3W82.B | IDUA – ASTRID

3W82.B | IDUA

General Structure Information

PDB ID	3w82
HGNC Gene Label(s)	IDUA
Structure Name	human alpha-l-iduronidase in complex with iduronic acid
Resolution	2.76Å
Reference	AUTH N.MAITA,T.TSUKIMURA,T.TANIGUCHI,S.SAITO,K.OHNO,H.TANIGUCHI,AUTH 2 H.SAKURABATITL HUMAN ALPHA-L-IDURONIDASE USES ITS OWN N-GLYCAN AS ATITL 2 SUBSTRATE-BINDING AND CATALYTIC MODULEREF PROC.NATL.ACAD.SCI.USA V. 110 14628 2013REFN ISSN 0027-8424PMID 23959878DOI 10.1073/PNAS.1306939110

Variant Set Distributions

ExAC Variants

Number Of Residues	616
Number Of SNVs	172
Number Of Permutations	36668
Optimal Distance Threshold	20.0
K Statistic	0.21
p-value	0.025

ClinVar

Number Of Residues	616
Number Of SNVs	14
Number Of Permutations	3065
Optimal Distance Threshold	12.0
K Statistic	0.176
p-value	0.001

COSMIC

Number Of Residues	616
Number Of SNVs	4
Number Of Permutations	396
Optimal Distance Threshold	13.0
K Statistic	0.167
p-value	0.789

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	172
Number Of ClinVar SNVs	14
Optimal Distance Threshold	12.0
K Statistic	0.119
p-value	0.005

Cosmic vs. ExAC

Number Of ExAC SNVs	172
Number Of COSMIC SNVs	3
Optimal Distance Threshold	13.0
K Statistic	0.265
p-value	0.338

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
4:980958		P>R	B:29	(52.68, 63.35, -18.74)
4:980971	rs10794537	H>Q	B:33	(63.49, 65.22, -21.80)
4:981598		P>S	B:54	(76.21, 32.30, 8.29)
4:981601		P>A	B:55	(73.52, 29.88, 10.00)
4:981602	rs199554923	P>L	B:55	(73.52, 29.88, 10.00)
4:981617		Q>R	B:60	(78.05, 23.78, 11.79)
4:981631		V>I	B:65	(79.13, 27.92, 2.57)
4:981634		L>F	B:66	(80.54, 24.21, 1.06)
4:981652		L>F	B:72	(72.79, 26.32, -7.20)
4:981661		A>T	B:75	(75.41, 30.47, -10.01)
4:981665		Y>C	B:76	(70.83, 31.31, -10.18)
4:981671		G>D	B:78	(77.25, 35.08, -11.68)
4:981673	rs58037052	A>T	B:79	(74.85, 34.76, -14.02)
4:981674		A>V	B:79	(74.85, 34.76, -14.02)
4:981676		V>I	B:80	(74.74, 38.56, -13.26)
4:981679		P>S	B:81	(75.05, 39.96, -16.74)
4:981684	rs148775298	H>Q	B:82	(77.99, 42.04, -18.75)
4:981686	rs141461803	R>H	B:83	(82.00, 40.76, -13.38)
4:981688	rs564306004 CM113552	G>S	B:84	(76.96, 42.76, -11.89)
4:981695		K>R	B:86	(82.80, 42.36, -8.30)
4:981700		V>F	B:88	(79.95, 37.86, -1.75)
4:981703		R>W	B:89	(79.74, 41.72, 3.64)
4:981734	rs147490060	T>I	B:99	(92.82, 24.95, 15.13)
4:981736	rs201345740	R>G	B:100	(94.93, 20.70, 13.89)
4:981737		R>K	B:100	(94.93, 20.70, 13.89)
4:994402	rs544130587	G>E	B:101	(96.99, 22.68, 18.64)
4:994411	rs368625868	G>A	B:104	(102.64, 25.44, 23.71)
4:994413		R>W	B:105	(102.48, 22.16, 23.56)
4:994440	rs372934646	L>M	B:114	(88.36, 29.31, 3.53)
4:994446	rs148946496	G>R	B:116	(86.24, 26.00, -0.78)
4:994455		D>Y	B:119	(87.95, 27.64, -4.81)
4:994456	rs537047205	D>A	B:119	(87.95, 27.64, -4.81)
4:994465	rs200237798	R>K	B:122	(88.23, 32.71, -9.07)
4:994467	rs577729544	E>K	B:123	(84.01, 28.12, -10.49)
4:994482		P>S	B:128	(85.80, 37.87, -1.42)
4:994681		M>L	B:133	(84.09, 37.46, 11.07)
4:994690	rs112571714	A>T	B:136	(89.39, 29.50, 14.78)
4:994694		S>L	B:137	(87.88, 26.59, 16.11)
4:994705		T>P	B:141	(89.16, 34.20, 23.59)
4:994713	rs373342547	F>L	B:143	(91.54, 40.12, 20.32)
4:994722		K>N	B:146	(100.75, 40.08, 24.37)
4:994733	rs144870444	F>S	B:150	(101.86, 39.05, 18.39)
4:994735		E>K	B:151	(98.38, 33.85, 17.73)
4:994744		D>Y	B:154	(100.86, 35.26, 12.24)
4:994762	rs138731804	A>T	B:160	(97.04, 36.24, 2.30)
4:994774	rs141349021	I>V	B:164	(98.51, 35.89, -3.00)
4:994777		G>S	B:165	(99.13, 31.83, -4.52)
4:995259		R>T	B:166	(94.69, 28.62, -4.24)
4:995264		G>R	B:168	(96.98, 36.11, -7.08)
4:995271	COSM4126889 COSM4126890	A>V	B:170	(96.10, 40.93, -8.96)
4:995273		H>D	B:171	(91.90, 38.19, -7.79)
4:995279		S>A	B:173	(94.64, 43.26, -4.73)
4:995297		T>S	B:179	(86.44, 44.82, 10.23)
4:995298		T>M	B:179	(86.44, 44.82, 10.23)
4:995306		E>K	B:182	(77.47, 45.08, 13.02)
4:995309		P>S	B:183	(81.49, 46.15, 16.19)
4:995315	rs147174054	H>D	B:185	(75.29, 45.68, 16.73)
4:995319		H>R	B:186	(77.26, 43.54, 21.15)
4:995333		V>L	B:191	(85.07, 36.78, 21.27)
4:995342		T>P	B:194	(87.19, 45.38, 24.25)
4:995343	rs575667885	T>S	B:194	(87.19, 45.38, 24.25)
4:995477	COSM1582630	N>K	B:200	(94.61, 45.53, 19.76)
4:995487		A>T	B:204	(96.52, 42.70, 13.28)
4:995490	rs140294059	C>S	B:205	(94.24, 43.04, 10.50)
4:995494		S>L	B:206	(96.96, 46.10, 9.07)
4:995499		G>S	B:208	(99.14, 41.20, 8.19)
4:995506	rs371021597	R>H	B:210	(102.38, 46.27, 5.30)
4:995524		L>P	B:216	(96.36, 43.80, 0.39)
4:995544	rs183347428	D>N	B:223	(78.24, 49.76, 12.46)
4:995547	rs367813829	S>P	B:224	(75.76, 52.91, 12.44)
4:995559		P>S	B:228	(77.97, 60.29, 20.16)
4:995563		P>L	B:229	(77.20, 57.82, 23.39)
4:995571		P>T	B:232	(81.55, 53.15, 20.72)
4:995578	rs201826605	S>T	B:234	(82.86, 52.81, 15.17)
4:995587	rs147353014	L>H	B:237	(88.65, 52.44, 14.49)
4:995606		D>E	B:243	(95.17, 60.43, 16.24)
4:995618	rs368241547	F>L	B:247	(99.92, 46.14, 19.57)
4:995634	rs546933529	G>C	B:253	(98.87, 55.95, 12.85)
4:995638		V>G	B:254	(96.69, 53.17, 11.47)
4:995640		R>W	B:255	(95.98, 50.26, 6.59)
4:995644	rs373037758	L>P	B:256	(91.46, 53.36, 7.15)
4:995654		I>M	B:259	(85.11, 54.56, 6.30)
4:995655		S>A	B:260	(82.58, 50.71, 6.52)
4:995658		L>F	B:261	(78.55, 52.67, 6.69)
4:995661	rs375305122	H>Y	B:262	(76.26, 48.85, 8.19)
4:995664	rs201268637	R>W	B:263	(72.78, 54.16, 8.64)
4:995770	rs369090960 CM042364	G>R	B:265	(65.52, 52.68, 5.58)
4:995783	rs202051939	S>C	B:269	(64.82, 55.34, -0.44)
4:995789		S>F	B:271	(66.74, 57.52, 4.50)
4:995805		E>D	B:276	(74.84, 57.75, 3.63)
4:995808		K>N	B:277	(74.49, 63.48, 3.33)
4:995819	COSM1059184	Q>R	B:281	(80.03, 66.57, 7.33)
4:995825	rs555091763	I>T	B:283	(83.76, 61.52, 9.18)
4:995837		F>C	B:287	(88.01, 62.11, 12.06)
4:995882		P>R	B:302	(65.28, 48.69, 2.30)
4:995902		P>T	B:309	(58.28, 38.03, 6.07)
4:995909	rs377684568	P>L	B:311	(55.16, 41.24, 0.54)
4:995923	COSM1619265 COSM1619266	V>M	B:316	(59.23, 44.29, -9.37)
4:995939		M>T	B:321	(63.47, 50.32, -3.68)
4:995942	rs76722191	V>E	B:322	(67.37, 48.52, -5.69)
4:996063	rs199801029 CM950680	A>P	B:327	(69.80, 56.63, -8.75)
4:996068		Q>H	B:328	(68.26, 58.20, -4.86)
4:996075		N>D	B:331	(71.51, 61.33, -9.81)
4:996085		L>R	B:334	(78.28, 60.43, -7.31)
4:996087		A>S	B:335	(76.65, 63.88, -9.71)
4:996091		N>T	B:336	(77.34, 67.87, -10.28)
4:996094		T>I	B:337	(77.89, 67.48, -5.80)
4:996114		A>T	B:344	(82.54, 53.68, -3.51)
4:996115	rs202191662	A>G	B:344	(82.54, 53.68, -3.51)
4:996121	rs121965033	L>R	B:346	(75.71, 50.24, -2.52)
4:996124		S>N	B:347	(75.79, 46.35, -0.56)
4:996128	COSM2989458 COSM2989459 CD951743 CM113557	N>K	B:348	(71.85, 45.29, -1.61)
4:996129	rs368454909 CM950681 CM022026 CD113571	D>N	B:349	(73.02, 41.97, 2.75)
4:996130	rs371397270	D>G	B:349	(73.02, 41.97, 2.75)
4:996132		N>D	B:350	(70.63, 40.29, -1.34)
4:996135		A>T	B:351	(72.70, 36.27, -0.45)
4:996138	COSM1670835 COSM1670836	F>L	B:352	(70.80, 35.98, 3.30)
4:996165	rs6831280	A>T	B:361	(59.38, 37.06, 1.31)
4:996169		Q>P	B:362	(62.90, 35.81, 3.04)
4:996177	rs527336882	L>V	B:365	(69.06, 37.58, -5.04)
4:996183		A>T	B:367	(63.92, 31.22, -4.62)
4:996186		R>C	B:368	(65.95, 27.49, -0.48)
4:996207		R>C	B:375	(62.66, 8.21, -4.10)
4:996213		P>S	B:377	(65.69, 14.62, -1.85)
4:996214	rs546808806	P>L	B:377	(65.69, 14.62, -1.85)
4:996217		H>R	B:378	(65.28, 18.33, -5.63)
4:996220		V>G	B:379	(67.55, 21.95, -4.36)
4:996223		Q>R	B:380	(65.09, 23.70, -8.00)
4:996232		R>H	B:383	(66.04, 35.02, -12.54)
4:996237		P>S	B:385	(62.61, 40.09, -9.64)
4:996555	rs11934801	G>R	B:409	(57.38, 71.46, -15.73)
4:996600		A>T	B:424	(77.41, 55.94, -22.62)
4:996645		L>V	B:439	(67.20, 52.28, -16.21)
4:996658		S>N	B:443	(59.15, 53.26, -7.12)
4:996673	rs565375837	A>D	B:448	(52.53, 48.79, -4.33)
4:996675	rs532731688	H>N	B:449	(50.51, 51.44, -5.83)
4:996690	rs73066479	V>I	B:454	(52.81, 56.11, -15.00)
4:996851		D>G	B:477	(55.40, 44.12, -14.61)
4:996853		N>D	B:478	(54.45, 42.48, -10.44)
4:996856		G>R	B:479	(52.31, 40.63, -14.23)
4:996857		G>E	B:479	(52.31, 40.63, -14.23)
4:996860		L>R	B:480	(54.21, 40.39, -17.42)
4:996862		C>R	B:481	(57.83, 39.69, -14.67)
4:996865		S>G	B:482	(56.30, 37.53, -10.92)
4:996873	rs4690224	D>E	B:484	(55.32, 35.17, -6.21)
4:996884	rs75427046	R>Q	B:488	(50.99, 33.26, -4.57)
4:996890	rs121965027	L>P	B:490	(50.49, 27.47, -9.98)
4:996895		R>G	B:492	(50.27, 28.80, -2.12)
4:996906		F>L	B:495	(57.22, 19.74, -2.18)
4:996908		P>R	B:496	(57.66, 22.25, -7.08)
4:996922		F>L	B:501	(60.14, 24.56, -10.88)
4:996925	rs570594115	R>W	B:502	(58.86, 23.56, -17.30)
4:997185		L>P	B:526	(59.18, 55.60, -26.75)
4:997190	rs199722340	P>A	B:528	(55.68, 54.34, -22.28)
4:997196		L>V	B:530	(55.42, 52.65, -16.66)
4:997223		H>Y	B:539	(70.44, 48.81, -25.17)
4:997248		P>Q	B:547	(81.18, 39.28, -34.41)
4:997253		G>R	B:549	(82.29, 36.18, -28.60)
4:997337		V>L	B:551	(80.87, 31.38, -24.46)
4:997340		T>S	B:552	(83.79, 30.95, -21.59)
4:997344		R>L	B:553	(84.63, 29.92, -16.84)
4:997350		R>H	B:555	(79.53, 25.47, -14.77)
4:997352		A>S	B:556	(76.66, 21.34, -15.67)
4:997353		A>V	B:556	(76.66, 21.34, -15.67)
4:997359		P>L	B:558	(73.26, 18.65, -11.25)
4:997367	COSM588802 CM034103	Q>K	B:561	(65.01, 12.73, -13.31)
4:997380	rs371671953	V>A	B:565	(71.88, 24.23, -14.23)
4:997395		D>G	B:570	(80.20, 37.24, -20.33)
4:997401		H>R	B:572	(86.60, 36.08, -23.43)
4:997403	rs146588560	V>L	B:573	(81.39, 38.05, -25.49)
4:997816		E>K	B:582	(71.94, 29.63, -29.92)
4:997823	rs141304503	Q>R	B:584	(73.40, 23.73, -29.94)
4:997824		Q>H	B:584	(73.40, 23.73, -29.94)
4:997829	rs187833337	S>F	B:586	(74.24, 16.08, -28.45)
4:997843	rs398123257	A>T	B:591	(73.60, 16.33, -34.03)
4:997844	rs138826105	A>V	B:591	(73.60, 16.33, -34.03)
4:997867		P>S	B:599	(64.56, 35.53, -25.35)
4:997874	rs200089576	T>I	B:601	(70.67, 38.31, -21.44)
4:997888	rs547144863	V>L	B:606	(66.93, 25.49, -16.32)
4:998056	rs553282198	A>T	B:613	(66.72, 13.83, -22.24)
4:998075	rs372137794	R>Q	B:619	(77.44, 23.61, -29.24)
4:998081		R>Q	B:621	(76.06, 30.35, -30.91)
4:998086		L>V	B:623	(72.58, 35.90, -30.87)
4:998129	rs371369206	P>L	B:637	(80.15, 16.74, -20.72)
4:998131		Y>H	B:638	(74.79, 15.92, -17.62)

3W82.B | IDUA.

3W82.B | IDUA

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
4:981024	rs794726877	G>D	B:51	(75.45, 39.33, 1.02)
4:981704	rs121965029	R>Q	B:89	(79.74, 41.72, 3.64)
4:995875	rs121965030	A>T	B:300	(71.82, 49.34, 1.67)
4:996063	rs199801029	A>P	B:327	(69.80, 56.63, -8.75)
4:996121	rs121965033	L>R	B:346	(75.71, 50.24, -2.52)
4:996129	rs368454909	D>N	B:349	(73.02, 41.97, 2.75)
4:996175	rs121965032	T>M	B:364	(66.54, 36.76, -1.17)
4:996180	rs121965024	T>P	B:366	(67.41, 33.22, -4.73)
4:996555	rs11934801	G>R	B:409	(57.38, 71.46, -15.73)
4:996890	rs121965027	L>P	B:490	(50.49, 27.47, -9.98)
4:996896	rs121965026	R>P	B:492	(50.27, 28.80, -2.12)
4:997137	rs794727017	P>R	B:510	(62.56, 40.72, -19.27)
4:997206	rs121965021	P>R	B:533	(55.96, 48.33, -9.57)
4:998093	rs587779401	Y>C	B:625	(70.75, 43.61, -30.32)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
4:995294	COSM735216	E>K	B:178	(85.54, 44.54, 6.30)
4:995923	COSM1619265	V>M	B:316	(59.23, 44.29, -9.37)
4:996165	COSM4159330	A>T	B:361	(59.38, 37.06, 1.31)
4:996204	COSM3993871	T>P	B:374	(62.23, 13.74, -4.85)