1NUD.A | TGM3 – ASTRID

1NUD.A | TGM3

General Structure Information

PDB ID	1nud
HGNC Gene Label(s)	TGM3
Structure Name	role of calcium ions in the activation and activity of the transglutaminase 3 enzyme (3 calciums, active form)
Resolution	2.7Å
Reference	AUTH B.AHVAZI,K.M.BOESHANS,W.IDLER,U.BAXA,P.M.STEINERTTITL ROLES OF CALCIUM IONS IN THE ACTIVATION ANDTITL 2 ACTIVITY OF THE TRANSGLUTAMINASE 3 ENZYMEREF J.BIOL.CHEM. V. 278 23834 2003REFN ISSN 0021-9258PMID 12679341DOI 10.1074/JBC.M301162200

Variant Set Distributions

ExAC Variants

Number Of Residues	673
Number Of SNVs	225
Number Of Permutations	71570
Optimal Distance Threshold	10.0
K Statistic	0.026
p-value	0.26

COSMIC

Number Of Residues	673
Number Of SNVs	16
Number Of Permutations	9393
Optimal Distance Threshold	38.0
K Statistic	0.342
p-value	0.152

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	225
Number Of COSMIC SNVs	12
Optimal Distance Threshold	38.0
K Statistic	-0.172
p-value	0.454

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:2290311		V>F	A:5	(-24.28, -18.32, -12.97)
20:2290318		S>N	A:7	(-23.26, -12.96, -14.09)
20:2290320		I>V	A:8	(-20.97, -12.22, -10.27)
20:2290324		N>S	A:9	(-21.88, -7.33, -9.52)
20:2290333	rs214803	T>K	A:12	(-15.93, -3.75, -5.39)
20:2290345		R>Q	A:16	(-12.95, -1.84, -1.35)
20:2290351	rs143797112	A>V	A:18	(-18.41, -0.51, 3.81)
20:2290371		S>T	A:25	(-4.40, -0.20, -4.83)
20:2290372	rs376878875	S>F	A:25	(-4.40, -0.20, -4.83)
20:2290380		E>Q	A:28	(-8.32, -7.96, -5.41)
20:2290387		I>T	A:30	(-10.45, -5.83, -0.01)
20:2290393		R>Q	A:32	(-12.16, -5.44, 6.99)
20:2290416		L>V	A:40	(-25.77, -8.46, -8.01)
20:2290423		I>N	A:42	(-27.38, -12.35, -13.48)
20:2290435		G>D	A:46	(-35.39, -18.67, -12.30)
20:2290448		N>K	A:50	(-37.25, -28.23, -5.96)
20:2290449	rs267605853 COSM3544672	E>K	A:51	(-34.04, -24.84, -7.88)
20:2290462		F>Y	A:55	(-22.97, -19.50, -1.88)
20:2290840		E>D	A:65	(-15.01, -28.04, 6.26)
20:2290851		T>M	A:69	(-10.33, -23.34, 6.33)
20:2290875	rs151028271	N>S	A:77	(-35.20, -15.91, 3.24)
20:2290878		G>D	A:78	(-32.33, -15.81, 6.59)
20:2290880		S>G	A:79	(-29.42, -15.48, 9.18)
20:2290904		L>F	A:87	(-32.71, -14.02, -1.38)
20:2290908		Q>R	A:88	(-31.59, -9.08, 0.42)
20:2290919		G>S	A:92	(-35.53, -11.47, -12.61)
20:2290920	rs544584169 COSM1229105	G>D	A:92	(-35.53, -11.47, -12.61)
20:2290937		S>C	A:98	(-26.40, -10.91, 1.86)
20:2290955	rs563060197	S>G	A:104	(-14.03, -16.22, 13.79)
20:2290958	rs146616453	A>T	A:105	(-12.59, -16.00, 10.36)
20:2290959		A>V	A:105	(-12.59, -16.00, 10.36)
20:2290965		I>T	A:107	(-6.96, -13.45, 7.81)
20:2290970	rs139117716	R>W	A:109	(-5.41, -13.99, -1.10)
20:2290971	COSM3673087	R>Q	A:109	(-5.41, -13.99, -1.10)
20:2290977		T>K	A:111	(-12.12, -19.26, -3.37)
20:2290979		M>V	A:112	(-16.90, -17.65, -3.69)
20:2290980		M>T	A:112	(-16.90, -17.65, -3.69)
20:2290986		L>R	A:114	(-22.29, -21.81, -6.79)
20:2290990		Q>H	A:115	(-23.46, -26.68, -4.77)
20:2290991		I>F	A:116	(-26.48, -25.11, -8.72)
20:2291006	rs551977439	G>S	A:121	(-28.92, -32.05, -10.25)
20:2291030		T>A	A:129	(-11.40, -14.20, -5.60)
20:2291031		T>M	A:129	(-11.40, -14.20, -5.60)
20:2291043		L>H	A:133	(-8.83, -8.38, 6.22)
20:2291051		P>A	A:136	(-11.15, -2.98, 13.60)
20:2291665		V>I	A:143	(-9.05, -6.28, 16.49)
20:2291672		M>T	A:145	(-10.22, 0.36, 18.20)
20:2291680	rs201965610	H>D	A:148	(-13.08, 7.61, 14.07)
20:2291702	rs555433935	V>A	A:155	(-5.75, 1.10, 10.87)
20:2291705		Q>R	A:156	(-7.01, 3.67, 7.88)
20:2291716	rs138092626	G>S	A:160	(4.84, 8.43, 10.38)
20:2291726		F>S	A:163	(9.47, 9.64, 18.59)
20:2291735		S>N	A:166	(18.94, 10.41, 23.58)
20:2291738		T>I	A:167	(17.81, 10.30, 27.48)
20:2291740		N>D	A:168	(20.26, 13.58, 26.88)
20:2291744	rs556533732	R>Q	A:169	(19.30, 15.49, 21.25)
20:2291754		M>I	A:172	(11.33, 13.16, 14.93)
20:2293554		D>G	A:183	(2.10, -5.78, -4.26)
20:2293556	rs372537861	I>V	A:184	(2.15, -3.63, 0.11)
20:2293565		I>V	A:187	(3.84, -8.67, -0.19)
20:2293578		I>S	A:191	(4.59, -12.83, 4.90)
20:2293601		R>C	A:199	(8.28, -24.09, 5.73)
20:2293602	COSM1025163	R>H	A:199	(8.28, -24.09, 5.73)
20:2293610	COSM328458	A>T	A:202	(-0.31, -25.28, 6.30)
20:2293620	rs140483456	D>A	A:205	(-0.83, -21.53, 9.52)
20:2293622	rs374185059	V>M	A:206	(-4.46, -21.21, 7.32)
20:2293625		A>T	A:207	(-6.37, -22.03, 10.94)
20:2293629	COSM384000	S>N	A:208	(-4.23, -19.97, 13.15)
20:2293645		K>N	A:213	(-2.90, -14.09, 19.67)
20:2293649	rs113905463	V>I	A:215	(-0.84, -13.08, 12.83)
20:2293653		G>A	A:216	(1.98, -11.41, 15.13)
20:2293655		R>W	A:217	(4.82, -15.20, 18.27)
20:2293656		R>Q	A:217	(4.82, -15.20, 18.27)
20:2293665	rs530116639 COSM385349	S>N	A:220	(7.73, -11.24, 14.92)
20:2293670	rs377549298	M>V	A:222	(8.76, -13.63, 8.51)
20:2297718		N>S	A:224	(13.45, -11.31, 11.10)
20:2297721	rs146227949	S>N	A:225	(16.24, -12.71, 7.95)
20:2297727		D>G	A:227	(15.53, -18.25, 11.64)
20:2297759	rs200714008	G>S	A:238	(28.81, 0.58, 10.79)
20:2297769		T>I	A:241	(29.24, -2.82, 2.43)
20:2297771	rs143810711	G>S	A:242	(26.12, -4.54, 0.42)
20:2297777	rs202051623	R>W	A:244	(19.88, 1.29, 1.42)
20:2297786		R>G	A:247	(20.00, 6.05, 10.67)
20:2297790	rs214814	S>N	A:248	(18.54, 5.27, 4.27)
20:2297798	rs372347727	G>S	A:251	(10.12, 2.89, 4.39)
20:2297804		V>M	A:253	(7.08, 0.34, 0.18)
20:2297808		E>V	A:254	(10.57, 0.39, -1.82)
20:2297818	rs368285192	K>N	A:257	(7.83, -3.66, -3.48)
20:2297832		S>Y	A:262	(14.79, -10.81, -4.32)
20:2297843		P>T	A:266	(17.87, -11.09, 2.41)
20:2297853	rs372374301	Y>C	A:269	(22.39, -4.51, 5.65)
20:2297856		G>D	A:270	(18.59, -3.12, 9.44)
20:2297873		A>S	A:276	(8.94, -1.51, 13.25)
20:2298001	rs200047268 COSM4097105	R>W	A:284	(-1.39, 0.37, 10.74)
20:2298002		R>Q	A:284	(-1.39, 0.37, 10.74)
20:2298022	rs145397721	R>W	A:291	(0.87, 2.41, 19.38)
20:2298041		N>S	A:297	(18.01, 3.90, 28.25)
20:2298050		H>P	A:300	(19.63, -7.67, 25.61)
20:2298062	rs562802461	R>Q	A:304	(15.38, -15.47, 32.79)
20:2298068		L>H	A:306	(15.48, -8.29, 36.01)
20:2298073	rs377223591	V>M	A:308	(21.97, -4.76, 32.71)
20:2298074		V>A	A:308	(21.97, -4.76, 32.71)
20:2298076		D>N	A:309	(26.13, -5.95, 33.26)
20:2298078		D>E	A:309	(26.13, -5.95, 33.26)
20:2298080	rs370570929	V>G	A:310	(27.83, -1.67, 32.01)
20:2298086	rs374601295	Y>C	A:312	(33.00, 1.86, 31.67)
20:2298088	COSM3910979	D>N	A:313	(39.00, 0.88, 31.60)
20:2298095		M>T	A:315	(42.41, 4.61, 31.32)
20:2298104	rs182697627	P>L	A:318	(34.20, 2.17, 26.74)
20:2298114		K>N	A:321	(33.43, -8.05, 29.44)
20:2298115		G>S	A:322	(28.82, -8.06, 27.85)
20:2298123		D>E	A:324	(23.79, -8.03, 28.88)
20:2298125		S>T	A:325	(22.98, -4.34, 26.27)
20:2306522		W>C	A:336	(-6.21, -2.59, 20.90)
20:2306526		V>L	A:338	(-8.62, -9.47, 22.91)
20:2306527		V>G	A:338	(-8.62, -9.47, 22.91)
20:2306533	rs372653108	S>C	A:340	(-8.26, -15.24, 25.00)
20:2306542		G>D	A:343	(-7.58, -12.36, 30.11)
20:2306553	rs139599978	G>S	A:347	(-5.99, -6.52, 27.12)
20:2306557		G>E	A:348	(-5.00, -4.57, 24.41)
20:2306565		V>L	A:351	(4.40, -6.12, 22.86)
20:2306570		L>F	A:352	(4.53, -7.16, 18.59)
20:2306581	rs200497601	P>L	A:356	(16.92, -9.59, 15.83)
20:2306598		G>R	A:362	(14.64, -20.54, 19.00)
20:2308768		V>L	A:363	(12.78, -18.54, 16.78)
20:2308780	rs368238578	G>S	A:367	(5.15, -11.94, 21.07)
20:2308781		G>D	A:367	(5.15, -11.94, 21.07)
20:2308784		P>L	A:368	(1.96, -11.49, 22.28)
20:2308786	rs375988138 COSM1410744	A>T	A:369	(3.11, -8.77, 25.58)
20:2308790		S>L	A:370	(0.37, -7.34, 27.99)
20:2308795	rs138643209	I>V	A:372	(-1.72, -4.36, 31.33)
20:2308796		I>T	A:372	(-1.72, -4.36, 31.33)
20:2308805	rs375529969 COSM4135246	R>Q	A:375	(2.24, -0.77, 35.50)
20:2308808		E>V	A:376	(1.31, -4.87, 37.46)
20:2308814		D>G	A:378	(2.30, -10.50, 35.66)
20:2308820		Q>P	A:380	(3.63, -15.20, 34.66)
20:2308826	rs184729354	N>S	A:382	(2.80, -16.17, 27.19)
20:2308831	rs189594278	D>N	A:384	(8.74, -13.18, 25.24)
20:2308850	rs373347908	A>E	A:390	(14.14, -5.83, 30.87)
20:2308856		V>A	A:392	(11.14, -1.38, 30.44)
20:2308861	COSM1664548	A>T	A:394	(16.27, -3.27, 34.34)
20:2308867	rs557862374 COSM723359	R>C	A:396	(23.37, 0.88, 34.35)
20:2308871		I>T	A:397	(25.14, -3.31, 37.37)
20:2308885		D>N	A:402	(42.24, -4.19, 34.85)
20:2308889		N>T	A:403	(42.54, -7.35, 31.12)
20:2308892	COSM212988	T>S	A:404	(46.02, -6.04, 33.60)
20:2308894	rs539884508	T>A	A:405	(44.29, -7.89, 36.80)
20:2308916	rs142429871	S>F	A:412	(27.02, 1.28, 40.41)
20:2308918		V>L	A:413	(23.16, 0.07, 41.15)
20:2308922	rs561607245	N>S	A:414	(20.53, 2.94, 38.08)
20:2308927	rs150302326	H>D	A:416	(15.35, 4.72, 38.86)
20:2308931		T>I	A:417	(18.46, 4.64, 33.85)
20:2308941		R>S	A:420	(14.25, 7.93, 30.87)
20:2308949	rs543974677	S>I	A:423	(7.63, 7.41, 22.88)
20:2308957		A>P	A:426	(0.11, 11.18, 18.37)
20:2308964		G>A	A:428	(-3.35, 13.38, 14.69)
20:2308975		R>C	A:432	(6.74, 12.80, 23.18)
20:2308978	rs372876095	M>L	A:433	(1.94, 9.71, 23.44)
20:2308984	COSM1025194	V>I	A:435	(3.42, 5.53, 26.92)
20:2308988		T>M	A:436	(6.28, 5.47, 30.54)
20:2309003	rs141010304	Y>F	A:441	(3.33, 1.04, 38.98)
20:2309011		G>S	A:444	(10.58, 6.28, 42.87)
20:2312657		Q>R	A:447	(4.78, 1.45, 43.75)
20:2312663	COSM3544714	R>K	A:449	(11.94, -1.43, 43.22)
20:2312767	rs371412856	G>R	A:484	(30.18, 14.46, 38.04)
20:2312774	rs199578917	L>P	A:486	(30.06, 15.44, 31.11)
20:2312788	rs201410609	M>L	A:491	(25.81, 23.96, 18.23)
20:2312791		L>M	A:492	(26.74, 19.09, 18.92)
20:2312807		E>G	A:497	(34.91, 22.05, 17.68)
20:2312827	rs367595459	L>I	A:504	(34.72, 17.62, 38.92)
20:2312842		R>G	A:509	(35.54, 15.84, 56.28)
20:2312845		D>Y	A:510	(39.40, 15.98, 53.38)
20:2312846		D>V	A:510	(39.40, 15.98, 53.38)
20:2312849		T>M	A:511	(42.12, 18.12, 50.45)
20:2312854	rs143127926	T>A	A:513	(44.45, 13.86, 44.90)
20:2312866		N>D	A:517	(41.31, 8.66, 33.11)
20:2312900	rs563551325	T>M	A:528	(28.40, -0.98, 19.07)
20:2312908		H>Y	A:531	(38.04, 3.92, 16.76)
20:2312909	rs140371240	H>R	A:531	(38.04, 3.92, 16.76)
20:2312930		A>V	A:538	(44.03, 14.63, 34.79)
20:2312936	rs373609319	M>K	A:540	(43.11, 17.51, 39.85)
20:2312944	rs375357846	D>N	A:543	(40.22, 22.10, 48.22)
20:2312946		D>E	A:543	(40.22, 22.10, 48.22)
20:2315772		H>Q	A:550	(39.12, 19.12, 31.78)
20:2315776		I>L	A:552	(36.46, 17.86, 26.57)
20:2315786		S>L	A:555	(38.31, 17.76, 15.93)
20:2315791	rs199889633 COSM247807	A>T	A:557	(39.50, 15.44, 12.05)
20:2315801		E>G	A:560	(35.84, 12.33, 9.93)
20:2315810		L>P	A:563	(31.16, 9.63, 12.87)
20:2315819	rs373901654	D>G	A:566	(24.74, 6.71, 14.47)
20:2315821		N>D	A:567	(25.91, 11.32, 14.02)
20:2315826		M>I	A:568	(26.22, 8.79, 18.69)
20:2315827	rs560860137	I>V	A:569	(30.52, 10.61, 20.50)
20:2315830		R>W	A:570	(29.70, 6.18, 24.84)
20:2315831	rs531290820 COSM2706108	R>Q	A:570	(29.70, 6.18, 24.84)
20:2315840	rs549533086	A>V	A:573	(34.98, 9.94, 32.95)
20:2315843		V>A	A:574	(37.25, 7.34, 35.20)
20:2315846		C>Y	A:575	(37.24, 9.85, 38.50)
20:2315851		V>F	A:577	(40.30, 9.38, 44.82)
20:2315855		P>L	A:578	(43.26, 8.28, 46.71)
20:2315857		D>N	A:579	(42.36, 4.74, 49.16)
20:2315868	rs137862904	E>D	A:582	(36.65, 3.83, 40.94)
20:2315875		V>M	A:585	(31.43, 10.72, 34.38)
20:2315876	COSM178343	V>A	A:585	(31.43, 10.72, 34.38)
20:2315881	rs187614014	R>W	A:587	(26.42, 13.14, 27.64)
20:2315882	rs374729253	R>Q	A:587	(26.42, 13.14, 27.64)
20:2315894		L>P	A:591	(26.81, 15.16, 16.31)
20:2315900	rs201851703	N>S	A:593	(23.02, 16.12, 9.98)
20:2315902		P>S	A:594	(23.91, 19.20, 7.69)
20:2315912		T>I	A:597	(15.30, 21.79, 3.12)
20:2320509	rs199983032	E>K	A:603	(-1.97, 25.41, -4.03)
20:2320515	rs150542876	R>C	A:605	(-4.80, 21.95, -6.57)
20:2320516		R>H	A:605	(-4.80, 21.95, -6.57)
20:2320521	rs370607077 COSM1565875	R>W	A:607	(-6.18, 14.23, -10.21)
20:2320522	rs374127604 COSM1410746 COSM76718	R>Q	A:607	(-6.18, 14.23, -10.21)
20:2320527	rs370304381	P>S	A:609	(1.24, 18.73, -11.21)
20:2320533		N>D	A:611	(6.50, 22.06, -8.71)
20:2320552		S>C	A:617	(24.33, 23.52, 2.49)
20:2320561		L>R	A:620	(32.57, 20.39, 4.98)
20:2320564	rs138448745	D>G	A:621	(36.51, 23.12, 4.28)
20:2320568		E>D	A:622	(35.71, 18.26, 2.40)
20:2320569		P>S	A:623	(34.14, 18.44, -1.47)
20:2320570	rs144316255	P>L	A:623	(34.14, 18.44, -1.47)
20:2320584		V>M	A:628	(21.87, 10.16, -3.86)
20:2320605	rs367606978	G>S	A:635	(0.03, 10.15, -2.33)
20:2320628		K>N	A:642	(17.72, 7.49, -7.62)
20:2321081	COSM1410747	V>M	A:645	(23.37, 14.87, -6.78)
20:2321084	rs147532262	P>S	A:646	(25.60, 17.14, -8.64)
20:2321094	rs114998364	G>E	A:649	(31.20, 22.22, -2.84)
20:2321097		P>L	A:650	(33.36, 23.79, -0.73)
20:2321106		G>E	A:653	(22.03, 26.23, -1.81)
20:2321111	rs151074346	R>W	A:655	(17.86, 24.47, -7.00)
20:2321112		R>Q	A:655	(17.86, 24.47, -7.00)
20:2321117	COSM1410748	R>C	A:657	(12.94, 21.37, -9.45)
20:2321118	rs190943274	R>H	A:657	(12.94, 21.37, -9.45)
20:2321123		D>H	A:659	(7.81, 17.39, -10.24)
20:2321130		L>P	A:661	(0.97, 13.61, -9.46)
20:2321133	rs369393628	P>L	A:662	(-0.80, 14.55, -6.01)
20:2321138	rs150949349	R>W	A:664	(-4.93, 9.66, -1.10)
20:2321139	rs149720612	R>Q	A:664	(-4.93, 9.66, -1.10)
20:2321150		K>Q	A:668	(-0.28, 13.28, 2.38)
20:2321163	rs146717993	A>V	A:672	(13.95, 12.68, 2.15)
20:2321165	rs140423684	D>N	A:673	(17.91, 10.34, 1.97)
20:2321167	rs186345115	D>E	A:673	(17.91, 10.34, 1.97)
20:2321172		S>F	A:675	(23.43, 10.55, 0.72)
20:2321174		C>R	A:676	(27.25, 11.99, 0.87)
20:2321183	rs145595091	F>L	A:679	(27.47, 14.59, 5.36)
20:2321192	rs560975159	I>F	A:682	(20.97, 13.86, 5.52)
20:2321196		K>R	A:683	(16.93, 12.13, 6.81)
20:2321204	rs45581032	L>M	A:686	(7.27, 18.71, 3.85)
20:2321206		L>F	A:686	(7.27, 18.71, 3.85)
20:2321213	COSM285687	D>N	A:689	(-1.77, 20.43, 2.80)
20:2321222	rs149044769	E>K	A:692	(-9.53, 18.45, -4.48)

1NUD.A | TGM3.

1NUD.A | TGM3

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:2290333	COSM1533216	T>K	A:12	(-15.93, -3.75, -5.39)
20:2290449	COSM3544672	E>K	A:51	(-34.04, -24.84, -7.88)
20:2290957	COSM1751349	S>R	A:104	(-14.03, -16.22, 13.79)
20:2290970	COSM4097102	R>W	A:109	(-5.41, -13.99, -1.10)
20:2293605	COSM50487	R>H	A:200	(6.86, -26.30, 11.38)
20:2293610	COSM328458	A>T	A:202	(-0.31, -25.28, 6.30)
20:2298005	COSM323800	S>F	A:285	(-2.47, -4.28, 6.30)
20:2298098	COSM1713076	G>E	A:316	(37.81, 5.28, 30.40)
20:2298103	COSM2152884	P>T	A:318	(34.20, 2.17, 26.74)
20:2298127	COSM3378997	V>I	A:326	(22.23, -0.29, 27.35)
20:2308868	COSM3707649	R>L	A:396	(23.37, 0.88, 34.35)
20:2315878	COSM4531098	E>K	A:586	(28.18, 7.99, 31.86)
20:2320521	COSM1565875	R>W	A:607	(-6.18, 14.23, -10.21)
20:2320522	COSM1410746	R>L	A:607	(-6.18, 14.23, -10.21)
20:2321085	COSM1229108	P>L	A:646	(25.60, 17.14, -8.64)
20:2321105	COSM3758487	G>R	A:653	(22.03, 26.23, -1.81)
20:2321117	COSM1410748	R>C	A:657	(12.94, 21.37, -9.45)