3IHP.B | USP5 – ASTRID

3IHP.B | USP5

General Structure Information

PDB ID	3ihp
HGNC Gene Label(s)	USP5
Structure Name	covalent ubiquitin-usp5 complex
Resolution	2.8Å
Reference	AUTH J.R.WALKER,G.V.AVVAKUMOV,S.XUE,C.BUTLER-COLE,AUTH 2 J.WEIGELT,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,AUTH 3 A.BOCHKAREV,S.DHE-PAGANONTITL COVALENT UBIQUITIN-USP5 COMPLEXREF TO BE PUBLISHEDREFN

Variant Set Distributions

ExAC Variants

Number Of Residues	681
Number Of SNVs	131
Number Of Permutations	77066
Optimal Distance Threshold	17.0
K Statistic	0.074
p-value	0.011

COSMIC

Number Of Residues	681
Number Of SNVs	7
Number Of Permutations	1587
Optimal Distance Threshold	22.0
K Statistic	0.048
p-value	0.298

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	131
Number Of COSMIC SNVs	8
Optimal Distance Threshold	17.0
K Statistic	-0.074
p-value	0.812

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
12:6961353		L>V	B:4	(-58.88, 29.76, 21.90)
12:6961366		A>V	B:8	(-61.65, 25.00, 17.01)
12:6961387		T>M	B:15	(-66.61, 19.87, 8.50)
12:6961404		A>P	B:21	(-82.76, 22.58, -1.95)
12:6961405	rs192268986	A>V	B:21	(-82.76, 22.58, -1.95)
12:6961414		R>Q	B:24	(-81.75, 16.47, 4.03)
12:6964566		E>A	B:38	(-89.62, 20.02, 22.25)
12:6964573		E>D	B:40	(-84.14, 16.59, 28.24)
12:6964599	rs149569083	T>M	B:49	(-74.55, 15.17, 7.34)
12:6964630		E>D	B:59	(-70.08, 10.97, 22.15)
12:6964640		N>D	B:63	(-66.64, 8.28, 18.17)
12:6964649	COSM4044483 COSM4044482	G>S	B:66	(-65.27, 12.92, 13.28)
12:6964653		Q>R	B:67	(-68.23, 16.08, 12.69)
12:6964656	COSM1704998 COSM1704997	R>Q	B:68	(-64.51, 18.70, 16.40)
12:6964667		H>Y	B:72	(-77.72, 22.49, 20.43)
12:6964674	COSM431762 COSM1133966	R>Q	B:74	(-82.19, 23.44, 24.10)
12:6964676		R>W	B:75	(-87.54, 23.40, 19.61)
12:6964677		R>Q	B:75	(-87.54, 23.40, 19.61)
12:6965228		E>K	B:118	(-85.33, 28.17, 18.23)
12:6965234		V>M	B:120	(-79.29, 28.44, 18.54)
12:6965255		D>N	B:127	(-63.89, 19.62, 24.98)
12:6965273		R>W	B:133	(-76.87, 32.71, 15.45)
12:6965274		R>Q	B:133	(-76.87, 32.71, 15.45)
12:6965285		G>W	B:137	(-65.76, 38.72, 15.31)
12:6965286		G>E	B:137	(-65.76, 38.72, 15.31)
12:6965289		G>V	B:138	(-62.46, 38.03, 14.84)
12:6965298		D>A	B:141	(-64.98, 38.63, 6.98)
12:6965312	COSM179597	R>W	B:146	(-68.78, 28.38, 5.04)
12:6965476		S>N	B:149	(-74.44, 30.71, 5.58)
12:6965484		E>K	B:152	(-78.91, 31.68, 7.86)
12:6965494		L>R	B:155	(-82.53, 27.48, 10.83)
12:6965497		S>L	B:156	(-84.50, 26.76, 6.52)
12:6965547		V>I	B:173	(-111.30, 34.31, 9.88)
12:6965550	COSM1676681 COSM1676680	R>W	B:174	(-112.83, 30.00, 7.02)
12:6965551		R>P	B:174	(-112.83, 30.00, 7.02)
12:6965582		K>N	B:184	(-130.61, 23.42, -2.62)
12:6965589		D>Y	B:187	(-134.93, 14.94, -4.02)
12:6965614		C>S	B:195	(-114.34, 5.37, 1.62)
12:6965889		K>N	B:201	(-114.71, 11.96, -14.39)
12:6965914	COSM1676683 COSM1676682	L>F	B:210	(-119.19, 16.48, -1.74)
12:6965918		N>S	B:211	(-121.77, 19.66, -4.46)
12:6965959		D>N	B:225	(-97.70, 25.44, -8.95)
12:6965966		S>T	B:227	(-100.70, 22.24, -7.08)
12:6965978		N>S	B:231	(-110.25, 21.70, -13.39)
12:6965999		R>Q	B:238	(-118.31, 27.70, -13.98)
12:6966011		Y>C	B:242	(-125.69, 23.07, -8.27)
12:6966019		A>T	B:245	(-118.09, 22.23, -1.53)
12:6966025		K>Q	B:247	(-111.53, 18.70, 0.84)
12:6966041	COSM95485	T>I	B:252	(-113.87, 16.20, 11.37)
12:6966048		D>E	B:254	(-114.73, 19.27, 15.63)
12:6966795		V>M	B:258	(-116.54, 24.68, 3.01)
12:6966861		G>S	B:280	(-125.03, 9.96, 5.14)
12:6966867		D>N	B:282	(-122.29, 11.45, 10.68)
12:6966870		M>V	B:283	(-119.95, 15.14, 11.83)
12:6967675		K>Q	B:318	(-106.77, -0.41, 34.03)
12:6967696		Y>H	B:325	(-97.75, -2.52, 28.86)
12:6967708	rs183579487	R>W	B:329	(-97.93, 9.90, 18.54)
12:6967709		R>Q	B:329	(-97.93, 9.90, 18.54)
12:6967739		S>C	B:339	(-101.31, -3.18, 14.95)
12:6967770		D>E	B:349	(-87.56, -14.21, 18.52)
12:6968641		D>N	B:356	(-81.58, -7.35, 23.46)
12:6968644		K>E	B:357	(-78.54, -7.61, 19.42)
12:6968652		E>D	B:359	(-75.48, -0.78, 21.73)
12:6968656	rs141770469	I>V	B:361	(-77.75, -2.45, 15.56)
12:6968663		Q>L	B:363	(-71.68, 0.28, 17.56)
12:6968675		T>M	B:367	(-73.27, 7.77, 7.94)
12:6968688		Q>H	B:371	(-82.36, 5.79, 5.32)
12:6968689		D>H	B:372	(-80.30, 1.36, 8.88)
12:6969346		E>K	B:388	(-91.51, 6.79, 26.16)
12:6969554		R>W	B:415	(-93.00, 10.93, 11.99)
12:6969555		R>Q	B:415	(-93.00, 10.93, 11.99)
12:6969567		A>D	B:419	(-90.40, 6.31, 5.85)
12:6969575		G>S	B:422	(-92.10, 2.83, 2.35)
12:6969622	COSM942989 COSM1152569	Q>H	B:437	(-101.62, -9.63, 4.57)
12:6969643		I>M	B:444	(-91.72, -10.59, 7.07)
12:6969644	rs149515919	N>H	B:445	(-90.28, -10.18, 2.88)
12:6969650		V>M	B:447	(-86.63, -9.05, 7.98)
12:6970118		R>K	B:449	(-85.12, -9.33, 1.38)
12:6970127		R>Q	B:452	(-78.57, -14.82, 3.47)
12:6970165	COSM1232090 COSM1232089	V>M	B:465	(-97.03, -26.24, 2.94)
12:6970187		L>Q	B:472	(-109.45, -39.06, -8.94)
12:6970220		V>A	B:483	(-92.10, -21.71, 2.33)
12:6970231		M>V	B:487	(-103.12, -20.52, 8.25)
12:6970246		P>S	B:492	(-117.35, -21.46, 5.25)
12:6970259		A>D	B:496	(-124.20, -20.54, 9.21)
12:6970615		L>V	B:503	(-132.37, -13.26, 5.85)
12:6970633		K>Q	B:509	(-131.62, -2.75, 6.64)
12:6970634		K>R	B:509	(-131.62, -2.75, 6.64)
12:6970637		R>Q	B:510	(-132.99, -4.57, 2.28)
12:6970645	COSM942990 COSM1586711	E>K	B:513	(-132.51, 2.55, 3.68)
12:6970656		K>N	B:516	(-133.99, 7.29, 6.10)
12:6970666		P>S	B:520	(-130.78, -2.27, 12.30)
12:6970672		L>V	B:522	(-124.99, -5.60, 13.72)
12:6970675		V>F	B:523	(-126.79, -9.33, 12.71)
12:6970676		V>A	B:523	(-126.79, -9.33, 12.71)
12:6970679		R>Q	B:524	(-121.54, -9.64, 13.05)
12:6970681		A>T	B:525	(-122.44, -14.30, 10.49)
12:6970682		A>V	B:525	(-122.44, -14.30, 10.49)
12:6970697		S>T	B:530	(-114.99, -26.35, 12.92)
12:6970747		S>C	B:547	(-102.51, -36.77, -16.17)
12:6970751		T>M	B:548	(-98.53, -37.66, -16.55)
12:6971650		S>A	B:564	(-94.05, -27.49, 9.61)
12:6971684		K>R	B:575	(-113.08, -11.68, 7.02)
12:6971700	rs148640344	L>F	B:580	(-121.60, -7.55, -7.77)
12:6971714		K>R	B:585	(-118.07, -8.41, 0.12)
12:6971717		K>T	B:586	(-115.83, -7.30, 5.34)
12:6972412	rs61761597	P>S	B:609	(-95.66, -46.78, 1.74)
12:6972415		G>R	B:610	(-98.38, -47.67, -1.86)
12:6972416		G>A	B:610	(-98.38, -47.67, -1.86)
12:6973010		E>D	B:634	(-86.90, -34.63, -41.32)
12:6973023		Q>E	B:639	(-94.45, -36.45, -45.60)
12:6973047		M>V	B:647	(-94.70, -27.51, -37.78)
12:6973048		M>T	B:647	(-94.70, -27.51, -37.78)
12:6973059	rs139483668	R>C	B:651	(-90.97, -29.16, -35.39)
12:6973060	COSM1512934 COSM1512933	R>H	B:651	(-90.97, -29.16, -35.39)
12:6973072		Y>C	B:655	(-87.19, -35.80, -29.88)
12:6973074		Y>H	B:656	(-90.72, -37.18, -27.93)
12:6973084		N>S	B:659	(-85.94, -40.26, -36.46)
12:6973106		M>I	B:666	(-99.09, -40.69, -38.94)
12:6973122		H>Y	B:672	(-99.41, -37.41, -28.32)
12:6973232		I>T	B:683	(-85.63, -27.17, -26.73)
12:6973276	COSM95486	D>N	B:698	(-73.60, -7.18, -21.67)
12:6973279		P>S	B:699	(-71.52, -6.84, -18.94)
12:6973280		P>H	B:699	(-71.52, -6.84, -18.94)
12:6973283		P>L	B:700	(-73.32, -6.55, -15.23)
12:6973286		P>R	B:701	(-73.64, -2.85, -13.76)
12:6973293	COSM942996 COSM1586705	D>E	B:703	(-72.35, -0.71, -9.03)
12:6973327		R>W	B:715	(-68.37, -11.64, -7.70)
12:6973328	rs181922891	R>Q	B:715	(-68.37, -11.64, -7.70)
12:6973337		A>V	B:718	(-74.72, -12.09, -8.15)
12:6973352		R>Q	B:723	(-76.57, -14.26, -17.48)
12:6973355		A>V	B:724	(-81.58, -13.94, -15.17)
12:6973358		T>M	B:725	(-82.79, -10.51, -14.42)
12:6973889		N>D	B:727	(-78.74, -6.46, -15.91)
12:6973901	COSM1232092 COSM1232091	R>W	B:731	(-86.18, -9.00, -12.65)
12:6973934		D>N	B:742	(-82.55, -24.58, -5.64)
12:6973950		A>G	B:747	(-73.30, -27.55, -3.88)
12:6974013		G>A	B:768	(-83.44, -26.80, 2.98)
12:6974033		P>A	B:775	(-95.40, -29.45, 18.68)
12:6974039		K>E	B:777	(-100.73, -28.29, 21.28)
12:6974364		T>I	B:789	(-118.63, -2.74, 6.88)
12:6974372		M>V	B:792	(-112.80, 0.71, 0.52)
12:6974374		M>I	B:792	(-112.80, 0.71, 0.52)
12:6974387		V>I	B:797	(-107.20, -2.73, 16.80)
12:6974412		R>K	B:805	(-103.10, -8.68, 31.31)
12:6975192		P>L	B:820	(-111.66, -10.27, 24.52)
12:6975236		S>G	B:835	(-92.31, -22.33, 22.64)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
12:6964621	COSM1747219	Q>H	B:56	(-77.04, 10.39, 25.55)
12:6965602	COSM1363952	R>Q	B:191	(-125.51, 6.64, -0.37)
12:6965959	COSM4739911	D>N	B:225	(-97.70, 25.44, -8.95)
12:6970735	COSM1747222	D>N	B:543	(-111.45, -28.99, -12.87)
12:6971695	COSM212499	G>S	B:579	(-119.37, -9.02, -5.76)
12:6973228	COSM3931731	L>F	B:682	(-89.02, -29.71, -28.42)
12:6973901	COSM1232092	R>W	B:731	(-86.18, -9.00, -12.65)
12:6974348	COSM253881	I>V	B:784	(-104.84, -7.93, 14.00)

3IHP.B | USP5.

3IHP.B | USP5

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants