4G8A.A | TLR4 – ASTRID

4G8A.A | TLR4

General Structure Information

PDB ID	4g8a
HGNC Gene Label(s)	TLR4
Structure Name	crystal structure of human tlr4 polymorphic variant d299g and t399i in complex with md-2 and lps
Resolution	2.4Å
Reference	AUTH U.OHTO,N.YAMAKAWA,S.AKASHI-TAKAMURA,K.MIYAKE,T.SHIMIZUTITL STRUCTURAL ANALYSES OF HUMAN TOLL-LIKE RECEPTOR 4TITL 2 POLYMORPHISMS D299G AND T399IREF J.BIOL.CHEM. V. 287 40611 2012REFN ISSN 0021-9258PMID 23055527DOI 10.1074/JBC.M112.404608

Variant Set Distributions

ExAC Variants

Number Of Residues	601
Number Of SNVs	140
Number Of Permutations	70236
Optimal Distance Threshold	31.0
K Statistic	0.365
p-value	0.243

COSMIC

Number Of Residues	601
Number Of SNVs	21
Number Of Permutations	18827
Optimal Distance Threshold	10.0
K Statistic	0.043
p-value	0.496

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	140
Number Of COSMIC SNVs	16
Optimal Distance Threshold	21.0
K Statistic	0.075
p-value	0.488

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:120466838	COSM120821	V>L	A:30	(-11.81, 21.77, -74.63)
9:120470844	rs200405562 COSM1554086	V>I	A:33	(-6.11, 14.70, -74.31)
9:120470853		I>V	A:36	(-5.84, 12.46, -78.37)
9:120470864	rs201589239	Q>H	A:39	(-15.47, 18.48, -75.19)
9:120470866	COSM76740	C>Y	A:40	(-16.52, 20.42, -79.59)
9:120470871		E>Q	A:42	(-23.44, 23.38, -76.13)
9:120470884	rs78848399	Y>C	A:46	(-24.48, 26.48, -88.49)
9:120470892	COSM140630	P>S	A:49	(-14.41, 20.94, -86.62)
9:120470895	COSM1643719	D>N	A:50	(-11.09, 22.98, -89.76)
9:120470900	rs148151027	N>K	A:51	(-9.43, 23.87, -85.94)
9:120470940	COSM334898	P>S	A:65	(-26.20, 23.24, -84.99)
9:120470949		H>D	A:68	(-26.39, 17.83, -93.72)
9:120470966	rs147453131	S>R	A:73	(-17.92, 15.15, -92.84)
9:120470998		D>A	A:84	(-20.57, 12.29, -79.46)
9:120474678	rs141943958	Q>R	A:91	(-32.91, 16.58, -90.33)
9:120474679		Q>H	A:91	(-32.91, 16.58, -90.33)
9:120474681		T>K	A:92	(-29.71, 14.51, -93.34)
9:120474683	rs56302444	I>V	A:93	(-26.71, 11.00, -92.58)
9:120474696		A>V	A:97	(-20.39, 10.67, -93.93)
9:120474699		Y>C	A:98	(-19.88, 8.85, -90.74)
9:120474713		H>Y	A:103	(-9.21, 3.64, -87.41)
9:120474720		S>C	A:105	(-15.23, 2.12, -82.37)
9:120474750		Q>R	A:115	(-36.19, 12.86, -91.14)
9:120474767	rs199985705	A>S	A:121	(-24.41, 6.31, -94.11)
9:120474768		A>V	A:121	(-24.41, 6.31, -94.11)
9:120474800		V>L	A:132	(-25.62, 4.91, -80.03)
9:120474806	rs370421152	V>M	A:134	(-30.84, 6.48, -78.62)
9:120474807		V>A	A:134	(-30.84, 6.48, -78.62)
9:120474815		N>Y	A:137	(-37.22, 9.27, -85.91)
9:120474819	rs188543451	L>P	A:138	(-35.48, 4.18, -85.76)
9:120474832		E>D	A:142	(-36.04, -3.63, -92.07)
9:120474843	rs201897073	I>T	A:146	(-26.39, -1.66, -89.90)
9:120474845	rs567339096	G>R	A:147	(-25.25, -4.85, -92.60)
9:120474866		E>K	A:154	(-22.41, -2.32, -78.29)
9:120474885	rs537921846	N>S	A:160	(-36.64, 4.87, -81.17)
9:120474891	rs200168998	I>T	A:162	(-38.99, 0.03, -83.26)
9:120474929	rs16906079	T>A	A:175	(-21.26, -12.33, -86.49)
9:120474941	rs201215262	H>Y	A:179	(-24.45, -6.10, -75.99)
9:120474950	rs373109368	L>V	A:182	(-34.98, -3.01, -78.79)
9:120474966		I>S	A:187	(-42.29, -3.77, -79.51)
9:120474991		L>F	A:195	(-37.03, -14.83, -83.83)
9:120474992	rs201943367	R>W	A:196	(-35.92, -15.86, -90.55)
9:120474993	rs200570847 COSM202374	R>Q	A:196	(-35.92, -15.86, -90.55)
9:120475002		H>R	A:199	(-34.21, -19.65, -85.18)
9:120475004	COSM3653627	Q>E	A:200	(-30.79, -18.47, -89.85)
9:120475013		L>V	A:203	(-22.76, -19.50, -82.48)
9:120475019	rs200246890	N>H	A:205	(-23.30, -14.02, -77.11)
9:120475055		F>L	A:217	(-48.75, -12.18, -78.22)
9:120475065	COSM752876	P>Q	A:220	(-46.48, -19.35, -78.40)
9:120475070	rs572758278	A>T	A:222	(-40.86, -17.79, -80.56)
9:120475094	rs200759610	K>E	A:230	(-28.95, -10.35, -70.56)
9:120475128		N>S	A:241	(-53.27, -11.71, -66.66)
9:120475133		M>V	A:243	(-46.41, -11.10, -66.81)
9:120475143	rs5030714	C>S	A:246	(-45.88, -12.88, -72.52)
9:120475146		I>T	A:247	(-43.72, -15.46, -69.41)
9:120475157	rs573699173	A>T	A:251	(-41.28, -21.16, -74.06)
9:120475175	rs201835255 COSM607565	R>C	A:257	(-28.63, -12.29, -65.91)
9:120475185	rs55799839	L>P	A:260	(-37.93, -9.82, -64.77)
9:120475210		N>K	A:268	(-46.05, -0.44, -61.95)
9:120475217		K>E	A:271	(-52.27, -8.27, -59.41)
9:120475225		D>E	A:273	(-49.90, -13.96, -57.94)
9:120475227	rs142144857	K>R	A:274	(-48.83, -18.05, -55.90)
9:120475230		S>C	A:275	(-49.06, -17.01, -60.95)
9:120475232	rs199885534	A>S	A:276	(-46.34, -14.65, -62.00)
9:120475248	rs138122523	C>Y	A:281	(-40.90, -23.67, -65.40)
9:120475254	rs201836189	L>S	A:283	(-37.64, -20.70, -69.58)
9:120475256	rs201497570	T>A	A:284	(-33.28, -22.73, -69.41)
9:120475259		I>V	A:285	(-33.14, -19.51, -66.19)
9:120475266	rs76014534	E>G	A:287	(-27.96, -15.65, -63.89)
9:120475286	rs139736045	D>N	A:294	(-44.74, -1.16, -56.52)
9:120475298	rs145284280	D>N	A:298	(-47.28, -11.20, -47.51)
9:120475299		D>A	A:298	(-47.28, -11.20, -47.51)
9:120475300		D>E	A:298	(-47.28, -11.20, -47.51)
9:120475301	COSM3653633	D>Y	A:299	(-44.84, -13.77, -49.64)
9:120475302	rs4986790	D>G	A:299	(-44.84, -13.77, -49.64)
9:120475304		I>V	A:300	(-41.49, -15.91, -51.22)
9:120475307	rs141534085	I>V	A:301	(-45.28, -19.35, -50.50)
9:120475308	rs201050092	I>T	A:301	(-45.28, -19.35, -50.50)
9:120475316		F>L	A:304	(-39.63, -16.75, -56.46)
9:120475327	COSM3779590	L>F	A:307	(-36.53, -19.72, -60.22)
9:120475331		N>Y	A:309	(-32.44, -24.90, -60.79)
9:120475332		N>S	A:309	(-32.44, -24.90, -60.79)
9:120475349	rs199637440	L>M	A:315	(-34.52, -10.08, -55.14)
9:120475355		S>R	A:317	(-35.92, -3.05, -55.06)
9:120475365		I>T	A:320	(-40.63, -9.30, -48.82)
9:120475381		D>E	A:325	(-41.11, -18.26, -47.06)
9:120475389	COSM326682	Y>C	A:328	(-38.54, -24.32, -50.32)
9:120475391		N>H	A:329	(-33.98, -26.56, -50.16)
9:120475392	rs5030715	N>T	A:329	(-33.98, -26.56, -50.16)
9:120475397	rs535260110	G>R	A:331	(-30.39, -24.36, -55.30)
9:120475398	rs376837568	G>E	A:331	(-30.39, -24.36, -55.30)
9:120475407		H>R	A:334	(-25.53, -15.57, -56.11)
9:120475409		L>I	A:335	(-28.88, -15.03, -52.68)
9:120475412	COSM390691	E>K	A:336	(-28.11, -10.36, -55.12)
9:120475413	rs544871818	E>G	A:336	(-28.11, -10.36, -55.12)
9:120475417		L>F	A:337	(-31.14, -10.07, -51.18)
9:120475431	rs5031050	F>Y	A:342	(-36.58, -7.92, -46.15)
9:120475434	rs200713994	G>V	A:343	(-39.61, -7.42, -41.61)
9:120475451		K>E	A:349	(-32.81, -23.01, -43.66)
9:120475454	rs200307408	L>F	A:350	(-30.03, -22.42, -48.81)
9:120475458		K>R	A:351	(-28.64, -27.32, -47.94)
9:120475471		R>S	A:355	(-20.81, -15.88, -53.65)
9:120475476		T>S	A:357	(-25.16, -10.43, -51.51)
9:120475487	rs61734367	N>D	A:361	(-31.27, -4.42, -47.49)
9:120475488		N>S	A:361	(-31.27, -4.42, -47.49)
9:120475489		N>K	A:361	(-31.27, -4.42, -47.49)
9:120475492		K>N	A:362	(-34.47, -0.15, -46.78)
9:120475503		A>G	A:366	(-32.07, -8.43, -36.74)
9:120475512		E>V	A:369	(-29.38, -18.50, -36.26)
9:120475524	rs370344294	P>R	A:373	(-23.84, -25.53, -45.54)
9:120475534		E>D	A:376	(-17.22, -20.35, -49.83)
9:120475547	rs201114738 COSM95363	S>G	A:381	(-23.03, -4.88, -46.15)
9:120475561	rs11536884	L>F	A:385	(-27.77, -5.63, -39.78)
9:120475571	rs201746544 COSM3926060	G>C	A:389	(-23.32, -12.69, -31.09)
9:120475575		C>S	A:390	(-20.62, -12.18, -33.32)
9:120475602	rs4986791	T>I	A:399	(-16.95, -25.10, -41.71)
9:120475608		L>Q	A:401	(-16.89, -18.34, -44.21)
9:120475610	rs539153708	K>E	A:402	(-13.02, -18.49, -47.56)
9:120475626	rs202089517	S>T	A:407	(-19.82, -3.34, -43.33)
9:120475637	rs145887797	V>I	A:411	(-24.72, -2.98, -32.79)
9:120475650	COSM607560	S>T	A:415	(-19.97, -13.59, -28.08)
9:120475655		N>D	A:417	(-13.55, -16.44, -30.64)
9:120475667	rs137906784	L>V	A:421	(-15.47, -19.21, -38.91)
9:120475688	rs376443096	D>Y	A:428	(-15.17, -5.62, -43.33)
9:120475719	rs142298021	S>N	A:438	(-11.64, -5.58, -24.88)
9:120475749		N>S	A:448	(-6.22, -18.61, -41.96)
9:120475761		L>R	A:452	(-9.13, -6.97, -40.06)
9:120475772		H>Y	A:456	(-14.20, 4.43, -38.50)
9:120475798	rs368504750	N>K	A:464	(-2.76, -6.04, -24.62)
9:120475809		N>S	A:468	(-4.22, -12.66, -29.65)
9:120475848	rs200621504	N>S	A:481	(-10.92, 3.30, -33.35)
9:120475880	rs200787883	F>V	A:492	(0.35, -4.77, -33.13)
9:120475884	rs144562288	T>I	A:493	(3.59, -9.35, -30.91)
9:120475887		E>A	A:494	(0.43, -13.05, -32.50)
9:120475920	rs199891172	Q>R	A:505	(-8.75, 8.88, -37.69)
9:120475936	rs5030719	Q>H	A:510	(1.98, 8.39, -25.84)
9:120475949	COSM233589	A>T	A:515	(4.65, -1.75, -30.82)
9:120475952		F>I	A:516	(5.19, -0.76, -34.36)
9:120476000		F>L	A:532	(1.43, 11.27, -31.90)
9:120476016	rs151068160	T>M	A:537	(12.48, 7.26, -34.94)
9:120476025	rs545104922	Y>C	A:540	(8.78, 3.76, -36.16)
9:120476039		S>T	A:545	(9.76, -3.58, -44.94)
9:120476069	rs202101018	H>N	A:555	(-0.83, 18.26, -33.20)
9:120476081		S>P	A:559	(12.33, 15.29, -32.08)
9:120476091	rs149793266	Q>R	A:562	(17.47, 13.41, -30.75)
9:120476096	rs200473735	L>I	A:564	(15.68, 11.97, -35.65)
9:120476099	rs201413217	Q>K	A:565	(19.59, 7.69, -35.63)
9:120476121	rs200676661	A>V	A:572	(10.47, 6.30, -49.10)
9:120476135		T>A	A:577	(2.00, 16.98, -44.05)
9:120476166		H>R	A:587	(12.71, 23.08, -31.60)
9:120476167	rs199700911	H>Q	A:587	(12.71, 23.08, -31.60)
9:120476223	COSM170668	R>Q	A:606	(0.56, 19.85, -47.47)
9:120476262	COSM3926065	P>L	A:619	(7.96, 27.00, -45.67)
9:120476271	rs146859162	S>N	A:622	(12.49, 27.90, -46.25)
9:120476283	rs201055270 COSM1173438	T>I	A:626	(21.26, 31.06, -38.32)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:120470847	COSM233588	P>S	A:34	(-3.24, 16.77, -75.63)
9:120474738	COSM3653625	G>A	A:111	(-31.18, 12.92, -80.60)
9:120474743	COSM95359	P>T	A:113	(-33.97, 14.63, -85.79)
9:120474783	COSM303395	S>L	A:126	(-14.41, -0.94, -90.86)
9:120475046	COSM3737332	P>A	A:214	(-45.88, -1.90, -75.18)
9:120475079	COSM1701623	E>K	A:225	(-34.41, -24.24, -80.74)
9:120475251	COSM72993	N>S	A:282	(-41.39, -23.70, -69.67)
9:120475302	COSM4988203	D>G	A:299	(-44.84, -13.77, -49.64)
9:120475379	COSM607563	D>Y	A:325	(-41.11, -18.26, -47.06)
9:120475463	COSM106873	L>F	A:353	(-25.78, -20.60, -50.97)
9:120475602	COSM4989617	T>I	A:399	(-16.95, -25.10, -41.71)
9:120475662	COSM335758	L>W	A:419	(-15.78, -21.13, -32.73)
9:120475663	COSM2150749	L>F	A:419	(-15.78, -21.13, -32.73)
9:120475722	COSM3903593	E>V	A:439	(-15.16, -8.23, -23.03)
9:120475728	COSM4402884	S>L	A:441	(-9.49, -12.91, -27.86)
9:120475736	COSM3395531	L>I	A:444	(-8.13, -16.57, -30.73)
9:120475841	COSM1459650	A>T	A:479	(-9.18, 3.75, -38.21)
9:120475851	COSM3926062	S>F	A:482	(-9.68, 4.25, -29.13)
9:120475859	COSM1701628	E>K	A:485	(-4.83, 6.12, -20.99)
9:120475865	COSM1267921	F>V	A:487	(-0.20, 3.35, -24.67)
9:120475890	COSM1104599	L>P	A:495	(0.29, -9.51, -36.11)
9:120475898	COSM3903596	L>V	A:498	(1.18, -6.86, -40.54)
9:120475949	COSM233589	A>T	A:515	(4.65, -1.75, -30.82)
9:120476223	COSM170668	R>Q	A:606	(0.56, 19.85, -47.47)

4G8A.A | TLR4

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants