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3D5E
Biol. Unit 2
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Asym.Unit (134 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (66 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR ACETYLHYDROLASE COVALENTLY INHIBITED BY PARAOXON
Authors
:
U. Samanta, B. J. Bahnson
Date
:
16 May 08 (Deposition) - 09 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (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, Secreted, Paraoxon
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
U. Samanta, B. J. Bahnson
Crystal Structure Of Human Plasma Platelet-Activating Factor Acetylhydrolase: Structural Implication To Lipoprotein Binding And Catalysis.
J. Biol. Chem. V. 283 31617 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: DIETHYL PHOSPHONATE (DEPa)
1b: DIETHYL PHOSPHONATE (DEPb)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
2f: FORMIC ACID (FMTf)
2g: FORMIC ACID (FMTg)
2h: FORMIC ACID (FMTh)
2i: FORMIC ACID (FMTi)
2j: FORMIC ACID (FMTj)
2k: FORMIC ACID (FMTk)
2l: FORMIC ACID (FMTl)
2m: FORMIC ACID (FMTm)
2n: FORMIC ACID (FMTn)
2o: FORMIC ACID (FMTo)
2p: FORMIC ACID (FMTp)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DEP
1
Ligand/Ion
DIETHYL PHOSPHONATE
2
FMT
9
Ligand/Ion
FORMIC ACID
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Sites
(10, 10)
Info
All Sites
01: AC9 (SOFTWARE)
02: BC1 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC5 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
01
AC9
SOFTWARE
GLY B:152 , LEU B:153 , SER B:273 , PHE B:274 , TRP B:298 , HIS B:351 , GLN B:352
BINDING SITE FOR RESIDUE DEP B 473
02
BC1
SOFTWARE
TRP B:298 , TYR B:324
BINDING SITE FOR RESIDUE FMT B 1
03
BC2
SOFTWARE
TYR B:335 , LYS B:342 , MET B:343 , HOH B:518
BINDING SITE FOR RESIDUE FMT B 6
04
BC3
SOFTWARE
ARG B:182 , TRP B:203 , LEU B:204 , TYR B:205
BINDING SITE FOR RESIDUE FMT B 7
05
BC4
SOFTWARE
SER B:230 , GLN B:231 , SER B:234 , ARG B:288 , HOH B:554
BINDING SITE FOR RESIDUE FMT B 8
06
BC5
SOFTWARE
ILE A:422 , ASN A:423 , GLU B:320 , GLN B:323 , ASN B:421 , ILE B:422
BINDING SITE FOR RESIDUE FMT B 9
07
BC6
SOFTWARE
PRO B:57 , ARG B:58 , ALA B:162 , ASP B:166
BINDING SITE FOR RESIDUE FMT B 10
08
BC7
SOFTWARE
PRO A:311 , LYS B:143 , ILE B:262 , ARG B:264 , HOH B:605 , HOH B:606
BINDING SITE FOR RESIDUE FMT B 13
09
BC8
SOFTWARE
SER B:234 , ARG B:288 , HOH B:590
BINDING SITE FOR RESIDUE FMT B 14
10
BC9
SOFTWARE
GLN B:393 , LYS B:394 , ASP B:403 , HOH B:498
BINDING SITE FOR RESIDUE FMT B 15
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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)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: LIPASE_SER (B:267-276)
;
View:
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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
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Exons
(0, 0)
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SCOP Domains
(0, 0)
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CATH Domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Chain B
Asymmetric Unit 1
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Asym.Unit (134 KB)
Header - Asym.Unit
Biol.Unit 1 (67 KB)
Header - Biol.Unit 1
Biol.Unit 2 (66 KB)
Header - Biol.Unit 2
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