3D59.A | PLA2G7

General Structure Information

PDB ID	3d59
HGNC Gene Label(s)	PLA2G7
Structure Name	crystal structure of human plasma platelet activating factor acetylhydrolase
Resolution	1.5Å
Reference	AUTH U.SAMANTA,B.J.BAHNSONTITL CRYSTAL STRUCTURE OF HUMAN PLASMATITL 2 PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE:TITL 3 STRUCTURAL IMPLICATION TO LIPOPROTEIN BINDING ANDTITL 4 CATALYSIS.REF J.BIOL.CHEM. V. 283 31617 2008REFN ISSN 0021-9258PMID 18784071DOI 10.1074/JBC.M804750200

Variant Set Distributions

ExAC Variants

Number Of Residues	372
Number Of SNVs	129
Number Of Permutations	14117
Optimal Distance Threshold	16.0
K Statistic	0.204
p-value	0.037

COSMIC

Number Of Residues	372
Number Of SNVs	8
Number Of Permutations	3218
Optimal Distance Threshold	16.0
K Statistic	0.107
p-value	1.0

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	129
Number Of COSMIC SNVs	7
Optimal Distance Threshold	10.0
K Statistic	-0.055
p-value	0.781

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:46684774	rs369097718 COSM139647	P>S	A:57	(14.58, 50.04, 22.72)
6:46684770	rs201369933	R>Q	A:58	(14.61, 55.42, 23.79)
6:46684764	rs139110249	N>I	A:60	(11.43, 54.36, 16.39)
6:46684759	rs139188438	P>S	A:62	(5.86, 60.06, 16.51)
6:46684749	rs539941099	V>A	A:65	(5.18, 56.11, 25.45)
6:46684725	rs143930998	D>G	A:73	(-12.06, 40.97, 38.39)
6:46684720		T>A	A:75	(-10.42, 37.56, 40.43)
6:46684262		T>A	A:79	(-8.20, 41.04, 33.14)
6:46684255		L>S	A:81	(-3.56, 44.68, 31.24)
6:46684252	rs144983904	R>H	A:82	(2.29, 46.69, 31.81)
6:46684246	rs368234407	Y>C	A:84	(2.85, 49.26, 26.81)
6:46684247	rs199793731	Y>H	A:84	(2.85, 49.26, 26.81)
6:46684244		Y>D	A:85	(-0.29, 55.04, 27.34)
6:46684231		D>G	A:89	(2.99, 64.87, 28.29)
6:46684222	rs1805017	R>H	A:92	(10.42, 61.83, 34.91)
6:46684223	rs189781341	R>C	A:92	(10.42, 61.83, 34.91)
6:46684219	rs200298077	L>P	A:93	(11.75, 57.36, 30.39)
6:46684213		T>N	A:95	(8.53, 52.19, 33.65)
6:46684211	COSM1312276	L>I	A:96	(9.99, 49.09, 37.16)
6:46684208		W>G	A:97	(12.19, 44.67, 32.54)
6:46684194		K>N	A:101	(9.82, 39.86, 45.37)
6:46684192		E>G	A:102	(7.37, 37.73, 43.81)
6:46684184		W>G	A:105	(11.03, 34.79, 44.53)
6:46684180		G>V	A:106	(9.96, 32.40, 38.74)
6:46684181		G>S	A:106	(9.96, 32.40, 38.74)
6:46684175	rs200052639	S>C	A:108	(14.51, 30.63, 38.98)
6:46684168	rs143012249	F>S	A:110	(11.15, 28.79, 33.10)
6:46684169	rs150329930	F>L	A:110	(11.15, 28.79, 33.10)
6:46684166	COSM1079926	L>F	A:111	(15.66, 28.94, 34.39)
6:46684151	rs191270134	L>F	A:116	(20.59, 31.04, 44.06)
6:46684146		M>I	A:117	(19.47, 33.02, 39.62)
6:46684147		M>R	A:117	(19.47, 33.02, 39.62)
6:46684127		L>I	A:124	(21.58, 42.20, 37.79)
6:46682283		M>I	A:128	(16.17, 47.60, 34.56)
6:46682276		P>S	A:131	(11.44, 53.17, 27.56)
6:46682273	rs145638062	A>S	A:132	(7.97, 54.66, 29.69)
6:46682250		R>S	A:139	(-2.57, 62.04, 21.80)
6:46682251		R>M	A:139	(-2.57, 62.04, 21.80)
6:46682233	rs370831021	P>L	A:145	(-5.20, 51.65, 17.05)
6:46682234		P>S	A:145	(-5.20, 51.65, 17.05)
6:46682227		V>A	A:147	(-2.56, 45.50, 20.15)
6:46682224	rs201022799 COSM1312275	V>A	A:148	(-4.06, 42.13, 22.40)
6:46682216	COSM3627981	H>D	A:151	(2.82, 35.73, 27.94)
6:46682213		G>C	A:152	(5.27, 33.28, 26.75)
6:46682207		G>R	A:154	(7.81, 32.23, 31.34)
6:46682204	rs149037413	A>T	A:155	(6.63, 35.00, 30.78)
6:46680070	rs183702131	L>I	A:159	(9.15, 40.50, 29.55)
6:46680060		A>V	A:162	(10.12, 46.75, 22.85)
6:46680058		I>L	A:163	(7.14, 44.98, 20.84)
6:46680039		S>F	A:169	(5.41, 55.27, 19.12)
6:46680033	rs548182444	G>E	A:171	(-0.51, 54.93, 17.79)
6:46680024		V>A	A:174	(-0.51, 47.88, 23.65)
6:46680019	COSM334717	A>T	A:176	(-0.16, 43.16, 27.82)
6:46680009		H>R	A:179	(-1.81, 34.73, 30.08)
6:46679353		D>E	A:181	(-2.17, 29.50, 31.97)
6:46679351	rs146433848	R>I	A:182	(0.29, 27.14, 36.73)
6:46679352		R>G	A:182	(0.29, 27.14, 36.73)
6:46679348		S>F	A:183	(2.24, 30.07, 31.42)
6:46679337	rs200283994	T>P	A:187	(0.71, 35.83, 38.27)
6:46679331		Y>H	A:189	(-4.94, 35.82, 42.71)
6:46679323	rs45454695	K>N	A:191	(-7.83, 35.36, 47.82)
6:46679321	rs201110141	D>G	A:192	(-10.76, 39.63, 48.83)
6:46679312		A>V	A:195	(-6.84, 42.29, 49.35)
6:46679310		A>S	A:196	(-6.88, 44.76, 46.82)
6:46679303	rs1805018	I>T	A:198	(-4.34, 45.71, 51.85)
6:46679301		G>R	A:199	(-1.92, 44.44, 48.59)
6:46679283	rs150039037	Y>H	A:205	(4.61, 31.07, 41.44)
6:46679273	rs377019028	T>N	A:208	(5.98, 21.81, 35.82)
6:46679274		T>S	A:208	(5.98, 21.81, 35.82)
6:46679262	rs139384606	E>K	A:212	(1.62, 11.58, 30.81)
6:46679243	rs201567357 COSM1079924	R>Q	A:218	(1.07, 23.15, 27.29)
6:46679238	rs200979587	E>K	A:220	(-7.19, 23.01, 28.02)
6:46678391	rs140695465	R>Q	A:223	(-8.96, 25.82, 23.92)
6:46678392	rs200057649 COSM2157343	R>W	A:223	(-8.96, 25.82, 23.92)
6:46678376		E>V	A:228	(-7.04, 35.21, 29.38)
6:46678373	rs200338780	C>Y	A:229	(-7.17, 37.73, 24.80)
6:46678374		C>R	A:229	(-7.17, 37.73, 24.80)
6:46678370	rs201934571	S>Y	A:230	(-11.25, 37.90, 24.35)
6:46678343		I>T	A:239	(-13.32, 51.05, 29.58)
6:46678340		D>G	A:240	(-14.31, 52.94, 24.69)
6:46678338		H>Y	A:241	(-18.36, 52.48, 24.45)
6:46678335		G>R	A:242	(-18.18, 53.64, 30.05)
6:46678329		P>A	A:244	(-17.96, 51.62, 35.38)
6:46678316		A>E	A:248	(-7.31, 46.52, 41.64)
6:46678312		L>F	A:249	(-3.92, 47.88, 40.68)
6:46678314		L>I	A:249	(-3.92, 47.88, 40.68)
6:46678311	rs371046823	D>N	A:250	(-3.85, 52.55, 43.81)
6:46678299	COSM3777715	D>H	A:254	(-8.41, 58.16, 35.23)
6:46678288		Q>H	A:257	(-7.72, 58.92, 30.50)
6:46677151	COSM3830679	S>F	A:261	(-9.81, 55.73, 23.06)
6:46677146		D>N	A:263	(-10.53, 52.50, 16.05)
6:46677142	rs200062469 COSM1079922	R>M	A:264	(-14.88, 49.69, 19.21)
6:46677130	rs200752820	A>V	A:268	(-4.93, 43.16, 16.86)
6:46677128		V>L	A:269	(-3.70, 39.42, 18.04)
6:46677119	rs201187668 COSM3874544	H>Y	A:272	(7.08, 35.05, 21.61)
6:46677109		G>D	A:275	(1.47, 33.48, 21.78)
6:46677110	COSM3627977	G>S	A:275	(1.47, 33.48, 21.78)
6:46677104		A>T	A:277	(-0.66, 30.02, 19.43)
6:46677100	rs147252565	T>M	A:278	(-2.60, 32.55, 21.64)
6:46677098	rs76863441	V>F	A:279	(-2.68, 34.65, 17.71)
6:46677093		I>M	A:280	(-3.72, 31.01, 15.70)
6:46677091	rs201256712 CM973406	Q>R	A:281	(-7.24, 29.36, 19.54)
6:46677085	rs200303358 CM114499	L>P	A:283	(-7.84, 34.93, 15.09)
6:46675897		C>S	A:291	(-5.19, 40.82, 12.40)
6:46675887		A>V	A:294	(3.07, 35.34, 14.90)
6:46675880		D>E	A:296	(9.00, 32.35, 16.73)
6:46675871		M>I	A:299	(2.04, 25.76, 16.24)
6:46675863	rs370455958	L>P	A:302	(-2.79, 24.61, 18.15)
6:46675860	rs200128572	G>D	A:303	(-5.69, 21.98, 17.24)
6:46675861	rs137868817	G>C	A:303	(-5.69, 21.98, 17.24)
6:46675855	rs201635666	E>K	A:305	(-9.65, 22.40, 15.65)
6:46675828		L>F	A:314	(-1.74, 35.13, 9.92)
6:46675818	rs201842579 CM044029	I>N	A:317	(7.58, 37.34, 12.30)
6:46675815		N>S	A:318	(9.82, 33.16, 12.07)
6:46675806		Y>C	A:321	(19.66, 30.66, 14.27)
6:46675785	rs200787788	I>N	A:328	(7.20, 25.25, 9.76)
6:46675778	rs199551268	K>N	A:330	(1.31, 22.38, 12.04)
6:46675776	rs201533861	M>R	A:331	(3.20, 27.75, 10.40)
6:46675766	rs200567003	C>W	A:334	(-2.67, 28.12, 7.84)
6:46675759	rs199662586	P>S	A:337	(-5.96, 30.23, -1.81)
6:46675746		R>T	A:341	(-2.50, 33.29, 5.78)
6:46673024		Q>R	A:352	(14.65, 35.20, 23.69)
6:46673021	rs201171111	N>S	A:353	(15.86, 38.44, 19.27)
6:46673012	rs202073418	D>G	A:356	(12.66, 42.78, 26.72)
6:46673013	rs200015160	D>Y	A:356	(12.66, 42.78, 26.72)
6:46673002	rs200974898	F>L	A:359	(17.40, 44.60, 24.40)
6:46672970		K>T	A:370	(20.75, 30.69, 23.78)
6:46672968		L>I	A:371	(19.50, 36.20, 25.46)
6:46672943	rs1051931	V>A	A:379	(18.58, 45.36, 13.70)
6:46672935		D>Y	A:382	(13.86, 47.83, 14.26)
6:46672931		L>P	A:383	(13.36, 44.21, 10.81)
6:46672927	rs138627259	S>R	A:384	(9.55, 42.88, 13.70)
6:46672926	rs371623990	N>D	A:385	(8.57, 46.40, 15.21)
6:46672919		A>V	A:387	(6.69, 44.55, 9.43)
6:46672917	rs201840347	S>A	A:388	(4.32, 44.58, 12.11)
6:46672913	rs34159425	L>S	A:389	(3.82, 48.87, 11.78)
6:46672895		H>R	A:395	(-4.45, 43.53, 6.60)
6:46672891		L>F	A:396	(-6.24, 47.36, 10.65)
6:46672427	rs142693692	H>R	A:399	(-5.52, 56.29, 6.94)
6:46672403		C>S	A:407	(9.42, 45.50, 1.68)
6:46672394	rs137883169	E>G	A:410	(7.12, 40.41, 0.54)
6:46672381	rs145290218	E>D	A:414	(20.63, 42.91, 4.41)
6:46672382		E>G	A:414	(20.63, 42.91, 4.41)
6:46672371	rs368877374 COSM1496387	P>S	A:418	(11.76, 35.13, 2.03)
6:46672350	rs200979188	T>A	A:425	(5.57, 20.30, 2.32)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:46684222	COSM451580	R>H	A:92	(10.42, 61.83, 34.91)
6:46684166	COSM1079926	L>I	A:111	(15.66, 28.94, 34.39)
6:46682255	COSM1754850	L>V	A:138	(-4.21, 59.16, 26.96)
6:46679303	COSM4415263	I>T	A:198	(-4.34, 45.71, 51.85)
6:46679243	COSM1079924	R>Q	A:218	(1.07, 23.15, 27.29)
6:46678359	COSM97015	LS>QS	A:234	(-14.11, 43.01, 26.32)
6:46678321	COSM276788	K>N	A:246	(-12.07, 50.46, 41.23)
6:46678293	COSM3627979	E>K	A:256	(-12.89, 57.96, 33.48)

3D59.A | PLA2G7

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants