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3F98
Biol. Unit 2
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, 28)
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
27
Ligand/Ion
FORMIC ACID
2
NTJ
1
Ligand/Ion
R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC9 (SOFTWARE)
03: CC3 (SOFTWARE)
04: DC6 (SOFTWARE)
05: DC7 (SOFTWARE)
06: DC8 (SOFTWARE)
07: DC9 (SOFTWARE)
08: EC1 (SOFTWARE)
09: EC2 (SOFTWARE)
10: EC3 (SOFTWARE)
11: EC4 (SOFTWARE)
12: EC5 (SOFTWARE)
13: EC6 (SOFTWARE)
14: EC7 (SOFTWARE)
15: EC8 (SOFTWARE)
16: EC9 (SOFTWARE)
17: FC1 (SOFTWARE)
18: FC2 (SOFTWARE)
19: FC3 (SOFTWARE)
20: FC4 (SOFTWARE)
21: FC5 (SOFTWARE)
22: FC6 (SOFTWARE)
23: FC7 (SOFTWARE)
24: FC8 (SOFTWARE)
25: FC9 (SOFTWARE)
26: GC1 (SOFTWARE)
27: GC2 (SOFTWARE)
28: GC3 (SOFTWARE)
29: GC4 (SOFTWARE)
30: GC5 (SOFTWARE)
31: GC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
CC3
SOFTWARE
ASP A:412 , HOH A:1271 , HOH A:1622 , ARG B:92
BINDING SITE FOR RESIDUE FMT A 540
04
DC6
SOFTWARE
PHE 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:1183
BINDING SITE FOR RESIDUE NTJ B 473
05
DC7
SOFTWARE
PHE B:72 , ASP B:73 , GLY B:78 , HOH B:1656
BINDING SITE FOR RESIDUE FMT B 501
06
DC8
SOFTWARE
PHE B:322 , VAL B:350 , HIS B:351 , HOH B:1047 , HOH B:1595
BINDING SITE FOR RESIDUE FMT B 502
07
DC9
SOFTWARE
ASP B:374 , ILE B:375 , FMT B:505 , HOH B:1637
BINDING SITE FOR RESIDUE FMT B 504
08
EC1
SOFTWARE
ARG B:347 , ASN B:415 , FMT B:504 , FMT B:515 , HOH B:1637
BINDING SITE FOR RESIDUE FMT B 505
09
EC2
SOFTWARE
GLU B:142 , LYS B:143 , LYS B:259 , HOH B:1683
BINDING SITE FOR RESIDUE FMT B 507
10
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
11
EC4
SOFTWARE
LYS B:55 , PHE B:359 , THR B:361 , LYS B:372
BINDING SITE FOR RESIDUE FMT B 514
12
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
13
EC6
SOFTWARE
PRO B:62 , TYR B:63 , HIS B:170 , LYS B:400 , PHE B:402 , HOH B:1400
BINDING SITE FOR RESIDUE FMT B 516
14
EC7
SOFTWARE
GLU B:212 , VAL B:379 , HOH B:1111 , HOH B:1182 , HOH B:1236
BINDING SITE FOR RESIDUE FMT B 517
15
EC8
SOFTWARE
GLN B:393 , LEU B:398 , HOH B:1629
BINDING SITE FOR RESIDUE FMT B 520
16
EC9
SOFTWARE
TYR B:335 , LYS B:339 , GLU B:340 , ARG B:341 , HOH B:1141 , HOH B:1536
BINDING SITE FOR RESIDUE FMT B 523
17
FC1
SOFTWARE
ASN B:76 , HOH B:1533 , HOH B:1567
BINDING SITE FOR RESIDUE FMT B 525
18
FC2
SOFTWARE
SER A:336 , ARG B:122 , FMT B:529 , HOH B:1325
BINDING SITE FOR RESIDUE FMT B 526
19
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
20
FC4
SOFTWARE
LYS B:55 , PRO B:57 , GLN B:211 , ASN B:378 , HOH B:1297 , HOH B:1572
BINDING SITE FOR RESIDUE FMT B 530
21
FC5
SOFTWARE
THR B:54 , LYS B:55 , MET B:128 , THR B:129 , HOH B:1132 , HOH B:1153 , HOH B:1189
BINDING SITE FOR RESIDUE FMT B 532
22
FC6
SOFTWARE
HIS B:179 , ASP B:181 , ARG B:182 , SER B:183 , ALA B:184 , THR B:187 , LEU B:204 , TYR B:205
BINDING SITE FOR RESIDUE FMT B 535
23
FC7
SOFTWARE
ARG B:309 , FMT B:549 , HOH B:1480
BINDING SITE FOR RESIDUE FMT B 537
24
FC8
SOFTWARE
PRO B:57 , ASN B:60 , GLN B:211 , ASN B:378 , ILE B:381 , ASP B:382 , HOH B:1101 , HOH B:1598
BINDING SITE FOR RESIDUE FMT B 542
25
FC9
SOFTWARE
HOH B:1632 , PHE C:72 , ASP C:73
BINDING SITE FOR RESIDUE FMT B 543
26
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
27
GC2
SOFTWARE
GLN B:257
BINDING SITE FOR RESIDUE FMT B 548
28
GC3
SOFTWARE
GLU B:305 , SER B:308 , ARG B:309 , FMT B:537 , HOH B:1157
BINDING SITE FOR RESIDUE FMT B 549
29
GC4
SOFTWARE
ILE B:239 , GLY B:242 , LYS B:243 , MET B:255 , GLU B:256 , LYS B:259 , HOH B:1486
BINDING SITE FOR RESIDUE FMT B 550
30
GC5
SOFTWARE
GLU B:265 , ARG B:290 , HIS B:395 , LEU B:396
BINDING SITE FOR RESIDUE FMT B 557
31
GC6
SOFTWARE
ASN B:318 , SER B:319 , GLU B:320 , GLN B:323 , THR B:345 , THR B:420 , ASN B:421 , ILE B:422
BINDING SITE FOR RESIDUE FMT B 586
[
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 B, )
2: VAR_047971 (K191N, chain B, )
3: VAR_011584 (I198T, chain B, )
4: VAR_004268 (V279F, chain B, )
5: VAR_011585 (Q281R, chain B, )
6: VAR_011586 (V379A, chain B, )
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
B
R
92
H
2
UniProt
VAR_047971
K
191
N
PAFA_HUMAN
Polymorphism
45454695
B
K
191
N
3
UniProt
VAR_011584
I
198
T
PAFA_HUMAN
Polymorphism
1805018
B
I
198
T
4
UniProt
VAR_004268
V
279
F
PAFA_HUMAN
Disease (PAFAD)
16874954
B
V
279
F
5
UniProt
VAR_011585
Q
281
R
PAFA_HUMAN
Disease (PAFAD)
---
B
Q
281
R
6
UniProt
VAR_011586
V
379
A
PAFA_HUMAN
Polymorphism
1051931
B
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 (B: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
-
B:267-276
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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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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Sorry, no Info available
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(currently selected atoms:
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)
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Chain B
Asymmetric Unit 1
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