1C9Y.A | OTC – ASTRID

1C9Y.A | OTC

General Structure Information

PDB ID	1c9y
HGNC Gene Label(s)	OTC
Structure Name	human ornithine transcarbamylase: crystallographic insights into substrate recognition and catalytic mechanism
Resolution	1.9Å
Reference	AUTH D.SHI,H.MORIZONO,M.AOYAGI,M.TUCHMAN,N.M.ALLEWELLTITL CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMYLASETITL 2 COMPLEXED WITH CARBAMOYL PHOSPHATE AND L-NORVALINE AT 1.9 ATITL 3 RESOLUTION.REF PROTEINS V. 39 271 2000REFN ISSN 0887-3585PMID 10813810DOI 10.1002/(SICI)1097-0134(20000601)39:4<271::AID-PROTDOI 2 10>3.3.CO;2-5

Variant Set Distributions

ExAC Variants

Number Of Residues	321
Number Of SNVs	38
Number Of Permutations	4787
Optimal Distance Threshold	6.0
K Statistic	0.02
p-value	0.857

ClinVar

Number Of Residues	321
Number Of SNVs	138
Number Of Permutations	15650
Optimal Distance Threshold	13.0
K Statistic	0.165
p-value	0.0

COSMIC

Number Of Residues	321
Number Of SNVs	6
Number Of Permutations	214
Optimal Distance Threshold	13.0
K Statistic	0.2
p-value	0.612

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	38
Number Of ClinVar SNVs	131
Optimal Distance Threshold	18.0
K Statistic	0.119
p-value	0.005

Cosmic vs. ExAC

Number Of ExAC SNVs	38
Number Of COSMIC SNVs	5
Optimal Distance Threshold	26.0
K Statistic	0.395
p-value	0.264

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
X:38226572	rs72554305 CM003028	Q>E	A:36	(2.40, -22.12, -39.17)
X:38226603	rs1800321	K>R	A:46	(12.26, -8.60, -33.67)
X:38226606	rs67939655	N>T	A:47	(10.27, -12.11, -33.66)
X:38226614	rs67486158	G>R	A:50	(4.15, -9.36, -42.43)
X:38229104	rs372906667	T>I	A:91	(-6.98, 0.99, -18.35)
X:38229118	rs184053962	S>P	A:96	(-8.67, -5.61, -23.59)
X:38229128		T>I	A:99	(-13.21, -8.22, -21.82)
X:38240664		S>N	A:123	(11.63, -17.61, -9.02)
X:38240670	rs72554356	T>M	A:125	(12.14, -20.11, -13.37)
X:38240681	rs140046498	R>C	A:129	(9.13, -24.70, -14.55)
X:38260544	rs72556255 CD921013	A>T	A:135	(-2.31, -21.80, -17.80)
X:38260589		T>S	A:150	(12.91, -15.82, -18.54)
X:38260618		I>M	A:159	(4.61, -15.54, -23.10)
X:38260639		L>F	A:166	(12.25, -2.40, -25.28)
X:38260670	rs148961194	L>F	A:177	(-7.04, -2.57, -37.38)
X:38262942		I>M	A:204	(6.20, 1.83, -34.95)
X:38262952	rs72558416 COSM1121088 CM961056	A>S	A:208	(6.20, -0.31, -40.71)
X:38262955	rs372179665	A>S	A:209	(8.22, -1.75, -43.30)
X:38262956	rs72558417 COSM3561621 CM950879	A>G	A:209	(8.22, -1.75, -43.30)
X:38262964		G>R	A:212	(5.01, -0.24, -46.56)
X:38262969		M>I	A:213	(4.11, 1.78, -43.51)
X:38262986		T>N	A:219	(13.47, 12.50, -30.80)
X:38267995		G>S	A:222	(19.00, 11.86, -25.98)
X:38268001	rs373196047 CM0910708	E>Q	A:224	(17.84, 9.36, -29.31)
X:38268036	rs4385598	Q>H	A:235	(17.48, -4.63, -42.09)
X:38268044		K>R	A:238	(17.69, -1.79, -47.77)
X:38268165		E>Q	A:252	(11.61, 17.84, -41.01)
X:38268172		A>V	A:254	(5.33, 15.96, -40.06)
X:38268175	rs72558440 CM001751	H>R	A:255	(6.84, 17.30, -44.75)
X:38268184	rs142592280	N>S	A:258	(-0.43, 10.20, -43.88)
X:38268219	rs72558451	Q>E	A:270	(12.06, 6.85, -17.36)
X:38268220	rs1800328	Q>R	A:270	(12.06, 6.85, -17.36)
X:38268247		Q>R	A:279	(14.08, 21.70, -19.74)
X:38268274		M>R	A:288	(-3.52, 22.00, -35.78)
X:38271121		K>E	A:292	(-0.26, 24.03, -41.67)
X:38271143		T>I	A:299	(-4.76, 10.91, -39.00)
X:38271188	rs137899554	E>A	A:314	(-7.32, 21.95, -31.79)
X:38271199		S>A	A:318	(-9.89, 16.11, -34.05)
X:38271230		E>G	A:328	(-12.58, -0.51, -29.89)
X:38280282	rs199568993	M>L	A:338	(-4.80, -14.86, -27.17)

[+] ClinVar Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
X:38226581	rs72554306	G>C	A:39	(2.63, -21.49, -29.65)
X:38226584	rs72554307	R>C	A:40	(5.10, -17.87, -32.45)
X:38226585	rs72554308	R>H	A:40	(5.10, -17.87, -32.45)
X:38226588	rs74518351	D>G	A:41	(5.97, -16.71, -27.65)
X:38226593	rs72554309	L>I	A:43	(8.00, -11.23, -26.66)
X:38226597	rs72554310	T>I	A:44	(8.74, -8.53, -30.46)
X:38226599	rs72554311	L>V	A:45	(6.16, -7.10, -33.91)
X:38226600	rs72554312	L>P	A:45	(6.16, -7.10, -33.91)
X:38226603	rs1800321	K>R	A:46	(12.26, -8.60, -33.67)
X:38226606	rs67939655	N>I	A:47	(10.27, -12.11, -33.66)
X:38226609	rs72554315	F>S	A:48	(6.11, -11.97, -35.49)
X:38226611	rs72554316	T>P	A:49	(6.55, -11.80, -40.89)
X:38226614	rs67486158	G>R	A:50	(4.15, -9.36, -42.43)
X:38226620	rs66521141	E>K	A:52	(3.52, -13.74, -39.34)
X:38226621	rs72554317	E>G	A:52	(3.52, -13.74, -39.34)
X:38226622	rs72554318	E>D	A:52	(3.52, -13.74, -39.34)
X:38226624	rs66677059	I>T	A:53	(1.84, -8.75, -38.45)
X:38226629	rs72554319	Y>D	A:55	(-3.60, -14.60, -39.53)
X:38226633	rs72554320	M>T	A:56	(-2.21, -11.02, -36.15)
X:38226636	rs72554321	L>Q	A:57	(-4.41, -7.25, -38.47)
X:38226645	rs72554323	S>L	A:60	(-8.81, -8.79, -35.68)
X:38226654	rs72554324	L>P	A:63	(-12.98, -11.99, -34.20)
X:38226666	rs72554325	I>R	A:67	(-18.38, -10.72, -32.06)
X:38229059	rs72554328	L>S	A:76	(-12.83, -19.73, -30.00)
X:38229063	rs72554329	L>F	A:77	(-10.65, -19.24, -25.75)
X:38229068	rs72554331	G>E	A:79	(-11.23, -24.04, -21.34)
X:38229070	rs72554332	K>E	A:80	(-8.57, -22.33, -22.96)
X:38229072	rs72554333	K>N	A:80	(-8.57, -22.33, -22.96)
X:38229079	rs72554336	G>R	A:83	(-2.25, -15.05, -17.13)
X:38229080	rs72554337	G>D	A:83	(-2.25, -15.05, -17.13)
X:38229091	rs72554338	E>K	A:87	(5.41, -5.41, -13.04)
X:38229096	rs72554339	K>N	A:88	(3.79, -1.27, -15.24)
X:38229100	rs72554340	S>G	A:90	(-3.60, -0.89, -16.93)
X:38229101	rs72554341	S>N	A:90	(-3.60, -0.89, -16.93)
X:38229102	rs72554342	S>R	A:90	(-3.60, -0.89, -16.93)
X:38229107	rs66550389	R>Q	A:92	(-6.14, 1.54, -22.19)
X:38229109	rs72554344	T>A	A:93	(-3.95, -3.84, -21.59)
X:38229113	rs72554345	R>T	A:94	(-7.18, -5.23, -16.36)
X:38229116	rs72554346	L>S	A:95	(-10.60, -3.56, -19.86)
X:38229124	rs72554347	E>K	A:98	(-10.41, -9.24, -18.08)
X:38240601	rs72554350	A>E	A:102	(-14.18, -13.74, -21.66)
X:38240610	rs72554351	G>V	A:105	(-14.73, -18.30, -22.82)
X:38240612	rs72554352	G>R	A:106	(-12.44, -17.52, -20.96)
X:38240613	rs67651903	G>E	A:106	(-12.44, -17.52, -20.96)
X:38240628	rs1800324	L>P	A:111	(-1.87, -12.20, -11.29)
X:38240646	rs66539573	H>L	A:117	(4.71, -15.82, -3.60)
X:38240670	rs72554356	T>M	A:125	(12.14, -20.11, -13.37)
X:38240673	rs72554358	D>G	A:126	(10.05, -21.64, -10.15)
X:38240682	rs66656800	R>H	A:129	(9.13, -24.70, -14.55)
X:38260533	rs72556252	L>S	A:131	(2.06, -19.82, -14.94)
X:38260535	rs72556253	S>P	A:132	(2.81, -23.73, -17.70)
X:38260536	rs72556254	S>F	A:132	(2.81, -23.73, -17.70)
X:38260545	rs72556256	A>E	A:135	(-2.31, -21.80, -17.80)
X:38260548	rs72556257	D>V	A:136	(-3.64, -22.15, -21.48)
X:38260550	rs72556258	A>T	A:137	(-1.41, -18.14, -21.32)
X:38260557	rs72556259	L>S	A:139	(-0.47, -10.73, -20.62)
X:38260559	rs72556260	A>P	A:140	(3.15, -9.60, -19.21)
X:38260563	rs68026851	R>Q	A:141	(2.00, -3.99, -18.52)
X:38260566	rs72556261	V>E	A:142	(7.06, -5.88, -17.70)
X:38260584	rs67016166	L>S	A:148	(8.97, -11.16, -21.27)
X:38260585	rs66741318	L>F	A:148	(8.97, -11.16, -21.27)
X:38260593	rs72556265	L>R	A:151	(8.28, -15.94, -18.69)
X:38260596	rs72556266	A>V	A:152	(9.47, -17.86, -22.75)
X:38260604	rs67890094	A>S	A:155	(7.33, -21.59, -20.47)
X:38260605	rs72556268	A>E	A:155	(7.33, -21.59, -20.47)
X:38260617	rs72556269	I>T	A:159	(4.61, -15.54, -23.10)
X:38260620	rs67954347	I>N	A:160	(1.61, -12.34, -24.58)
X:38260622	rs72556270	N>D	A:161	(4.47, -7.92, -24.39)
X:38260623	rs72556271	N>S	A:161	(4.47, -7.92, -24.39)
X:38260625	rs66626662	G>R	A:162	(1.86, -5.92, -22.14)
X:38260626	rs72556272	G>E	A:162	(1.86, -5.92, -22.14)
X:38260631	rs72556273	S>P	A:164	(8.07, -3.35, -22.08)
X:38260634	rs72556275	D>Y	A:165	(10.76, -0.62, -20.36)
X:38260644	rs66867430	H>P	A:168	(2.99, -2.04, -26.26)
X:38260645	rs72556276	H>Q	A:168	(2.99, -2.04, -26.26)
X:38260646	rs72556277	P>A	A:169	(3.75, -5.32, -29.39)
X:38260647	rs72556278	P>L	A:169	(3.75, -5.32, -29.39)
X:38260655	rs72556279	I>F	A:172	(1.42, -1.35, -33.06)
X:38260657	rs72556280	I>M	A:172	(1.42, -1.35, -33.06)
X:38260661	rs72556281	A>P	A:174	(-4.49, -1.48, -32.91)
X:38260665	rs68033093	D>V	A:175	(-2.23, 1.39, -33.88)
X:38260667	rs72556282	Y>H	A:176	(-0.19, -0.69, -37.87)
X:38260668	rs72556283	Y>C	A:176	(-0.19, -0.69, -37.87)
X:38260674	rs72556284	T>M	A:178	(-7.34, 1.90, -36.65)
X:38260677	rs72556286	L>P	A:179	(-4.57, 3.26, -39.78)
X:38260681	rs72556287	Q>H	A:180	(-7.38, -1.08, -42.88)
X:38262872	rs72556290	E>G	A:181	(-10.70, 0.22, -39.86)
X:38262875	rs72556291	H>L	A:182	(-9.48, 6.25, -41.91)
X:38262877	rs72556292	Y>D	A:183	(-6.21, 6.00, -44.27)
X:38262878	rs72556293	Y>C	A:183	(-6.21, 6.00, -44.27)
X:38262892	rs72556294	G>R	A:188	(2.49, 4.21, -48.17)
X:38262893	rs72556295	G>V	A:188	(2.49, 4.21, -48.17)
X:38262901	rs72556296	L>F	A:191	(3.84, 6.58, -39.86)
X:38262902	rs72556297	L>R	A:191	(3.84, 6.58, -39.86)
X:38262906	rs72556298	S>R	A:192	(4.64, 11.03, -38.17)
X:38262907	rs67284661	W>R	A:193	(6.72, 9.01, -32.40)
X:38262913	rs67294955	G>R	A:195	(8.85, 12.19, -29.24)
X:38262916	rs66642398	D>N	A:196	(10.35, 9.42, -26.14)
X:38262917	rs72556300	D>V	A:196	(10.35, 9.42, -26.14)
X:38262919	rs72556301	G>R	A:197	(12.25, 6.88, -27.50)
X:38262920	rs72556302	G>E	A:197	(12.25, 6.88, -27.50)
X:38262923	rs72558403	N>I	A:198	(9.08, 5.04, -26.55)
X:38262924	rs72558404	N>K	A:198	(9.08, 5.04, -26.55)
X:38262925	rs72558405	N>D	A:199	(7.67, 1.49, -25.66)
X:38262926	rs72558406	N>S	A:199	(7.67, 1.49, -25.66)
X:38262932	rs72558407	L>P	A:201	(9.15, 4.51, -31.83)
X:38262934	rs72558408	H>Y	A:202	(11.47, 0.87, -29.93)
X:38262935	rs72558409	H>P	A:202	(11.47, 0.87, -29.93)
X:38262938	rs72558410	S>C	A:203	(6.87, -1.31, -31.92)
X:38262943	rs72558411	M>V	A:205	(11.17, 1.18, -35.49)
X:38262945	rs796052012	M>I	A:205	(11.17, 1.18, -35.49)
X:38262947	rs72558412	M>R	A:206	(10.50, -3.69, -35.06)
X:38262948	rs72558413	M>I	A:206	(10.50, -3.69, -35.06)
X:38262950	rs72558414	S>N	A:207	(6.26, -2.86, -38.01)
X:38262951	rs72558415	S>R	A:207	(6.26, -2.86, -38.01)
X:38262952	rs72558416	A>T	A:208	(6.20, -0.31, -40.71)
X:38262956	rs72558417	A>V	A:209	(8.22, -1.75, -43.30)
X:38262958	rs72558418	K>Q	A:210	(7.39, -5.81, -41.73)
X:38262970	rs72558420	H>Y	A:214	(7.08, 5.23, -45.76)
X:38262973	rs72558421	L>F	A:215	(9.01, 6.04, -39.82)
X:38262976	rs72558423	Q>E	A:216	(8.90, 10.71, -41.18)
X:38262980	rs72558424	A>E	A:217	(11.05, 10.31, -36.26)
X:38262988	rs72558425	P>A	A:220	(14.40, 14.78, -28.14)
X:38262989	rs72558426	P>L	A:220	(14.40, 14.78, -28.14)
X:38268004	rs72558428	P>T	A:225	(15.65, 5.63, -30.73)
X:38268005	rs67120076	P>L	A:225	(15.65, 5.63, -30.73)
X:38268029	rs72558429	A>V	A:233	(14.72, -0.39, -39.04)
X:38268047	rs67283833	E>V	A:239	(14.39, -5.86, -46.28)
X:38268142	rs72558436	L>Q	A:244	(13.90, 5.43, -41.52)
X:38268151	rs72558437	T>K	A:247	(14.61, 14.02, -36.61)
X:38268168	rs67330615	A>T	A:253	(8.48, 14.38, -39.01)
X:38268175	rs72558440	H>P	A:255	(6.84, 17.30, -44.75)
X:38268190	rs72558441	L>S	A:260	(0.34, 12.97, -36.69)
X:38268196	rs67333670	T>K	A:262	(2.31, 11.15, -29.56)
X:38268198	rs72558442	D>N	A:263	(3.31, 8.82, -25.84)
X:38268199	rs72558443	D>G	A:263	(3.31, 8.82, -25.84)
X:38268201	rs72558444	T>A	A:264	(4.10, 10.17, -22.52)
X:38268202	rs67156896	T>N	A:264	(4.10, 10.17, -22.52)
X:38268204	rs72558445	W>R	A:265	(6.76, 14.95, -23.35)
X:38268205	rs72558446	W>L	A:265	(6.76, 14.95, -23.35)
X:38268210	rs72558448	S>R	A:267	(7.14, 6.68, -19.34)
X:38268214	rs72558449	M>T	A:268	(4.94, 3.67, -16.77)
X:38268217	rs72558450	G>E	A:269	(9.55, 4.67, -14.54)
X:38268220	rs1800328	Q>P	A:270	(12.06, 6.85, -17.36)
X:38268240	rs72558454	R>W	A:277	(12.02, 13.33, -19.94)
X:38268241	rs66724222	R>Q	A:277	(12.02, 13.33, -19.94)
X:38268278	rs72558456	K>N	A:289	(1.03, 25.27, -36.18)
X:38271140	rs72558461	W>S	A:298	(-4.43, 15.45, -40.11)
X:38271150	rs72558462	L>F	A:301	(-2.53, 7.67, -33.51)
X:38271151	rs72558463	H>Y	A:302	(-1.80, 8.91, -27.60)
X:38271152	rs67993095	H>L	A:302	(-1.80, 8.91, -27.60)
X:38271153	rs67870244	H>Q	A:302	(-1.80, 8.91, -27.60)
X:38271154	rs67468335	C>R	A:303	(-1.43, 4.91, -26.76)
X:38271155	rs72558464	C>Y	A:303	(-1.43, 4.91, -26.76)
X:38271159	rs72558465	L>F	A:304	(-3.96, 6.50, -24.55)
X:38271161	rs67501347	P>H	A:305	(-2.17, 7.32, -20.98)
X:38271166	rs796052013	K>E	A:307	(-0.42, 13.10, -20.29)
X:38271176	rs72558467	E>G	A:310	(1.79, 14.79, -25.20)
X:38271178	rs72558468	V>M	A:311	(-1.32, 16.63, -27.51)
X:38271190	rs72558470	V>F	A:315	(-5.14, 17.48, -32.23)
X:38271191	rs67414444	V>D	A:315	(-5.14, 17.48, -32.23)
X:38271194	rs72558471	F>S	A:316	(-6.85, 13.88, -27.93)
X:38271200	rs72558472	S>F	A:318	(-9.89, 16.11, -34.05)
X:38271206	rs72558474	R>L	A:320	(-8.39, 14.76, -39.53)
X:38271223	rs72558476	E>K	A:326	(-6.08, 3.65, -31.18)
X:38271235	rs72558478	R>G	A:330	(-5.30, -2.63, -27.23)
X:38271241	rs72558480	W>R	A:332	(-12.52, -6.54, -31.17)
X:38271252	rs281865553	M>I	A:335	(-9.80, -11.22, -29.06)
X:38280276	rs72558486	A>S	A:336	(-6.41, -12.40, -32.23)
X:38280279	rs72558487	V>L	A:337	(-3.11, -12.66, -30.17)
X:38280285	rs72558488	V>L	A:339	(-7.26, -17.13, -31.30)
X:38280288	rs72558489	S>P	A:340	(-3.31, -17.21, -32.97)
X:38280292	rs72558490	L>P	A:341	(-0.86, -17.86, -29.92)
X:38280298	rs72558491	T>K	A:343	(-6.53, -21.82, -31.73)
X:38280303	rs66469337	Y>H	A:345	(-10.78, -19.29, -36.18)
X:38280304	rs72558492	Y>C	A:345	(-10.78, -19.29, -36.18)
X:38280309	rs72558493	P>T	A:347	(-10.10, -16.58, -40.75)
X:38280331	rs72558495	F>C	A:354	(-3.29, -4.95, -45.48)

1C9Y.A | OTC.

1C9Y.A | OTC

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
X:38226603	COSM3759494	K>R	A:46	(12.26, -8.60, -33.67)
X:38229107	COSM276565	R>Q	A:92	(-6.14, 1.54, -22.19)
X:38240676	COSM3379624	T>M	A:127	(6.50, -18.40, -11.58)
X:38260563	COSM1467886	R>Q	A:141	(2.00, -3.99, -18.52)
X:38260574	COSM246308	Q>K	A:145	(11.72, -7.63, -22.98)
X:38268198	COSM1625876	D>Y	A:263	(3.31, 8.82, -25.84)
X:38268220	COSM32797	Q>R	A:270	(12.06, 6.85, -17.36)