2R02.A | PDCD6IP

General Structure Information

PDB ID	2r02
HGNC Gene Label(s)	PDCD6IP
Structure Name	crystal structure of alix/aip1 in complex with the hiv-1 ypltsl late domain
Resolution	2.6Å
Reference	AUTH Q.ZHAI,R.D.FISHER,H.Y.CHUNG,D.G.MYSZKA,AUTH 2 W.I.SUNDQUIST,C.P.HILLTITL STRUCTURAL AND FUNCTIONAL STUDIES OF ALIXTITL 2 INTERACTIONS WITH YPX(N)L LATE DOMAINS OF HIV-1TITL 3 AND EIAV.REF NAT.STRUCT.MOL.BIOL. V. 15 43 2008REFN ISSN 1545-9993PMID 18066081DOI 10.1038/NSMB1319

Variant Set Distributions

ExAC Variants

Number Of Residues	697
Number Of SNVs	122
Number Of Permutations	84860
Optimal Distance Threshold	22.0
K Statistic	0.167
p-value	0.333

COSMIC

Number Of Residues	697
Number Of SNVs	6
Number Of Permutations	3742
Optimal Distance Threshold	8.0
K Statistic	0.067
p-value	0.805

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	122
Number Of COSMIC SNVs	6
Optimal Distance Threshold	8.0
K Statistic	0.05
p-value	0.743

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
3:33840234	rs200697599	I>T	A:5	(-2.42, -26.33, -26.52)
3:33840252		K>R	A:11	(-14.82, -16.30, -37.11)
3:33840253		K>N	A:11	(-14.82, -16.30, -37.11)
3:33840375	rs550876351	A>G	A:52	(-25.50, -15.48, -28.16)
3:33840381		V>G	A:54	(-22.13, -17.59, -32.77)
3:33840390	rs368462021	P>L	A:57	(-15.83, -13.51, -30.91)
3:33840398		K>Q	A:60	(-12.67, -16.36, -21.95)
3:33853568		Y>H	A:72	(-24.84, -29.58, -30.14)
3:33853577		I>F	A:75	(-29.34, -27.32, -33.50)
3:33853581		C>Y	A:76	(-29.68, -31.58, -32.08)
3:33853601	rs145549670	P>S	A:83	(-37.80, -30.89, -43.66)
3:33855084		D>N	A:100	(-6.52, -18.92, -41.59)
3:33855105		G>S	A:107	(-5.46, -16.72, -45.54)
3:33855111		V>I	A:109	(-11.35, -20.54, -46.42)
3:33863449	rs371038293	L>F	A:113	(-23.16, -25.84, -46.80)
3:33863461		G>R	A:117	(-24.47, -30.67, -39.91)
3:33863470		K>E	A:120	(-24.55, -30.48, -35.72)
3:33863498		A>G	A:129	(-12.62, -24.44, -27.94)
3:33863533		D>N	A:141	(-1.63, -23.89, -7.61)
3:33863557	rs368375025	A>S	A:149	(-9.11, -28.71, -16.45)
3:33866683		A>G	A:156	(-12.74, -31.38, -25.65)
3:33866685		S>G	A:157	(-11.35, -34.78, -26.41)
3:33866691		A>T	A:159	(-15.97, -33.06, -28.95)
3:33866731	rs144962999	S>N	A:172	(-22.37, -33.57, -48.37)
3:33866734		R>Q	A:173	(-19.58, -31.23, -50.60)
3:33866740		P>L	A:175	(-14.60, -30.42, -45.03)
3:33866745		V>M	A:177	(-8.76, -28.15, -42.36)
3:33866755		S>Y	A:180	(-10.89, -32.82, -40.70)
3:33866766		V>I	A:184	(-10.60, -33.37, -34.98)
3:33866785		I>T	A:190	(-3.67, -32.25, -27.93)
3:33866799		A>S	A:195	(-5.62, -34.23, -19.00)
3:33866819	COSM4116993	L>F	A:201	(0.07, -31.31, -11.90)
3:33866826		T>A	A:204	(2.68, -33.66, -7.66)
3:33867987		A>V	A:211	(5.24, -44.89, -8.80)
3:33867998		K>Q	A:215	(3.31, -45.44, -13.95)
3:33868033		D>E	A:226	(1.05, -40.47, -30.28)
3:33868034	rs143264432	A>T	A:227	(0.47, -35.88, -31.25)
3:33868050		Q>L	A:232	(6.49, -34.85, -37.98)
3:33868067		P>A	A:238	(-1.69, -23.50, -35.14)
3:33870348		V>L	A:241	(0.88, -26.83, -31.77)
3:33870353		F>L	A:242	(5.50, -29.25, -34.22)
3:33870363		A>T	A:246	(7.83, -31.29, -28.20)
3:33870366		A>T	A:247	(8.31, -29.91, -25.03)
3:33870367		A>V	A:247	(8.31, -29.91, -25.03)
3:33870382		M>T	A:252	(6.12, -35.23, -19.33)
3:33870383		M>I	A:252	(6.12, -35.23, -19.33)
3:33870391		N>S	A:255	(8.76, -35.45, -14.93)
3:33870399		Y>N	A:258	(13.03, -36.71, -10.42)
3:33870402		H>N	A:259	(9.24, -39.00, -10.17)
3:33870406		Q>R	A:260	(11.41, -44.81, -11.92)
3:33870411	rs148065975	I>V	A:262	(13.12, -41.19, -6.35)
3:33870424		Q>R	A:266	(13.43, -45.53, -2.45)
3:33870450		A>T	A:275	(20.79, -43.08, -15.77)
3:33877560		V>M	A:287	(13.54, -28.18, -23.73)
3:33877563	COSM4116994	A>T	A:288	(15.72, -24.94, -22.71)
3:33877566		S>P	A:289	(17.74, -24.55, -25.80)
3:33877569		R>C	A:290	(15.46, -27.18, -29.55)
3:33877576	rs138586886	D>G	A:292	(13.19, -20.84, -24.98)
3:33877590		V>L	A:297	(12.40, -25.92, -17.33)
3:33877606		D>V	A:302	(17.76, -26.32, -10.57)
3:33877617		R>C	A:306	(19.08, -29.71, -6.42)
3:33877623	COSM116109	L>V	A:308	(22.98, -35.87, -10.96)
3:33877626	rs3792594	A>T	A:309	(25.27, -34.49, -7.69)
3:33877647		D>N	A:316	(31.83, -41.47, -7.20)
3:33877653		I>V	A:318	(30.00, -44.49, -0.78)
3:33877654		I>T	A:318	(30.00, -44.49, -0.78)
3:33877668		V>I	A:323	(26.02, -46.23, -14.96)
3:33877677	rs371977368	L>F	A:326	(19.31, -45.59, -21.55)
3:33877684	rs139871869	D>G	A:328	(19.99, -52.43, -20.73)
3:33877690		D>V	A:330	(13.31, -52.16, -17.26)
3:33877695		I>V	A:332	(8.68, -46.35, -17.26)
3:33877696	rs142953386	I>T	A:332	(8.68, -46.35, -17.26)
3:33877731		N>H	A:344	(-24.74, -38.05, -24.96)
3:33877732		N>S	A:344	(-24.74, -38.05, -24.96)
3:33879703		F>L	A:355	(-39.02, -26.25, -31.02)
3:33879709	COSM314038	K>N	A:357	(-44.60, -30.57, -27.47)
3:33879711		M>T	A:358	(-42.80, -30.15, -33.51)
3:33879719		V>M	A:361	(-41.26, -35.29, -40.31)
3:33879726		V>A	A:363	(-44.97, -39.15, -37.93)
3:33879747	rs371668410	Y>C	A:370	(-53.28, -44.76, -42.18)
3:33879749	rs200837933	N>D	A:371	(-55.10, -41.19, -44.73)
3:33879770	rs3203777	V>I	A:378	(-62.86, -47.07, -47.87)
3:33879779		S>P	A:381	(-64.96, -51.10, -50.78)
3:33879782		I>L	A:382	(-67.89, -47.96, -51.02)
3:33879804		T>S	A:389	(-76.51, -52.45, -56.01)
3:33879807		T>S	A:390	(-76.26, -50.61, -60.01)
3:33879810	rs149124708	L>W	A:391	(-75.41, -55.13, -61.91)
3:33883487		Q>R	A:427	(-87.72, -39.11, -50.91)
3:33883488	rs546345810	Q>H	A:427	(-87.72, -39.11, -50.91)
3:33883492	rs148256302	G>S	A:429	(-90.69, -36.19, -55.37)
3:33883502	rs146976979	T>I	A:432	(-87.19, -33.00, -54.69)
3:33883516	rs370556565	I>F	A:437	(-82.08, -29.49, -61.85)
3:33883529		P>H	A:441	(-77.51, -23.59, -62.59)
3:33883544		R>Q	A:446	(-72.53, -19.44, -55.46)
3:33883566		E>D	A:453	(-65.42, -11.01, -58.08)
3:33885611		R>K	A:456	(-62.02, -7.50, -61.06)
3:33885619		D>H	A:459	(-56.12, -8.24, -63.55)
3:33885637		D>N	A:465	(-47.64, -1.81, -60.98)
3:33885685	rs377593608	S>P	A:481	(-47.56, -7.58, -59.73)
3:33885700		K>E	A:486	(-46.57, -17.00, -60.59)
3:33886917		T>I	A:493	(-55.78, -22.10, -64.13)
3:33886920	rs372822946	N>S	A:494	(-56.51, -25.59, -60.97)
3:33886946		V>M	A:503	(-70.17, -28.16, -66.47)
3:33886962	rs200000172	Q>R	A:508	(-73.50, -36.31, -67.49)
3:33886968		K>I	A:510	(-79.47, -31.03, -67.26)
3:33886974	rs371176638	C>F	A:512	(-80.62, -38.38, -66.84)
3:33886980	rs200882224	Q>R	A:514	(-84.47, -34.32, -70.18)
3:33886988		R>C	A:517	(-89.92, -35.08, -65.54)
3:33886989		R>H	A:517	(-89.92, -35.08, -65.54)
3:33887000		V>M	A:521	(-94.27, -37.93, -62.96)
3:33887010	rs369799746	C>S	A:524	(-95.32, -39.80, -57.98)
3:33887027		L>V	A:530	(-100.32, -45.36, -60.79)
3:33887031		N>S	A:531	(-103.98, -48.70, -61.33)
3:33887054		P>A	A:539	(-103.98, -63.52, -65.31)
3:33887064		T>S	A:542	(-101.30, -71.77, -62.84)
3:33887076		S>N	A:546	(-95.28, -72.40, -58.42)
3:33893987	rs9813017	N>S	A:550	(-92.03, -69.85, -53.48)
3:33894001		L>V	A:555	(-83.80, -66.33, -54.53)
3:33895371		V>F	A:631	(-81.86, -70.29, -64.67)
3:33895396		M>R	A:639	(-94.70, -70.95, -66.62)
3:33895397		M>I	A:639	(-94.70, -70.95, -66.62)
3:33895405	rs147601956	S>C	A:642	(-96.45, -63.76, -74.91)
3:33895407		N>D	A:643	(-100.23, -61.28, -74.89)
3:33895408		N>S	A:643	(-100.23, -61.28, -74.89)
3:33895450		A>V	A:657	(-88.51, -50.00, -61.94)
3:33895452		T>A	A:658	(-86.06, -48.31, -64.43)
3:33895458		Y>H	A:660	(-87.03, -46.60, -56.89)
3:33895465	rs141828459	N>S	A:662	(-83.51, -43.59, -62.46)
3:33895479		V>L	A:667	(-81.41, -37.67, -55.36)
3:33896665		N>S	A:678	(-71.88, -25.88, -51.37)
3:33896714	rs202202188	I>M	A:694	(-51.81, -10.14, -51.59)
3:33896724	COSM304865	R>W	A:698	(-47.72, -4.89, -53.67)
3:33896725		R>Q	A:698	(-47.72, -4.89, -53.67)

2R02.A | PDCD6IP.

2R02.A | PDCD6IP

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
3:33840270	COSM1617495	L>P	A:17	(-32.66, -19.56, -37.85)
3:33866751	COSM4152422	I>V	A:179	(-14.08, -29.63, -39.42)
3:33866819	COSM4116993	L>F	A:201	(0.07, -31.31, -11.90)
3:33877666	COSM172966	R>Q	A:322	(27.68, -50.03, -14.76)
3:33879764	COSM186030	D>N	A:376	(-57.08, -46.46, -51.77)
3:33879770	COSM149352	V>I	A:378	(-62.86, -47.07, -47.87)