3D4J.A | MVD – ASTRID

3D4J.A | MVD

General Structure Information

PDB ID	3d4j
HGNC Gene Label(s)	MVD
Structure Name	crystal structure of human mevalonate diphosphate decarboxylase
Resolution	2.4Å
Reference	AUTH N.E.VOYNOVA,Z.FU,K.P.BATTAILE,T.J.HERDENDORF,AUTH 2 J.J.KIM,H.M.MIZIORKOTITL HUMAN MEVALONATE DIPHOSPHATE DECARBOXYLASE:TITL 2 CHARACTERIZATION, INVESTIGATION OF THE MEVALONATETITL 3 DIPHOSPHATE BINDING SITE, AND CRYSTAL STRUCTURE.REF ARCH.BIOCHEM.BIOPHYS. V. 480 58 2008REFN ISSN 0003-9861PMID 18823933DOI 10.1016/J.ABB.2008.08.024

Variant Set Distributions

ExAC Variants

Number Of Residues	374
Number Of SNVs	141
Number Of Permutations	64920
Optimal Distance Threshold	12.0
K Statistic	0.076
p-value	0.129

COSMIC

Number Of Residues	374
Number Of SNVs	3
Number Of Permutations	108
Optimal Distance Threshold	26.0
K Statistic	0.667
p-value	0.899

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:88729467		A>T	A:8	(33.32, -8.93, -10.35)
16:88729463	rs142431370	A>V	A:9	(32.98, -7.03, -7.33)
16:88729457		T>I	A:11	(29.41, -3.25, -2.96)
16:88729445		P>L	A:15	(19.69, -0.36, 6.63)
16:88729446		P>S	A:15	(19.69, -0.36, 6.63)
16:88729433	rs532101272	A>V	A:19	(10.96, -1.33, 16.45)
16:88725119	COSM404692	R>H	A:27	(5.39, -19.19, 14.72)
16:88725120	rs200509037	R>C	A:27	(5.39, -19.19, 14.72)
16:88725117		D>N	A:28	(9.58, -21.87, 14.11)
16:88725092		N>S	A:36	(4.21, -10.82, 16.92)
16:88725078	rs146412581	V>I	A:41	(11.63, 3.05, 11.22)
16:88725061		D>E	A:46	(23.58, 9.24, 5.17)
16:88724418		A>V	A:54	(30.88, -9.97, -3.12)
16:88724416	rs200435526	V>I	A:55	(33.60, -12.12, -5.09)
16:88724409		S>T	A:57	(34.71, -18.20, -8.50)
16:88724410	rs369603174	S>G	A:57	(34.71, -18.20, -8.50)
16:88724404	rs375979090	D>H	A:59	(38.07, -23.23, -7.51)
16:88724397	rs202087443	T>N	A:61	(39.56, -20.57, -0.96)
16:88724390		D>E	A:63	(32.33, -20.63, 1.15)
16:88724388	COSM3402539	R>Q	A:64	(37.25, -17.67, 3.22)
16:88724383	rs200434281	W>R	A:66	(36.49, -12.56, 5.46)
16:88724376	rs371763667	N>S	A:68	(34.23, -5.99, 11.36)
16:88724374		G>R	A:69	(37.70, -9.21, 10.36)
16:88724370		R>Q	A:70	(37.15, -10.06, 14.01)
16:88724371		R>G	A:70	(37.15, -10.06, 14.01)
16:88724355		G>V	A:75	(28.51, -23.21, 9.89)
16:88724334		C>S	A:82	(21.19, -17.48, 4.11)
16:88724331		L>P	A:83	(24.37, -19.28, 2.22)
16:88724328	rs200508667	R>Q	A:84	(20.39, -24.08, 2.85)
16:88724329	rs150594289	R>W	A:84	(20.39, -24.08, 2.85)
16:88724324	rs199644137	E>D	A:85	(16.76, -19.58, 0.99)
16:88723987	rs200100993	R>H	A:87	(23.93, -21.00, -2.74)
16:88723988	rs201753135	R>C	A:87	(23.93, -21.00, -2.74)
16:88723984	rs376547753	C>Y	A:88	(17.37, -22.38, -3.57)
16:88723975	rs544260643	R>Q	A:91	(17.79, -22.69, -8.84)
16:88723927	rs539888157	S>I	A:107	(29.23, -20.15, -10.66)
16:88723913	rs147252211	V>M	A:112	(31.67, -12.15, 1.94)
16:88723906	rs372683488 COSM3513198	S>L	A:114	(31.27, -6.84, 6.03)
16:88723904		V>L	A:115	(31.91, -3.11, 7.41)
16:88723896		N>K	A:117	(29.12, 3.03, 10.60)
16:88723898		N>D	A:117	(29.12, 3.03, 10.60)
16:88723888		T>M	A:120	(29.58, -2.52, 19.61)
16:88723882		A>V	A:122	(25.52, 2.05, 20.07)
16:88723879		G>D	A:123	(23.26, -0.42, 19.77)
16:88723864		A>V	A:128	(19.60, -7.18, 10.64)
16:88723861	rs370500274	A>V	A:129	(21.67, -5.11, 8.83)
16:88723859		G>S	A:130	(23.68, -7.68, 7.88)
16:88723855		Y>F	A:131	(22.35, -11.91, 8.34)
16:88722710		Y>H	A:136	(20.22, -6.04, -2.11)
16:88722706		T>S	A:137	(25.02, -8.41, -2.01)
16:88722698	rs143689631	R>C	A:140	(23.03, -7.75, -7.66)
16:88722689		G>S	A:143	(20.20, -12.44, -10.04)
16:88722686		V>M	A:144	(18.02, -12.94, -7.19)
16:88722674	rs138878057	L>F	A:148	(15.29, -11.24, -0.46)
16:88722671		S>T	A:149	(12.34, -11.70, 2.86)
16:88722668	rs150275437	E>K	A:150	(12.49, -16.93, 3.03)
16:88722656	rs141463390	R>W	A:154	(16.13, -19.09, 7.57)
16:88722650		S>P	A:156	(17.79, -12.11, 11.07)
16:88722641		A>T	A:159	(16.32, -8.47, 8.36)
16:88722634	rs144010349	R>Q	A:161	(12.02, -5.00, 9.99)
16:88722635	rs146629473	R>W	A:161	(12.02, -5.00, 9.99)
16:88722631	COSM1679326	S>N	A:162	(16.20, -3.64, 6.35)
16:88722625		Y>C	A:164	(11.59, -3.27, 1.65)
16:88722623		G>R	A:165	(12.28, 1.97, 3.10)
16:88722620		G>S	A:166	(10.98, 3.58, 5.87)
16:88722602		M>L	A:172	(3.04, -13.50, 11.81)
16:88722598	rs372043528	G>E	A:173	(2.29, -15.35, 9.15)
16:88722595		E>G	A:174	(-1.68, -17.73, 8.10)
16:88722591	rs567533965	Q>H	A:175	(2.00, -19.95, 4.97)
16:88722586		D>G	A:177	(5.80, -22.64, 4.68)
16:88722587		D>N	A:177	(5.80, -22.64, 4.68)
16:88722584		G>R	A:178	(7.49, -19.90, 5.74)
16:88722576		D>E	A:180	(3.37, -15.99, 4.72)
16:88722571		I>T	A:182	(6.88, -11.39, 4.26)
16:88722569	rs142098957	A>T	A:183	(8.22, -7.88, 4.20)
16:88722560		V>M	A:186	(3.76, 0.88, 5.38)
16:88722557	rs369371155	A>S	A:187	(5.76, 3.89, 3.95)
16:88722551	rs569320748	E>K	A:189	(11.77, 6.80, 2.05)
16:88722542	rs144072796	W>R	A:192	(6.26, 11.36, 9.18)
16:88722534	rs375844540	E>D	A:194	(8.91, 16.36, 8.75)
16:88722530	COSM1709502	R>C	A:196	(14.14, 13.87, 12.08)
16:88722527		V>M	A:197	(15.72, 9.11, 14.82)
16:88722521		I>V	A:199	(20.49, 6.67, 18.94)
16:88722518		L>F	A:200	(20.14, 8.47, 23.50)
16:88722515		V>L	A:201	(24.60, 5.81, 23.78)
16:88722131		A>V	A:204	(26.57, 0.46, 30.51)
16:88722132	rs112697935	A>T	A:204	(26.57, 0.46, 30.51)
16:88722107		T>I	A:212	(17.82, -15.37, 20.63)
16:88722098		M>T	A:215	(12.93, -14.15, 22.36)
16:88722096	rs370299302	R>W	A:216	(14.48, -19.50, 23.35)
16:88722092	rs574614800	A>G	A:217	(12.18, -17.53, 27.91)
16:88722076	rs374443480	S>R	A:222	(5.27, -14.96, 29.65)
16:88722069		L>V	A:225	(4.38, -12.82, 25.56)
16:88721822		R>W	A:228	(2.38, -8.24, 23.02)
16:88721813	rs371091142	S>A	A:231	(-5.08, -9.76, 22.35)
16:88721810		V>M	A:232	(-2.35, -6.57, 21.97)
16:88721800		A>V	A:235	(-4.43, -3.71, 16.86)
16:88721797	rs377645347 COSM1609769	R>H	A:236	(-0.70, -1.82, 20.07)
16:88721798	COSM974730	R>C	A:236	(-0.70, -1.82, 20.07)
16:88721794		M>T	A:237	(0.51, -3.57, 13.55)
16:88721791	rs60803836	A>V	A:238	(-3.35, -1.15, 12.59)
16:88721780	rs200296577	R>C	A:242	(-3.82, 5.87, 11.98)
16:88721770		R>Q	A:245	(-1.35, 4.88, 6.44)
16:88721771	COSM1380425	R>W	A:245	(-1.35, 4.88, 6.44)
16:88721764	rs143846527	R>Q	A:247	(1.49, 12.32, 7.56)
16:88721758		F>S	A:249	(4.50, 12.38, 16.59)
16:88721752	COSM1215983	S>N	A:251	(-0.83, 8.75, 17.95)
16:88721747	rs202128233	A>T	A:253	(4.30, 8.42, 20.19)
16:88721741		L>V	A:255	(1.42, 3.20, 20.10)
16:88721734		M>K	A:257	(5.87, 5.47, 24.55)
16:88721722		N>S	A:261	(6.74, 0.31, 28.08)
16:88721713		H>R	A:264	(11.26, -3.79, 28.18)
16:88721710		A>V	A:265	(6.99, -6.16, 30.60)
16:88721689		P>L	A:272	(14.38, -16.06, 34.98)
16:88721672	rs34519538	N>H	A:278	(19.56, 1.55, 32.93)
16:88721654		I>V	A:284	(15.67, 9.09, 29.38)
16:88721629		N>S	A:292	(5.62, 15.70, 26.30)
16:88721627		A>T	A:293	(3.71, 17.97, 29.92)
16:88721618	rs150857520	G>R	A:296	(0.92, 19.83, 26.26)
16:88721211		A>V	A:301	(9.26, 9.41, 21.73)
16:88721201		F>L	A:304	(13.97, 1.84, 25.47)
16:88721197		A>T	A:306	(17.99, -5.26, 24.25)
16:88721193	rs554003292	G>D	A:307	(18.77, -2.28, 26.21)
16:88721185		A>T	A:310	(17.54, 5.53, 23.79)
16:88721182	rs200147810	V>M	A:311	(15.27, 5.17, 20.45)
16:88721169	rs148321136	L>P	A:315	(8.93, 16.20, 14.56)
16:88721166		D>G	A:316	(11.92, 18.95, 12.39)
16:88721164		D>N	A:317	(9.95, 21.26, 15.21)
16:88721137	rs368231679	V>L	A:326	(19.51, 15.45, 26.96)
16:88721130		H>R	A:328	(19.71, 19.79, 32.26)
16:88721127	rs370676684	G>V	A:329	(20.57, 15.78, 32.35)
16:88721128	rs188551104	G>S	A:329	(20.57, 15.78, 32.35)
16:88721123		F>L	A:330	(21.66, 13.00, 31.07)
16:88721112	rs374779531	S>L	A:334	(33.51, 19.16, 28.87)
16:88721108		N>K	A:335	(32.79, 17.99, 24.89)
16:88721104	rs377428809	D>N	A:337	(33.42, 17.62, 20.75)
16:88721100		T>M	A:338	(31.98, 13.30, 19.94)
16:88719811		L>P	A:340	(26.09, 15.84, 18.87)
16:88719799		Q>R	A:344	(22.98, 18.92, 10.91)
16:88719790	rs138484696	P>L	A:347	(22.84, 24.67, 19.87)
16:88719782		L>V	A:350	(16.71, 24.95, 28.44)
16:88719770	rs145850660	L>V	A:354	(11.47, 23.06, 30.27)
16:88719760	rs151006109	A>V	A:357	(9.47, 20.52, 34.39)
16:88719755	rs145441544	A>P	A:359	(12.53, 17.73, 37.62)
16:88719752		M>L	A:360	(16.16, 15.81, 36.12)
16:88719746		P>T	A:362	(22.15, 16.42, 36.95)
16:88719742		T>I	A:363	(23.46, 12.14, 35.41)
16:88719736		G>A	A:365	(27.62, 10.68, 31.75)
16:88719737	rs113497258	G>S	A:365	(27.62, 10.68, 31.75)
16:88719718	rs546761521	I>T	A:371	(23.20, 8.82, 16.87)
16:88718989	rs189127618	D>H	A:383	(29.09, 3.24, -8.34)
16:88718983		P>T	A:385	(35.83, 0.56, -7.68)
16:88718979	rs367729578	C>Y	A:386	(37.62, 2.40, -4.48)
16:88718976		A>V	A:387	(34.55, 0.56, -2.22)
16:88718977	COSM974728	A>T	A:387	(34.55, 0.56, -2.22)
16:88718956	rs374698190	G>S	A:394	(40.64, -10.30, -0.40)

3D4J.A | MVD.

3D4J.A | MVD

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
16:88722120	COSM3712186	L>M	A:208	(22.94, -7.29, 28.12)
16:88721798	COSM974730	R>C	A:236	(-0.70, -1.82, 20.07)
16:88719745	COSM2922243	P>L	A:362	(22.15, 16.42, 36.95)