3F96 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR ACETYLHYDROLASE COVALENTLY INHIBITED BY SARIN

Authors :   U. Samanta, B. J. Bahnson

Date :   13 Nov 08 (Deposition) - 23 Jun 09 (Release) - 28 Jul 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, Sarin, 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)

Molecule 1 - PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
	Chains	:	A, B
	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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SGB	2	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SGB	1	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SGB	1	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

(no "Site" information available for 3F96)

(no "SS Bond" information available for 3F96)

Asymmetric Unit

No.	Residues
1	Phe A:72	-	Asp A:73
2	Phe B:72	-	Asp B:73

Asymmetric Unit (6, 12)

								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/B	R	92	H
2	UniProt	VAR_047971	K	191	N	PAFA_HUMAN	Polymorphism	45454695	A/B	K	191	N
3	UniProt	VAR_011584	I	198	T	PAFA_HUMAN	Polymorphism	1805018	A/B	I	198	T
4	UniProt	VAR_004268	V	279	F	PAFA_HUMAN	Disease (PAFAD)	76863441	A/B	V	279	F
5	UniProt	VAR_011585	Q	281	R	PAFA_HUMAN	Disease (PAFAD)	201256712	A/B	Q	281	R
6	UniProt	VAR_011586	V	379	A	PAFA_HUMAN	Polymorphism	1051931	A/B	V	379	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (6, 6)

								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)	76863441	A	V	279	F
5	UniProt	VAR_011585	Q	281	R	PAFA_HUMAN	Disease (PAFAD)	201256712	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)

Biological Unit 2 (6, 6)

								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)	76863441	B	V	279	F
5	UniProt	VAR_011585	Q	281	R	PAFA_HUMAN	Disease (PAFAD)	201256712	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)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	PAFA_HUMAN	267-276	2	A:267-276 B:267-276

Biological Unit 1 (1, 1)

	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 -

Biological Unit 2 (1, 1)

	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

(no "Exon" information available for 3F96)

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:371
 aligned with PAFA_HUMAN | Q13093 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:371
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
           PAFA_HUMAN    54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINT 424
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh.hhhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee.......hhhhhhh....eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------H--------------------------------------------------------------------------------------------------N------T--------------------------------------------------------------------------------F-R-------------------------------------------------------------------------------------------------A--------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f96 A  54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHsFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINT 424
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
                                                                                                                                                                                                                                                     273-SGB

Chain B from PDB  Type:PROTEIN  Length:371
 aligned with PAFA_HUMAN | Q13093 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:371
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
           PAFA_HUMAN    54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINT 424
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee......eeeeeeeee.......ee...hhhhhhhhhhhhh.hhhhhhhhhhhhh..ee..ee.........eeeeeee.........hhhhhhhhhhh..eeeee........eeee..hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh....eeeee.......hhhhhhh....eeeeee....hhhhhhhhhh.......eeeeee...hhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------H--------------------------------------------------------------------------------------------------N------T--------------------------------------------------------------------------------F-R-------------------------------------------------------------------------------------------------A--------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f96 B  54 TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHsFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINT 424
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
                                                                                                                                                                                                                                                     273-SGB

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 '\|'

(no "SCOP Domain" information available for 3F96)

(no "CATH Domain" information available for 3F96)

(no "Pfam Domain" information available for 3F96)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	Sites
(no "Sites" information available for 3f96)

	Cis Peptide Bonds
		Phe A:72 - Asp A:73	[ RasMol ]
		Phe B:72 - Asp B:73	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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Access by PDB/NDB ID
	3f96
		Family and Domain Information	:	ProDom \| SYSTERS
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	PAFA_HUMAN \| Q13093
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	3.1.1.47
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	614278
		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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	PAFA_HUMAN \| Q13093
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3d59	THE SAME WILD TYPE PROTEIN
3d5e	THE SAME PROTEIN COMPLEXED WITH PARAOXON
3f97	THE SAME PROTEIN COMPLEXED WITH SOMAN
3f98	THE SAME PROTEIN COMPLEXED WITH TABUN
3f9c	THE SAME PROTEIN COMPLEXED WITH DIISOPROPYLFLUOROPHOSPHATE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 12)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (16, 16)

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