3A6P.A | XPO5 – ASTRID

3A6P.A | XPO5

General Structure Information

PDB ID	3a6p
HGNC Gene Label(s)	XPO5
Structure Name	crystal structure of exportin-5:rangtp:pre-mirna complex
Resolution	2.92Å
Reference	AUTH C.OKADA,E.YAMASHITA,S.J.LEE,S.SHIBATA,J.KATAHIRA,A.NAKAGAWA,AUTH 2 Y.YONEDA,T.TSUKIHARATITL A HIGH-RESOLUTION STRUCTURE OF THE PRE-MICRORNA NUCLEARTITL 2 EXPORT MACHINERYREF SCIENCE V. 326 1275 2009REFN ISSN 0036-8075PMID 19965479DOI 10.1126/SCIENCE.1178705

Variant Set Distributions

ExAC Variants

Number Of Residues	1072
Number Of SNVs	197
Number Of Permutations	44856
Optimal Distance Threshold	6.0
K Statistic	0.005
p-value	0.555

COSMIC

Number Of Residues	1072
Number Of SNVs	6
Number Of Permutations	2206
Optimal Distance Threshold	10.0
K Statistic	0.067
p-value	0.987

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	197
Number Of COSMIC SNVs	5
Optimal Distance Threshold	10.0
K Statistic	0.083
p-value	0.937

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:43543513		R>Q	A:30	(18.20, 145.61, 20.06)
6:43543499	rs376796788	K>E	A:35	(13.26, 150.98, 11.04)
6:43541329		E>K	A:39	(15.03, 153.05, 5.83)
6:43541304		C>Y	A:47	(26.19, 155.89, 2.27)
6:43541305		C>S	A:47	(26.19, 155.89, 2.27)
6:43541302		V>F	A:48	(30.20, 156.17, 0.57)
6:43541298		P>L	A:49	(30.39, 159.29, 2.67)
6:43541292		G>V	A:51	(31.57, 154.61, 5.71)
6:43541286	rs373359039	R>K	A:53	(33.38, 160.20, 8.44)
6:43541276		E>D	A:56	(38.30, 155.94, 9.14)
6:43541257	rs370390582	V>I	A:63	(32.27, 151.39, 14.67)
6:43541237		Q>H	A:69	(28.49, 145.95, 7.23)
6:43541227		H>Y	A:73	(24.28, 147.18, 1.41)
6:43540310		R>Q	A:78	(22.44, 151.56, -3.10)
6:43540302	rs61762966	G>S	A:81	(22.34, 153.26, -8.63)
6:43540263		V>I	A:94	(38.47, 150.37, -0.61)
6:43540257		E>K	A:96	(43.90, 154.32, -0.19)
6:43538730		G>A	A:101	(43.50, 152.09, 6.64)
6:43538691		D>G	A:114	(36.11, 139.84, 6.83)
6:43538688	rs370633103	A>V	A:115	(35.16, 143.58, 6.10)
6:43538621		I>M	A:137	(48.26, 144.48, -11.72)
6:43538596		G>R	A:146	(53.38, 144.37, 2.81)
6:43538393	rs377741530	I>T	A:156	(40.41, 139.18, -1.27)
6:43538390		L>H	A:157	(42.48, 135.66, -3.63)
6:43538364		T>A	A:166	(32.47, 126.29, -3.30)
6:43538351		L>P	A:170	(26.98, 134.69, -8.39)
6:43538309	rs377472859	Q>R	A:184	(41.78, 132.48, -18.44)
6:43538302		M>I	A:186	(45.30, 129.76, -11.77)
6:43538301		E>K	A:187	(50.32, 130.16, -14.53)
6:43538295	rs373327142	I>L	A:189	(46.39, 133.41, -9.13)
6:43538289		S>G	A:191	(52.69, 131.99, -8.77)
6:43538286		F>V	A:192	(50.71, 135.85, -5.39)
6:43536471	rs201099159	T>S	A:209	(65.60, 131.90, 16.90)
6:43536465		T>A	A:211	(65.76, 137.86, 20.70)
6:43536461	rs201591158	S>F	A:212	(65.93, 141.54, 18.89)
6:43535090		A>V	A:217	(58.47, 136.62, 12.94)
6:43535085	rs375060795	A>T	A:219	(54.44, 138.58, 10.58)
6:43535082		N>D	A:220	(56.82, 136.95, 7.93)
6:43535079	rs553233595	C>R	A:221	(54.04, 133.53, 10.22)
6:43535075		R>Q	A:222	(49.09, 135.76, 10.84)
6:43535067	rs200090185	V>I	A:225	(48.96, 130.91, 7.92)
6:43535052	rs567783691	T>A	A:230	(44.40, 130.93, 0.30)
6:43535049		L>V	A:231	(46.74, 127.62, -1.29)
6:43535024		S>F	A:239	(44.57, 122.31, -12.79)
6:43535025		S>P	A:239	(44.57, 122.31, -12.79)
6:43535020		M>I	A:240	(47.12, 118.75, -11.12)
6:43535022		M>V	A:240	(47.12, 118.75, -11.12)
6:43535018	rs34324334	S>N	A:241	(49.05, 121.98, -13.91)
6:43534986		E>K	A:252	(58.57, 119.51, -2.19)
6:43534983	rs570153052	I>L	A:253	(57.07, 123.97, 0.24)
6:43534958		Q>R	A:261	(55.94, 123.54, 15.14)
6:43534943		G>V	A:266	(48.18, 123.94, 6.95)
6:43534931		C>Y	A:270	(46.96, 121.70, 1.74)
6:43534916		V>A	A:275	(45.54, 113.66, -1.67)
6:43533439		L>S	A:290	(53.92, 112.94, -2.16)
6:43533418		H>R	A:297	(63.06, 113.43, 4.98)
6:43533401		A>T	A:303	(55.65, 110.70, 11.72)
6:43530050		H>Q	A:315	(51.34, 116.81, 18.11)
6:43530022	rs540772244	V>L	A:325	(47.48, 112.89, 4.42)
6:43530012	rs373915842	A>V	A:328	(44.72, 109.24, 0.95)
6:43530003		N>S	A:331	(43.53, 105.08, -0.83)
6:43529991		A>G	A:335	(44.23, 103.42, -7.39)
6:43529989		L>V	A:336	(47.16, 105.12, -9.30)
6:43528732	COSM3777696	D>N	A:342	(52.25, 104.36, -16.37)
6:43528724	rs200225049	E>D	A:344	(55.62, 100.98, -11.61)
6:43528707	rs529074766	G>E	A:350	(58.85, 101.95, 3.16)
6:43528704		K>I	A:351	(60.33, 106.08, 3.75)
6:43528674		T>N	A:361	(51.50, 101.88, 17.07)
6:43528675		T>A	A:361	(51.50, 101.88, 17.07)
6:43528033	COSM484119	R>H	A:368	(44.56, 102.47, 17.36)
6:43528020		Q>H	A:372	(42.42, 99.58, 9.80)
6:43528015		T>I	A:374	(44.56, 102.00, 3.93)
6:43527979	rs61762965	R>H	A:386	(52.19, 89.16, -5.01)
6:43527980		R>C	A:386	(52.19, 89.16, -5.01)
6:43527959		I>V	A:393	(55.21, 95.53, 7.75)
6:43527955		I>T	A:394	(52.58, 91.56, 8.26)
6:43527948		K>N	A:396	(56.19, 95.73, 12.86)
6:43527937		A>V	A:400	(49.20, 95.99, 16.75)
6:43527932	rs370562231	M>V	A:402	(47.76, 91.47, 19.53)
6:43526304		S>R	A:416	(45.54, 102.97, 29.33)
6:43526280		F>V	A:424	(40.66, 115.48, 22.57)
6:43526252	rs201473380	N>S	A:433	(31.64, 100.91, 23.35)
6:43523654		D>N	A:454	(52.57, 85.64, 7.33)
6:43523634	rs368000134	Q>H	A:460	(54.93, 81.74, 16.06)
6:43523633	rs377017230	M>V	A:461	(52.19, 85.99, 17.18)
6:43523629		A>G	A:462	(48.58, 83.02, 18.54)
6:43523630	rs372441079	A>S	A:462	(48.58, 83.02, 18.54)
6:43523626	rs200605932	G>A	A:463	(50.39, 80.90, 20.41)
6:43523602	rs575516907	S>L	A:471	(50.39, 81.32, 32.90)
6:43523599		T>S	A:472	(48.74, 84.84, 34.22)
6:43521177	rs370740144	Q>P	A:502	(44.03, 90.20, 27.84)
6:43521165		M>R	A:506	(43.68, 85.14, 23.09)
6:43521141		I>T	A:514	(43.50, 78.70, 13.27)
6:43521142		I>V	A:514	(43.50, 78.70, 13.27)
6:43521126	COSM1079630	R>Q	A:519	(40.28, 79.32, 4.63)
6:43521120		L>P	A:521	(48.86, 76.71, 5.01)
6:43521117	rs553230160	N>S	A:522	(48.86, 73.49, 1.56)
6:43521110		E>D	A:524	(50.88, 68.89, 3.74)
6:43519177		N>S	A:529	(53.45, 68.92, 16.28)
6:43519174	rs61739889	D>G	A:530	(52.92, 73.42, 17.49)
6:43519171		G>A	A:531	(48.56, 72.33, 17.83)
6:43519168		I>T	A:532	(48.67, 68.87, 19.47)
6:43519163	rs199686881	L>V	A:534	(48.21, 74.90, 21.74)
6:43519159		L>S	A:535	(44.38, 71.01, 21.81)
6:43519139		D>N	A:542	(40.30, 73.98, 35.29)
6:43519127		P>S	A:546	(31.67, 81.10, 33.63)
6:43519112		C>G	A:551	(37.12, 81.39, 26.03)
6:43519108	rs186877420	V>A	A:552	(38.20, 77.35, 26.88)
6:43519102		T>S	A:554	(36.24, 79.20, 21.52)
6:43519099		N>T	A:555	(40.27, 78.37, 22.36)
6:43519097		V>I	A:556	(38.63, 73.71, 21.62)
6:43519082		P>S	A:561	(41.12, 71.23, 13.23)
6:43519052		P>A	A:571	(37.95, 61.56, 23.85)
6:43517661		S>C	A:580	(30.05, 72.40, 29.66)
6:43517641		E>K	A:587	(24.37, 77.03, 43.34)
6:43517302	rs368843561	R>Q	A:595	(23.22, 86.38, 30.45)
6:43517303		R>W	A:595	(23.22, 86.38, 30.45)
6:43517266		S>F	A:607	(30.62, 73.30, 19.81)
6:43517255	rs530175692	M>V	A:611	(32.13, 68.45, 16.36)
6:43517248		R>H	A:613	(28.50, 71.75, 10.67)
6:43517240		P>A	A:616	(31.74, 63.88, 10.17)
6:43516185		M>V	A:625	(30.24, 57.18, 23.11)
6:43516151	rs563408450	N>S	A:636	(16.00, 64.06, 34.03)
6:43516142		L>P	A:639	(18.99, 67.97, 33.62)
6:43516130		M>T	A:643	(17.53, 75.23, 23.27)
6:43516118		A>V	A:647	(21.45, 70.43, 20.10)
6:43516119		A>S	A:647	(21.45, 70.43, 20.10)
6:43516113		M>V	A:649	(18.67, 65.42, 19.20)
6:43516107	rs200950847	A>S	A:651	(24.35, 66.26, 16.43)
6:43516101		V>I	A:653	(21.03, 63.95, 12.98)
6:43516071	COSM3874371	E>K	A:663	(16.48, 51.62, 5.70)
6:43516067		R>H	A:664	(22.55, 52.38, 9.20)
6:43516068		R>C	A:664	(22.55, 52.38, 9.20)
6:43516061		K>R	A:666	(14.01, 55.09, 8.14)
6:43516059		V>M	A:667	(16.12, 52.72, 11.79)
6:43516016		L>H	A:681	(0.83, 61.10, 17.66)
6:43516011	COSM1312242	Q>E	A:683	(-6.31, 60.41, 22.69)
6:43515419		I>V	A:696	(-6.18, 78.44, 26.46)
6:43515415	rs202182348	A>V	A:697	(-5.58, 74.93, 29.20)
6:43515412	rs377740264	Y>S	A:698	(-1.12, 71.74, 27.95)
6:43515406		G>A	A:700	(-2.42, 79.35, 31.19)
6:43515400		D>V	A:702	(-7.20, 79.51, 31.82)
6:43515382		P>R	A:708	(-1.34, 84.86, 41.82)
6:43515367		P>L	A:713	(1.52, 73.31, 36.02)
6:43514449		R>Q	A:734	(20.92, 69.93, 10.79)
6:43514435		T>P	A:739	(26.91, 65.51, -1.43)
6:43514403		F>L	A:749	(19.79, 58.09, -0.30)
6:43514402	rs375413374	V>M	A:750	(18.36, 57.32, -6.10)
6:43514390		T>A	A:754	(14.72, 64.80, -14.04)
6:43514374		P>L	A:759	(19.16, 63.40, -9.33)
6:43514372		I>V	A:760	(14.78, 62.38, -7.80)
6:43514365		R>H	A:762	(14.58, 57.77, -0.67)
6:43514354		T>A	A:766	(9.87, 61.46, 4.91)
6:43514350	rs372504431	E>G	A:767	(7.74, 57.15, 7.10)
6:43514324		L>M	A:776	(2.15, 71.06, 12.66)
6:43514317	rs375364641	A>G	A:778	(-3.50, 71.74, 14.01)
6:43514318		A>T	A:778	(-3.50, 71.74, 14.01)
6:43514312		I>V	A:780	(-0.41, 76.21, 12.73)
6:43501740	rs367681038	H>Y	A:783	(-1.05, 80.06, 17.53)
6:43501734		T>P	A:785	(-7.87, 81.00, 16.06)
6:43501712		L>R	A:792	(-7.44, 87.47, 22.85)
6:43501674	rs373758989	M>V	A:805	(6.13, 92.35, 20.49)
6:43501664	rs35794454	A>V	A:808	(12.83, 93.07, 23.61)
6:43501665		A>T	A:808	(12.83, 93.07, 23.61)
6:43501652		A>G	A:812	(14.67, 96.38, 18.74)
6:43501648		I>M	A:813	(12.10, 97.10, 15.64)
6:43499292		E>A	A:822	(27.12, 91.25, 34.76)
6:43499290		L>F	A:823	(26.98, 87.66, 32.47)
6:43499286	rs201138656	N>S	A:824	(28.15, 87.45, 37.25)
6:43499284		D>N	A:825	(23.30, 89.34, 37.90)
6:43499265		T>N	A:831	(7.72, 87.16, 34.31)
6:43499266		T>A	A:831	(7.72, 87.16, 34.31)
6:43499263	rs377196219	V>I	A:832	(4.19, 84.47, 34.21)
6:43499256		E>G	A:834	(7.93, 88.22, 29.61)
6:43498561		F>L	A:848	(4.85, 78.86, 10.12)
6:43498530		M>T	A:858	(10.60, 65.99, 2.44)
6:43498512		T>S	A:864	(3.02, 64.85, -3.79)
6:43498504		D>N	A:867	(-5.59, 67.86, -0.79)
6:43498486		L>F	A:873	(-5.25, 77.69, 2.40)
6:43498467	rs566775169	N>S	A:879	(-7.11, 84.32, 11.45)
6:43498455		I>T	A:883	(-2.51, 87.36, 12.14)
6:43498447		Y>H	A:886	(3.87, 90.89, 15.75)
6:43496630		P>L	A:904	(9.00, 71.13, -7.91)
6:43496618	rs373330630	Y>C	A:908	(5.38, 75.81, -9.97)
6:43496606		V>A	A:912	(2.35, 77.35, -5.89)
6:43496607		V>I	A:912	(2.35, 77.35, -5.89)
6:43496596		I>M	A:915	(-1.20, 78.98, -1.95)
6:43496592	rs370480839	G>R	A:917	(-3.39, 84.12, -4.98)
6:43495925		Q>K	A:932	(-5.41, 104.21, 3.41)
6:43495426		M>V	A:956	(6.34, 105.32, 16.10)
6:43495392		R>Q	A:967	(11.14, 97.13, 3.11)
6:43495382		M>I	A:970	(7.17, 93.80, -2.32)
6:43493605		D>V	A:1013	(9.23, 79.02, -15.14)
6:43493583		K>N	A:1020	(-0.08, 81.41, -18.09)
6:43493580		H>Q	A:1021	(-3.42, 81.38, -13.41)
6:43492943		T>A	A:1026	(-4.99, 90.61, -11.12)
6:43492939	rs527438448	A>V	A:1027	(-2.57, 90.40, -7.81)
6:43492934		L>I	A:1029	(-0.30, 93.67, -12.11)
6:43492918		N>S	A:1034	(-0.84, 100.00, -5.36)
6:43492909		A>G	A:1037	(1.62, 104.87, -3.46)
6:43492706		V>M	A:1059	(-0.13, 91.44, -20.27)
6:43492694		T>S	A:1063	(-7.34, 91.23, -22.58)
6:43492680		D>E	A:1067	(-10.84, 100.24, -16.06)
6:43492681		D>G	A:1067	(-10.84, 100.24, -16.06)
6:43492678		A>V	A:1068	(-6.92, 98.79, -16.54)
6:43492672		T>M	A:1070	(-6.97, 104.04, -17.04)
6:43492648		K>T	A:1078	(-1.13, 107.93, -7.67)
6:43492619		G>R	A:1088	(15.20, 108.10, -7.61)
6:43492616		C>R	A:1089	(11.87, 107.71, -7.38)
6:43492573		A>G	A:1103	(3.44, 100.14, -25.49)
6:43492353	rs112085617	I>M	A:1111	(-3.52, 106.52, -22.46)
6:43492346		V>I	A:1114	(-4.97, 110.35, -17.94)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:43540271	COSM1634815	K>M	A:91	(38.21, 151.46, -6.90)
6:43540256	COSM1634814	E>A	A:96	(43.90, 154.32, -0.19)
6:43535018	COSM50776	S>N	A:241	(49.05, 121.98, -13.91)
6:43523660	COSM3627723	R>C	A:452	(45.67, 85.78, 2.06)
6:43499223	COSM307595	E>V	A:845	(9.01, 82.03, 14.75)
6:43495386	COSM4153426	V>D	A:969	(5.51, 91.52, 0.42)

3A6P.A | XPO5.

3A6P.A | XPO5

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants