3I8E.A | DDB1 – ASTRID

3I8E.A | DDB1

General Structure Information

PDB ID	3i8e
HGNC Gene Label(s)	DDB1
Structure Name	crystal structure of ddb1 in complex with the h-box motif of wdr42a
Resolution	3.4Å
Reference	AUTH T.LI,E.I.ROBERT,P.C.VAN BREUGEL,M.STRUBIN,N.ZHENGTITL A PROMISCUOUS ALPHA-HELICAL MOTIF ANCHORS VIRAL HIJACKERSTITL 2 AND SUBSTRATE RECEPTORS TO THE CUL4-DDB1 UBIQUITIN LIGASETITL 3 MACHINERY.REF NAT.STRUCT.MOL.BIOL. V. 17 105 2010REFN ISSN 1545-9993PMID 19966799DOI 10.1038/NSMB.1719

Variant Set Distributions

ExAC Variants

Number Of Residues	1114
Number Of SNVs	153
Number Of Permutations	76937
Optimal Distance Threshold	7.0
K Statistic	0.009
p-value	0.303

COSMIC

Number Of Residues	1114
Number Of SNVs	12
Number Of Permutations	15850
Optimal Distance Threshold	13.0
K Statistic	0.061
p-value	0.655

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	153
Number Of COSMIC SNVs	10
Optimal Distance Threshold	13.0
K Statistic	0.052
p-value	0.216

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:61099151	rs35597036	S>L	A:25	(6.85, -6.09, 70.70)
11:61099148		A>V	A:26	(4.66, -8.02, 73.59)
11:61099146	rs141900083	E>K	A:27	(7.36, -10.08, 72.30)
11:61099129		L>F	A:32	(10.01, 5.35, 75.20)
11:61099125		A>T	A:34	(11.82, 12.17, 75.69)
11:61099115		T>M	A:37	(10.51, 17.91, 70.35)
11:61099107	rs371829600	E>Q	A:40	(15.16, 8.77, 71.15)
11:61099100		Y>C	A:42	(16.33, 3.58, 71.96)
11:61099098	rs536135424	V>M	A:43	(15.00, -2.33, 71.78)
11:61099067	rs200876024	K>R	A:53	(11.66, 5.45, 64.57)
11:61099052	rs371977932	Y>C	A:58	(4.76, 19.65, 64.85)
11:61099046		K>T	A:60	(7.62, 21.42, 74.75)
11:61099033		M>I	A:64	(5.85, 10.00, 78.11)
11:61099024		F>L	A:67	(-1.95, 3.06, 77.46)
11:61099023		R>G	A:68	(-1.08, -3.66, 77.48)
11:61099016		K>R	A:70	(-8.69, -4.74, 79.52)
11:61097546		G>R	A:71	(-8.12, -5.76, 74.09)
11:61097519		L>V	A:80	(0.16, 16.28, 76.88)
11:61097512	rs370677190	A>V	A:82	(2.58, 22.17, 76.47)
11:61097500		A>V	A:86	(-3.69, 15.11, 73.30)
11:61097498		C>S	A:87	(-2.03, 11.93, 71.75)
11:61097495	rs142240695	I>V	A:88	(-3.49, 7.77, 71.81)
11:61097487		E>D	A:90	(-0.12, 1.94, 67.49)
11:61097479		Q>R	A:93	(6.70, -3.09, 61.43)
11:61097465	COSM300045	I>V	A:98	(8.97, 1.80, 60.42)
11:61097459		I>V	A:100	(4.48, 6.14, 64.82)
11:61097452		T>M	A:102	(-2.76, 8.81, 65.49)
11:61097446		A>V	A:104	(-6.18, 9.49, 69.38)
11:61097052	COSM296905	R>H	A:111	(-11.06, 29.45, 76.38)
11:61097013		I>S	A:124	(-3.20, 6.25, 83.21)
11:61097014		I>V	A:124	(-3.20, 6.25, 83.21)
11:61096999		R>W	A:129	(-12.84, 2.58, 83.78)
11:61096983		R>H	A:134	(-2.61, 19.37, 88.11)
11:61096940		D>E	A:148	(-15.68, 5.55, 71.62)
11:61096897	rs570670012	H>Y	A:163	(-1.09, 24.02, 95.96)
11:61096870		G>C	A:172	(-7.29, -1.76, 94.88)
11:61094347	COSM1509317 COSM1355218	V>I	A:190	(-3.21, 13.00, 102.57)
11:61094337		Y>C	A:193	(-11.31, 13.02, 96.23)
11:61094328		S>C	A:196	(-17.62, 8.36, 89.46)
11:61094307		N>S	A:203	(-17.64, 10.55, 95.56)
11:61094266		S>T	A:217	(7.20, 16.02, 96.73)
11:61094263		M>V	A:218	(6.85, 12.32, 95.16)
11:61093165		G>V	A:227	(-1.02, -1.10, 98.45)
11:61093166	COSM94122	G>W	A:227	(-1.02, -1.10, 98.45)
11:61093103		I>V	A:248	(11.58, 6.06, 107.75)
11:61091588		N>H	A:262	(11.45, 3.69, 88.92)
11:61091584	COSM3450688 COSM193274	R>Q	A:263	(7.75, -0.18, 89.74)
11:61091500		M>K	A:291	(-0.06, -16.73, 105.31)
11:61091489		V>I	A:295	(1.09, -9.43, 101.76)
11:61091480		K>E	A:298	(7.70, -5.66, 109.65)
11:61090563	rs138285473	S>T	A:309	(24.14, 11.85, 86.22)
11:61090547	rs200092392	L>S	A:314	(15.24, 6.99, 86.70)
11:61090545		T>A	A:315	(14.42, 3.62, 83.79)
11:61090518		V>I	A:324	(20.28, 7.98, 83.92)
11:61090496	rs373709587	S>C	A:331	(22.54, 10.84, 79.85)
11:61090492		Q>H	A:332	(24.30, 7.59, 82.54)
11:61089844		A>G	A:349	(29.49, 2.86, 84.13)
11:61089815		I>V	A:359	(23.77, 26.08, 76.42)
11:61089098		E>D	A:398	(49.48, 16.17, 58.06)
11:61089100		E>K	A:398	(49.48, 16.17, 58.06)
11:61084024		R>Q	A:414	(51.80, -6.56, 51.29)
11:61084025		R>W	A:414	(51.80, -6.56, 51.29)
11:61084015	COSM138822	P>R	A:417	(54.58, -12.06, 52.38)
11:61083997		D>V	A:423	(56.38, -2.30, 52.69)
11:61083989	rs146943545	V>M	A:426	(51.76, 1.75, 43.23)
11:61083973		G>V	A:431	(50.95, 8.09, 31.81)
11:61083850		N>K	A:439	(63.36, 2.83, 54.63)
11:61083826		E>D	A:447	(63.54, -0.14, 38.93)
11:61083812		V>A	A:452	(55.35, -1.07, 33.19)
11:61083813	rs373150519	V>M	A:452	(55.35, -1.07, 33.19)
11:61083782		N>S	A:462	(46.96, -7.23, 47.56)
11:61083780		V>M	A:463	(46.86, -10.71, 44.13)
11:61083770		Q>R	A:466	(53.62, -15.79, 46.71)
11:61081939		R>K	A:477	(53.80, -7.03, 33.45)
11:61081936		L>S	A:478	(51.85, -11.03, 36.99)
11:61081930		S>F	A:480	(55.78, -13.07, 42.27)
11:61081927		Q>R	A:481	(56.49, -12.34, 46.46)
11:61081887	rs375517104	Q>H	A:494	(42.73, -7.67, 18.08)
11:61081883		K>Q	A:496	(41.65, -3.93, 21.15)
11:61081848	rs200688468	Q>H	A:507	(37.48, -12.06, 40.99)
11:61081819	rs56006697	Y>C	A:517	(37.55, -10.31, 28.20)
11:61081804	rs185730554	H>R	A:522	(45.40, -19.58, 40.09)
11:61081798	COSM1580766	Q>R	A:524	(53.87, -18.70, 39.14)
11:61081794	COSM929431	E>D	A:525	(48.94, -19.19, 36.54)
11:61081793		L>F	A:526	(47.11, -14.86, 33.93)
11:61081782		I>M	A:529	(37.54, -17.48, 32.11)
11:61081667	COSM1355212	E>D	A:535	(23.52, -2.69, 24.73)
11:61081645		I>V	A:543	(34.88, -7.12, 41.41)
11:61081639		P>S	A:545	(34.89, -10.62, 47.91)
11:61081628		D>E	A:548	(28.88, -14.56, 50.91)
11:61081629		D>G	A:548	(28.88, -14.56, 50.91)
11:61081627		S>G	A:549	(32.66, -15.20, 50.20)
11:61081623		N>S	A:550	(36.12, -17.03, 51.54)
11:61081624		N>D	A:550	(36.12, -17.03, 51.54)
11:61081621		G>R	A:551	(37.82, -14.32, 47.64)
11:61081617		L>P	A:552	(35.30, -15.94, 44.92)
11:61081578	COSM1704114	S>L	A:565	(23.03, 2.80, 33.04)
11:61081572		R>H	A:567	(23.23, -2.95, 32.91)
11:61081547	rs570804153	E>D	A:575	(23.05, -13.85, 33.35)
11:61081411		T>I	A:595	(29.33, -5.04, 53.90)
11:61081403		S>R	A:598	(22.92, -5.68, 58.60)
11:61081399		S>N	A:599	(22.89, -4.70, 54.72)
11:61081394		Y>D	A:601	(24.53, -1.12, 51.54)
11:61081366		A>V	A:610	(25.73, 13.18, 41.73)
11:61081338		E>D	A:619	(21.04, -13.98, 47.55)
11:61081163		R>H	A:626	(15.82, 6.79, 42.37)
11:61081130		V>A	A:637	(36.19, 8.54, 43.35)
11:61081115	rs376616995	R>H	A:642	(41.66, 0.08, 58.42)
11:61081116		R>C	A:642	(41.66, 0.08, 58.42)
11:61081109		L>P	A:644	(35.60, 1.42, 63.69)
11:61081049		H>R	A:664	(20.74, -0.61, 60.08)
11:61080986		D>G	A:685	(56.94, 0.65, 59.35)
11:61079536	rs376923688 COSM929430	S>N	A:697	(49.43, 18.61, 44.17)
11:61079533		T>I	A:698	(50.06, 17.15, 47.57)
11:61079534		T>A	A:698	(50.06, 17.15, 47.57)
11:61079492		I>L	A:712	(31.37, 16.68, 70.79)
11:61079473		Y>C	A:718	(34.36, 17.73, 87.25)
11:61079465		P>A	A:721	(29.92, 27.27, 83.69)
11:61079347	rs147859470	V>A	A:729	(46.31, 38.40, 72.12)
11:61079317	rs190054116	R>H	A:739	(33.64, 26.78, 94.30)
11:61079314		I>T	A:740	(28.19, 24.74, 95.94)
11:61079315		I>V	A:740	(28.19, 24.74, 95.94)
11:61079309		V>L	A:742	(29.53, 23.30, 103.05)
11:61079302		D>V	A:744	(32.77, 24.78, 108.47)
11:61079299	COSM929428	T>M	A:745	(32.60, 23.19, 112.53)
11:61079295		S>R	A:746	(34.91, 26.69, 112.29)
11:61079291		G>S	A:748	(33.48, 28.09, 107.24)
11:61079273		P>T	A:754	(37.57, 17.79, 93.16)
11:61077800		N>H	A:790	(36.03, 31.52, 90.16)
11:61077790		I>T	A:793	(42.73, 31.65, 82.69)
11:61077791	rs373866581	I>V	A:793	(42.73, 31.65, 82.69)
11:61077416		Q>H	A:806	(38.41, 33.00, 95.01)
11:61077405		N>S	A:810	(28.69, 36.38, 99.82)
11:61077370	rs372773947	G>S	A:822	(41.23, 52.98, 74.38)
11:61077345	rs367819676	I>T	A:830	(36.31, 43.42, 82.24)
11:61077346		I>V	A:830	(36.31, 43.42, 82.24)
11:61077331	rs201599936	M>V	A:835	(27.73, 41.60, 96.96)
11:61077295		R>C	A:847	(34.04, 44.20, 92.54)
11:61077291		I>T	A:848	(33.74, 46.94, 87.60)
11:61077288		V>A	A:849	(37.48, 43.83, 88.13)
11:61077289		V>L	A:849	(37.48, 43.83, 88.13)
11:61076538		T>S	A:860	(44.28, 43.16, 89.87)
11:61076508		V>M	A:870	(27.22, 44.20, 86.84)
11:61076484	COSM386431	G>R	A:878	(36.84, 52.23, 74.21)
11:61076462		N>S	A:885	(20.26, 47.19, 89.19)
11:61076456	rs187902800	T>M	A:887	(21.67, 52.38, 85.78)
11:61071486		T>A	A:895	(45.83, 57.78, 80.67)
11:61071445		N>K	A:908	(15.78, 50.78, 82.69)
11:61071428		L>P	A:914	(23.69, 45.07, 76.77)
11:61071360		P>A	A:937	(29.21, 62.29, 69.59)
11:61070222		A>T	A:982	(6.73, 56.89, 59.47)
11:61070156		V>I	A:1004	(16.95, 31.35, 74.26)
11:61070086	rs535718507	S>L	A:1027	(24.73, 34.03, 60.94)
11:61070071		T>M	A:1032	(19.18, 26.16, 74.31)
11:61070065	rs144788672	N>S	A:1034	(16.82, 21.47, 76.24)
11:61070058		M>I	A:1036	(18.82, 23.51, 70.41)
11:61069822		T>S	A:1041	(19.35, 33.51, 58.77)
11:61069798	rs182128993	N>S	A:1049	(6.98, 35.22, 49.47)
11:61069784		M>L	A:1054	(7.70, 25.45, 50.14)
11:61069772		L>I	A:1058	(5.33, 20.78, 53.23)
11:61069756		K>R	A:1063	(2.66, 12.51, 57.75)
11:61068385		E>K	A:1079	(-1.32, 32.89, 80.25)
11:61068330		F>S	A:1097	(10.94, 18.73, 49.74)
11:61068316		R>C	A:1102	(10.04, 12.32, 42.69)
11:61067641		I>M	A:1130	(15.40, 18.61, 45.17)
11:61067639		K>R	A:1131	(19.34, 21.75, 43.40)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:61097501	COSM3376013	A>T	A:86	(-3.69, 15.11, 73.30)
11:61094352	COSM929436	R>Q	A:188	(2.30, 20.10, 102.29)
11:61090509	COSM1704115	R>C	A:327	(17.77, 19.04, 83.36)
11:61083828	COSM929433	E>K	A:447	(63.54, -0.14, 38.93)
11:61081798	COSM1580766	Q>R	A:524	(53.87, -18.70, 39.14)
11:61081668	COSM1355213	E>G	A:535	(23.52, -2.69, 24.73)
11:61081077	COSM3710366	R>C	A:655	(31.42, 19.40, 48.83)
11:61079499	COSM2152473	K>N	A:709	(27.90, 17.55, 60.35)
11:61079464	COSM1355211	P>Q	A:721	(29.92, 27.27, 83.69)
11:61079340	COSM3355832	Q>H	A:731	(46.42, 32.02, 72.31)
11:61077397	COSM1746373	A>T	A:813	(30.52, 36.72, 88.71)
11:61070162	COSM169713	E>K	A:1002	(13.71, 25.61, 72.91)
11:61067618	COSM689333	R>Q	A:1138	(25.01, 23.36, 51.26)

3I8E.A | DDB1.

3I8E.A | DDB1

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