2OBD.A | CETP – ASTRID

2OBD.A | CETP

General Structure Information

PDB ID	2obd
HGNC Gene Label(s)	CETP
Structure Name	crystal structure of cholesteryl ester transfer protein
Resolution	2.1Å
Reference	AUTH X.QIU,A.MISTRY,M.J.AMMIRATI,B.A.CHRUNYK,R.W.CLARK,AUTH 2 Y.CONG,J.S.CULP,D.E.DANLEY,T.B.FREEMAN,AUTH 3 K.F.GEOGHEGAN,M.C.GRIFFOR,S.J.HAWRYLIK,C.M.HAYWARD,AUTH 4 P.HENSLEY,L.R.HOTH,G.A.KARAM,M.E.LIRA,D.B.LLOYD,AUTH 5 K.M.MCGRATH,K.J.STUTZMAN-ENGWALL,A.K.SUBASHI,AUTH 6 T.A.SUBASHI,J.F.THOMPSON,I.K.WANG,H.ZHAO,A.P.SEDDONTITL CRYSTAL STRUCTURE OF CHOLESTERYL ESTER TRANSFERTITL 2 PROTEIN REVEALS A LONG TUNNEL AND FOUR BOUND LIPIDTITL 3 MOLECULES.REF NAT.STRUCT.MOL.BIOL. V. 14 106 2007REFN ISSN 1545-9993PMID 17237796DOI 10.1038/NSMB1197

Variant Set Distributions

ExAC Variants

Number Of Residues	472
Number Of SNVs	144
Number Of Permutations	48399
Optimal Distance Threshold	11.0
K Statistic	0.05
p-value	0.339

COSMIC

Number Of Residues	472
Number Of SNVs	4
Number Of Permutations	74
Optimal Distance Threshold	13.0
K Statistic	0.167
p-value	0.734

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	144
Number Of COSMIC SNVs	3
Optimal Distance Threshold	37.0
K Statistic	0.483
p-value	0.583

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:56995959	rs574035014	S>L	A:6	(-3.11, -6.47, 25.71)
16:56995964	rs201234837 COSM1742997	E>K	A:8	(-3.57, 0.99, 25.98)
16:56995973		I>V	A:11	(6.87, 3.06, 29.25)
16:56995976		V>M	A:12	(6.60, -1.64, 29.91)
16:56995980		C>Y	A:13	(8.44, -2.43, 33.87)
16:56995982		R>C	A:14	(8.51, -7.94, 32.33)
16:56995983	rs147758502	R>H	A:14	(8.51, -7.94, 32.33)
16:56996000		L>F	A:20	(12.27, -10.35, 43.24)
16:56996004		L>P	A:21	(15.52, -14.08, 44.21)
16:56996006		V>L	A:22	(18.74, -10.17, 44.17)
16:56996930	rs141121785	E>K	A:26	(18.77, -6.46, 51.22)
16:56996937	rs200956328	A>V	A:28	(16.07, -7.82, 56.86)
16:56996939		K>E	A:29	(18.38, -4.52, 55.57)
16:56996942		V>M	A:30	(12.85, -3.84, 55.36)
16:56996954	rs549487844	A>T	A:34	(9.61, -1.90, 60.92)
16:56996959	rs201282006	F>L	A:35	(10.16, -4.81, 64.35)
16:56996964		R>Q	A:37	(10.62, 3.86, 61.90)
16:56996985	rs142464301	T>M	A:44	(-1.47, -0.02, 82.16)
16:56996990		E>K	A:46	(-5.61, -1.52, 89.59)
16:56996993		K>E	A:47	(-6.36, -7.28, 87.80)
16:56996996	rs369294786	A>P	A:48	(-7.24, -8.60, 91.45)
16:56996999		M>V	A:49	(-3.76, -9.97, 91.86)
16:56997003		M>K	A:50	(-5.06, -15.05, 93.89)
16:56997017		V>I	A:55	(-2.03, -5.06, 92.00)
16:56997026		G>R	A:58	(3.47, -1.44, 84.52)
16:57003303	rs371180917	Q>R	A:63	(12.71, 0.40, 73.93)
16:57003304		Q>H	A:63	(12.71, 0.40, 73.93)
16:57003316		L>F	A:67	(16.14, -7.56, 65.54)
16:57003320		I>V	A:69	(16.07, -12.06, 60.54)
16:57003341		L>V	A:76	(5.49, -14.26, 42.39)
16:57003345		V>A	A:77	(0.84, -15.52, 43.59)
16:57003375		Q>R	A:87	(11.78, -17.97, 58.33)
16:57003380	rs371258270 COSM169707	V>M	A:89	(12.03, -12.73, 63.91)
16:57003402		T>I	A:96	(10.40, -0.61, 83.52)
16:57003419		T>A	A:102	(-3.27, -0.79, 96.30)
16:57003528		G>V	A:108	(4.84, -2.02, 100.91)
16:57003551	rs150236668	E>K	A:116	(14.66, -8.62, 78.79)
16:57003554		I>F	A:117	(9.86, -9.27, 76.36)
16:57003557	rs138898516	D>N	A:118	(12.65, -13.21, 74.67)
16:57003583		N>K	A:126	(0.77, -11.76, 51.27)
16:57003837	rs554738455	G>S	A:134	(-0.86, 6.60, 38.85)
16:57003852	rs201778606	D>N	A:139	(-1.97, -2.81, 49.92)
16:57003853		D>V	A:139	(-1.97, -2.81, 49.92)
16:57003858		P>S	A:141	(-4.20, -7.15, 53.85)
16:57003879		H>Y	A:148	(7.86, -19.78, 67.59)
16:57003897		L>F	A:154	(12.00, -10.12, 85.90)
16:57003910	rs145690607	R>Q	A:158	(11.78, -9.48, 92.20)
16:57003913		E>G	A:159	(7.60, -14.24, 91.36)
16:57004949		G>R	A:161	(3.24, -14.70, 92.37)
16:57004955		I>F	A:163	(4.53, -11.26, 87.84)
16:57004979		I>V	A:171	(-0.07, -9.13, 79.27)
16:57004995		K>M	A:176	(1.23, -12.03, 70.89)
16:57005006	rs557660317	K>E	A:180	(-0.45, -7.89, 63.68)
16:57005236	rs138670739	C>G	A:184	(1.90, -5.11, 59.76)
16:57005249	rs373779560	N>S	A:188	(2.01, -1.52, 54.83)
16:57005254		I>V	A:190	(8.66, 0.82, 54.23)
16:57005268		M>I	A:194	(10.64, 1.17, 49.11)
16:57005272	rs371233223 COSM3510426	D>N	A:196	(6.90, 6.84, 45.90)
16:57005279		V>D	A:198	(11.23, 3.68, 42.38)
16:57005908	rs201438792	S>R	A:204	(14.06, 11.97, 37.52)
16:57005913		L>R	A:206	(12.59, 10.10, 32.03)
16:57005925		D>A	A:210	(11.37, 23.15, 31.33)
16:57005928	rs141794398	I>T	A:211	(11.96, 18.23, 29.78)
16:57005934		V>A	A:213	(7.67, 12.21, 32.37)
16:57005943		S>F	A:216	(0.86, 7.58, 34.70)
16:57005948	rs150550739	T>S	A:218	(-2.43, 2.32, 32.04)
16:57005960	COSM1200872	V>I	A:222	(0.62, -7.68, 36.10)
16:57005973		S>F	A:226	(7.67, -15.16, 36.31)
16:57005978	rs139570047	L>M	A:228	(6.37, -7.53, 38.50)
16:57007243	COSM3402380	G>C	A:234	(5.11, 8.37, 28.23)
16:57007244	rs144460063	G>V	A:234	(5.11, 8.37, 28.23)
16:57007247	rs375348327	H>R	A:235	(2.53, 10.94, 27.50)
16:57007280		P>H	A:246	(-3.39, 8.06, 21.52)
16:57007286	rs139594305	P>L	A:248	(0.68, 2.47, 22.33)
16:57007289	rs561462414	T>S	A:249	(-0.76, -1.93, 21.83)
16:57007293	COSM3510428	F>L	A:250	(2.79, -4.46, 25.76)
16:57007295		S>L	A:251	(2.54, -7.87, 23.70)
16:57007304		L>R	A:254	(7.00, -8.77, 22.75)
16:57007310	rs201503514	G>E	A:256	(11.00, -12.12, 28.55)
16:57007312		D>N	A:257	(10.97, -14.58, 31.97)
16:57007318	rs147566657	R>C	A:259	(18.19, -10.70, 31.49)
16:57007319		R>P	A:259	(18.19, -10.70, 31.49)
16:57007325		L>R	A:261	(15.11, -5.28, 34.49)
16:57007346		R>Q	A:268	(3.25, 6.08, 19.77)
16:57007351	COSM971754	F>V	A:270	(11.92, 7.35, 21.21)
16:57007355		H>R	A:271	(7.01, 11.93, 18.24)
16:57007361	rs369941536	L>P	A:273	(12.12, 13.17, 23.72)
16:57007364	rs200375648	A>D	A:274	(11.76, 14.96, 19.90)
16:57007382		D>G	A:280	(13.89, 23.58, 24.90)
16:57007387	rs142459781	R>C	A:282	(17.50, 20.94, 24.78)
16:57007388		R>H	A:282	(17.50, 20.94, 24.78)
16:57007394		M>T	A:284	(21.08, 23.85, 18.72)
16:57007414		E>K	A:291	(34.88, 23.92, 19.44)
16:57009022	rs140547417	E>K	A:297	(42.67, 18.14, 15.96)
16:57009032		G>D	A:300	(42.18, 13.39, 11.84)
16:57009039		N>K	A:302	(45.12, 19.78, 10.95)
16:57012003		V>I	A:311	(37.70, 26.46, 2.89)
16:57012007		V>A	A:312	(39.61, 27.62, 6.53)
16:57012009	rs375653767	G>S	A:313	(42.46, 29.29, 5.96)
16:57012012	rs5881	G>S	A:314	(44.13, 31.62, 7.53)
16:57012018		P>S	A:316	(41.79, 29.01, 11.62)
16:57012023		S>R	A:317	(40.84, 30.93, 15.14)
16:57012028		A>G	A:319	(35.66, 29.67, 12.49)
16:57012043		H>R	A:324	(19.39, 24.98, 13.07)
16:57012057		P>T	A:329	(13.31, 15.28, 14.88)
16:57012060		K>E	A:330	(10.80, 12.35, 11.59)
16:57012067		S>Y	A:332	(11.80, 5.26, 13.80)
16:57012075		N>Y	A:335	(14.21, -5.01, 13.25)
16:57012087		V>M	A:339	(15.49, 5.71, 12.04)
16:57012091		V>G	A:340	(16.90, 9.80, 13.11)
16:57012094	rs190187567	N>S	A:341	(14.36, 12.01, 9.39)
16:57012103	rs200134880	V>A	A:344	(19.54, 20.16, 9.16)
16:57012123	rs374078713	P>S	A:351	(36.64, 34.50, 8.04)
16:57012126		R>C	A:352	(39.12, 34.76, 4.31)
16:57012127	rs144949752	R>H	A:352	(39.12, 34.76, 4.31)
16:57012134	rs138725242	D>E	A:354	(38.09, 41.13, 2.15)
16:57012154	rs36122917	Y>C	A:361	(28.78, 27.68, 1.09)
16:57015071		D>V	A:366	(17.01, 15.92, 4.71)
16:57015073		I>V	A:367	(20.69, 14.00, 7.75)
16:57015076	rs34855278	V>M	A:368	(18.58, 9.70, 7.37)
16:57015085	rs147412224	V>I	A:371	(21.42, 4.30, 15.29)
16:57015091	rs5880	A>P	A:373	(23.00, 0.77, 20.97)
16:57015098	COSM558220	Y>C	A:375	(25.56, 0.96, 29.34)
16:57015106	rs375325271	K>E	A:378	(29.11, 2.94, 34.14)
16:57015107		K>R	A:378	(29.11, 2.94, 34.14)
16:57015113	rs566897355	L>H	A:380	(25.54, 5.42, 25.48)
16:57015115	rs369075950	F>V	A:381	(29.30, 3.23, 23.53)
16:57015116		F>S	A:381	(29.30, 3.23, 23.53)
16:57015564		T>I	A:390	(18.87, 14.71, 0.89)
16:57015566		P>T	A:391	(20.62, 18.02, -0.46)
16:57015582		N>S	A:396	(26.91, 31.12, -2.24)
16:57016081	rs145141976	S>T	A:401	(32.04, 29.80, -4.92)
16:57016086	rs202026395	E>K	A:403	(30.44, 22.69, -7.38)
16:57016092	rs5882	V>I	A:405	(34.31, 25.04, -2.00)
16:57016105		L>Q	A:409	(31.81, 22.17, 3.19)
16:57016108		Q>R	A:410	(28.29, 17.72, 2.19)
16:57016113		M>V	A:412	(33.02, 18.72, 7.00)
16:57016114	COSM192145	M>K	A:412	(33.02, 18.72, 7.00)
16:57016116		I>V	A:413	(28.40, 17.67, 6.92)
16:57016117		I>T	A:413	(28.40, 17.67, 6.92)
16:57016131		I>V	A:418	(27.25, 12.44, 11.16)
16:57016145		M>I	A:422	(26.54, 10.23, 16.91)
16:57016149	rs111642444	R>W	A:424	(29.00, 16.90, 20.90)
16:57017243	rs536221680 COSM3672286	E>K	A:426	(27.48, 8.95, 23.11)
16:57017264		M>V	A:433	(21.41, 8.51, 32.95)
16:57017279	rs2228667	V>M	A:438	(22.41, 5.02, 36.53)
16:57017292	rs2303790	D>G	A:442	(26.22, -3.70, 38.49)
16:57017314		I>M	A:449	(16.79, -4.99, 21.51)
16:57017319	rs1800777	R>Q	A:451	(13.03, -5.53, 17.35)
16:57017514		L>Q	A:456	(13.79, -4.01, 24.13)
16:57017527		D>E	A:460	(21.12, -8.64, 34.72)
16:57017528		F>L	A:461	(19.86, -5.69, 39.18)
16:57017544		H>R	A:466	(26.00, 0.98, 49.92)
16:57017552	rs5887	V>M	A:469	(21.83, 0.99, 54.62)
16:57017555		D>N	A:470	(22.69, 4.88, 53.25)

2OBD.A | CETP.

2OBD.A | CETP

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:57007387	COSM159958	R>C	A:282	(17.50, 20.94, 24.78)
16:57012109	COSM1378506	V>A	A:346	(24.72, 23.55, 8.08)
16:57015091	COSM4986487	A>P	A:373	(23.00, 0.77, 20.97)
16:57017319	COSM4986488	R>Q	A:451	(13.03, -5.53, 17.35)
16:57017553	COSM3818137	V>G	A:469	(21.83, 0.99, 54.62)