER
PS00120
Lipases, serine active site.
PAFA_HUMAN
267-276
1
A:267-276
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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