3BG3.A | PC – ASTRID

3BG3.A | PC

General Structure Information

PDB ID	3bg3
HGNC Gene Label(s)	PC
Structure Name	crystal structure of human pyruvate carboxylase (missing the biotin carboxylase domain at the n-terminus)
Resolution	2.8Å
Reference	AUTH S.XIANG,L.TONGTITL CRYSTAL STRUCTURES OF HUMAN AND STAPHYLOCOCCUSTITL 2 AUREUS PYRUVATE CARBOXYLASE AND MOLECULAR INSIGHTSTITL 3 INTO THE CARBOXYLTRANSFER REACTION.REF NAT.STRUCT.MOL.BIOL. V. 15 295 2008REFN ISSN 1545-9993PMID 18297087DOI 10.1038/NSMB.1393

Variant Set Distributions

ExAC Variants

Number Of Residues	679
Number Of SNVs	182
Number Of Permutations	69113
Optimal Distance Threshold	16.0
K Statistic	0.087
p-value	0.172

ClinVar

Number Of Residues	679
Number Of SNVs	10
Number Of Permutations	4622
Optimal Distance Threshold	18.0
K Statistic	0.6
p-value	0.0

COSMIC

Number Of Residues	679
Number Of SNVs	11
Number Of Permutations	9575
Optimal Distance Threshold	13.0
K Statistic	0.018
p-value	0.627

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	182
Number Of ClinVar SNVs	10
Optimal Distance Threshold	18.0
K Statistic	0.485
p-value	0.0

Cosmic vs. ExAC

Number Of ExAC SNVs	182
Number Of COSMIC SNVs	8
Optimal Distance Threshold	15.0
K Statistic	-0.075
p-value	0.614

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:66620719		H>Y	A:502	(-6.04, -48.18, -38.48)
11:66620302	rs555210692	V>I	A:507	(-2.02, -57.75, -38.95)
11:66620297		M>I	A:508	(1.88, -55.38, -38.05)
11:66620298		M>K	A:508	(1.88, -55.38, -38.05)
11:66620286	rs199667095	P>Q	A:512	(-2.76, -63.72, -38.31)
11:66620277		P>L	A:515	(-8.95, -67.95, -38.55)
11:66620269	rs569110648	V>I	A:518	(-1.28, -74.18, -40.25)
11:66620257		P>S	A:522	(2.97, -66.92, -46.63)
11:66620247	rs146840773	T>M	A:525	(7.28, -66.40, -53.98)
11:66620242		P>A	A:527	(2.31, -66.04, -58.50)
11:66620239	rs200433873	V>I	A:528	(4.05, -67.35, -62.77)
11:66620232	rs370248734	P>L	A:530	(1.05, -66.65, -68.03)
11:66620128		P>L	A:536	(-10.13, -60.40, -78.48)
11:66620122	rs151174961	P>L	A:538	(-11.00, -67.29, -78.20)
11:66620095	rs142036463	R>Q	A:547	(-25.56, -66.53, -81.31)
11:66620093		E>Q	A:548	(-28.35, -70.99, -79.84)
11:66620083		E>A	A:551	(-33.28, -75.84, -75.48)
11:66620084		E>K	A:551	(-33.28, -75.84, -75.48)
11:66620080	rs45555439	G>D	A:552	(-28.77, -75.21, -77.71)
11:66620071	rs148613404	R>Q	A:555	(-29.15, -78.42, -79.51)
11:66620062		R>Q	A:558	(-24.54, -85.33, -77.10)
11:66620059		N>S	A:559	(-23.55, -82.72, -81.20)
11:66620053	rs369291198 COSM930978	P>L	A:561	(-17.42, -85.30, -80.66)
11:66620051	COSM1356333	G>R	A:562	(-15.52, -85.20, -77.59)
11:66620033	rs199969388	T>A	A:568	(-12.98, -77.24, -60.41)
11:66620015		H>Y	A:574	(-10.72, -73.34, -53.27)
11:66619999		A>V	A:579	(-10.71, -73.80, -46.75)
11:66620000		A>T	A:579	(-10.71, -73.80, -46.75)
11:66619993		R>H	A:581	(-10.02, -69.63, -46.54)
11:66619987	rs119103242 COSM194466 CM092838	R>H	A:583	(-8.04, -63.00, -51.78)
11:66619988		R>C	A:583	(-8.04, -63.00, -51.78)
11:66619979	rs371922891 COSM930977	D>N	A:586	(-5.31, -64.80, -56.18)
11:66619976		L>F	A:587	(-9.29, -66.06, -58.82)
11:66619972		K>R	A:588	(-8.90, -60.80, -60.75)
11:66619968	rs143725101	K>N	A:589	(-3.46, -62.12, -61.49)
11:66619964	rs139795235	A>T	A:591	(-8.56, -64.71, -65.95)
11:66619918	rs372105187	N>T	A:606	(-16.85, -69.55, -60.54)
11:66619415	rs28940589	A>T	A:610	(-18.46, -72.33, -49.58)
11:66619411		T>M	A:611	(-17.66, -69.52, -52.06)
11:66619405	rs147396184	D>V	A:613	(-19.99, -68.31, -46.32)
11:66619403		V>I	A:614	(-15.78, -68.16, -47.05)
11:66619396	rs577138625	M>T	A:616	(-18.96, -62.70, -46.45)
11:66619394		R>C	A:617	(-18.10, -66.64, -42.04)
11:66619376	COSM3452218	P>S	A:623	(-19.70, -62.80, -53.27)
11:66619369	rs199568784	R>Q	A:625	(-17.11, -56.60, -55.93)
11:66619370		R>W	A:625	(-17.11, -56.60, -55.93)
11:66619366		R>Q	A:626	(-15.24, -63.79, -56.41)
11:66619339		P>L	A:635	(-15.85, -63.03, -72.10)
11:66619340		P>S	A:635	(-15.85, -63.03, -72.10)
11:66619323		Q>H	A:640	(-20.95, -74.24, -63.33)
11:66619312		R>P	A:644	(-25.89, -75.88, -51.11)
11:66619310		G>R	A:645	(-31.42, -76.17, -53.67)
11:66619303		N>S	A:647	(-30.32, -75.80, -48.97)
11:66619301		A>S	A:648	(-29.28, -72.56, -51.76)
11:66619288		T>S	A:652	(-31.34, -74.81, -44.16)
11:66619271	COSM930972	V>M	A:658	(-35.35, -66.24, -51.47)
11:66619263		F>L	A:660	(-37.62, -68.78, -57.48)
11:66618737		A>V	A:666	(-27.02, -64.53, -60.57)
11:66618734	rs138760063	K>T	A:667	(-28.38, -64.94, -65.32)
11:66618710	rs375528540	R>H	A:675	(-23.68, -78.70, -60.66)
11:66618711		R>C	A:675	(-23.68, -78.70, -60.66)
11:66618665		M>T	A:690	(-34.65, -77.45, -61.69)
11:66618659		A>V	A:692	(-35.13, -71.12, -60.03)
11:66618650		S>T	A:695	(-37.23, -68.71, -64.28)
11:66618651		S>G	A:695	(-37.23, -68.71, -64.28)
11:66618645		G>R	A:697	(-32.27, -68.66, -67.84)
11:66618639		V>M	A:699	(-27.99, -73.91, -68.02)
11:66618624	COSM544731	I>V	A:704	(-28.12, -87.54, -59.27)
11:66618615		T>A	A:707	(-23.94, -93.49, -52.41)
11:66618606		V>M	A:710	(-24.10, -99.56, -59.13)
11:66618600	rs185412729	D>N	A:712	(-22.36, -104.50, -55.31)
11:66618597		P>A	A:713	(-24.98, -106.79, -56.81)
11:66618590	COSM690394	R>H	A:715	(-24.22, -101.91, -51.63)
11:66618587		T>I	A:716	(-30.45, -103.13, -52.65)
11:66618585		K>Q	A:717	(-30.98, -98.19, -50.21)
11:66618564		M>V	A:724	(-32.16, -94.94, -64.26)
11:66618557		L>S	A:726	(-33.93, -89.95, -59.67)
11:66618552	rs193271416	E>K	A:728	(-36.40, -91.65, -66.01)
11:66618547		E>D	A:729	(-38.83, -88.33, -62.35)
11:66618539		R>Q	A:732	(-41.37, -86.66, -66.65)
11:66618531		T>A	A:735	(-32.75, -81.22, -67.52)
11:66618369	rs145400751	T>M	A:750	(-17.16, -101.12, -63.51)
11:66618360		T>I	A:753	(-19.30, -98.65, -67.75)
11:66618356		M>I	A:754	(-23.16, -100.35, -65.06)
11:66618352		V>F	A:756	(-22.83, -93.78, -68.46)
11:66618343		L>F	A:759	(-27.88, -92.77, -68.25)
11:66618339	rs543756586 COSM4035881	R>Q	A:760	(-26.10, -91.95, -73.66)
11:66618340	rs563526275 COSM2041157	R>W	A:760	(-26.10, -91.95, -73.66)
11:66618333	rs574858955	R>H	A:762	(-34.98, -94.63, -71.21)
11:66618334	COSM2041156	R>C	A:762	(-34.98, -94.63, -71.21)
11:66618325		D>N	A:765	(-30.00, -87.03, -77.60)
11:66618296		D>E	A:774	(-8.90, -88.55, -56.58)
11:66618280	rs572440768 COSM3703637	V>M	A:780	(-8.37, -90.59, -63.82)
11:66618271		M>L	A:783	(-13.94, -89.74, -65.33)
11:66618258		A>V	A:787	(-15.67, -91.38, -71.74)
11:66618255		Q>L	A:788	(-14.81, -95.26, -73.53)
11:66618247		A>T	A:791	(-19.48, -88.79, -71.54)
11:66618241		V>L	A:793	(-18.79, -83.18, -69.35)
11:66618238	rs148086243	V>L	A:794	(-15.28, -84.54, -67.16)
11:66618168		T>I	A:817	(-7.75, -88.14, -74.30)
11:66618165		R>T	A:818	(-3.31, -86.35, -76.78)
11:66618151		D>Y	A:823	(-8.92, -85.53, -77.92)
11:66617927		M>V	A:828	(-0.28, -80.61, -72.44)
11:66617924		E>K	A:829	(2.33, -76.65, -73.86)
11:66617920		R>H	A:830	(-2.79, -73.72, -73.85)
11:66617921	rs141730205	R>C	A:830	(-2.79, -73.72, -73.85)
11:66617917		V>A	A:831	(-2.20, -77.67, -68.68)
11:66617918	COSM930970	V>M	A:831	(-2.20, -77.67, -68.68)
11:66617884	COSM26593	R>Q	A:842	(-1.66, -75.09, -52.97)
11:66617885	COSM1676217	R>W	A:842	(-1.66, -75.09, -52.97)
11:66617873		A>T	A:846	(-0.03, -72.49, -46.17)
11:66617861		C>G	A:850	(-4.55, -80.13, -46.30)
11:66617858		T>A	A:851	(-0.78, -81.07, -47.26)
11:66617820		E>D	A:863	(-15.56, -98.37, -44.37)
11:66617804		G>S	A:869	(-14.35, -81.90, -47.63)
11:66617798		Y>H	A:871	(-11.65, -87.65, -45.28)
11:66617785		H>R	A:875	(-7.40, -85.56, -41.34)
11:66617773		H>R	A:879	(-3.88, -85.25, -37.24)
11:66617761		L>P	A:883	(-2.39, -85.24, -31.67)
11:66617755		S>C	A:885	(-5.95, -91.73, -33.51)
11:66617734		K>T	A:892	(-14.94, -95.96, -37.23)
11:66617735		K>E	A:892	(-14.94, -95.96, -37.23)
11:66617731		A>V	A:893	(-19.04, -92.92, -35.75)
11:66617728		Y>F	A:894	(-19.52, -90.37, -40.92)
11:66617726		V>M	A:895	(-20.04, -95.78, -40.22)
11:66617723		E>K	A:896	(-21.69, -96.28, -35.95)
11:66617716		N>S	A:898	(-25.03, -93.48, -42.21)
11:66617712		Q>H	A:899	(-26.26, -97.72, -40.63)
11:66617702	COSM3452216	D>N	A:903	(-28.08, -95.86, -45.35)
11:66617575		S>P	A:911	(-22.79, -84.59, -44.38)
11:66617566		V>M	A:914	(-23.54, -87.88, -40.21)
11:66617560		D>H	A:916	(-22.82, -83.09, -36.24)
11:66617527		S>G	A:927	(-22.39, -96.76, -28.59)
11:66617524		R>W	A:928	(-25.86, -98.15, -33.85)
11:66617520	rs565678903	A>G	A:929	(-26.71, -99.24, -29.27)
11:66617512	COSM1219409	E>K	A:932	(-30.23, -96.42, -30.80)
11:66617502	rs139540331	A>V	A:935	(-32.57, -91.07, -27.34)
11:66617487		F>C	A:940	(-29.21, -86.18, -29.76)
11:66617481	rs370436212 COSM1356329	R>H	A:942	(-30.16, -76.66, -34.18)
11:66617476	COSM1356328	V>M	A:944	(-29.87, -84.17, -35.61)
11:66617449	COSM930967	G>R	A:953	(-36.46, -83.79, -45.50)
11:66617440		H>D	A:956	(-35.01, -93.69, -50.63)
11:66617436		G>E	A:957	(-37.17, -94.63, -47.49)
11:66617416	rs192822072	R>C	A:964	(-38.79, -89.40, -36.73)
11:66617245		V>A	A:995	(-31.21, -48.29, -45.57)
11:66617240	rs565301304	R>W	A:997	(-29.04, -52.73, -40.09)
11:66617221	rs145046106	T>M	A:1003	(-26.80, -53.31, -53.59)
11:66617218	rs531674975	P>L	A:1004	(-29.78, -55.50, -54.82)
11:66617193		M>I	A:1012	(-28.80, -66.37, -47.60)
11:66617194	rs373157029	M>T	A:1012	(-28.80, -66.37, -47.60)
11:66617186		D>N	A:1015	(-24.68, -62.21, -38.03)
11:66617178	rs542809148	F>L	A:1017	(-24.19, -58.53, -44.71)
11:66617173		H>R	A:1019	(-20.01, -59.51, -37.83)
11:66617165		D>N	A:1022	(-19.43, -53.83, -39.33)
11:66617162	rs200315043	F>L	A:1023	(-13.55, -55.79, -41.64)
11:66617159		T>P	A:1024	(-15.84, -53.08, -44.72)
11:66617122	rs141237842	R>H	A:1036	(2.54, -61.93, -49.35)
11:66617119	rs140320331	L>H	A:1037	(-0.02, -57.60, -47.69)
11:66617105		P>S	A:1042	(3.53, -55.57, -43.63)
11:66617096		A>T	A:1045	(11.50, -52.05, -44.42)
11:66617092		E>G	A:1046	(8.42, -54.62, -47.40)
11:66617089		E>V	A:1047	(8.71, -50.02, -50.63)
11:66616828		R>Q	A:1054	(-12.45, -46.58, -59.73)
11:66616819	rs148661980	T>M	A:1057	(-0.50, -45.48, -56.76)
11:66616814		H>N	A:1059	(4.41, -45.83, -53.46)
11:66616796		V>M	A:1065	(6.07, -51.49, -33.79)
11:66616790	rs527559823	D>N	A:1067	(6.71, -49.76, -26.77)
11:66616781	rs372116771	R>W	A:1070	(0.51, -46.54, -19.30)
11:66616775	COSM3739246	G>S	A:1072	(-2.81, -51.23, -24.92)
11:66616751		L>V	A:1080	(2.42, -43.11, -47.07)
11:66616747		N>S	A:1081	(3.63, -41.28, -50.58)
11:66616740	rs374682909	Q>H	A:1083	(4.38, -37.90, -45.83)
11:66616718		D>Y	A:1091	(-2.17, -55.69, -28.28)
11:66616579		G>S	A:1110	(-17.27, -47.10, 7.90)
11:66616570		G>R	A:1113	(-8.66, -50.53, 7.21)
11:66616561		M>V	A:1116	(0.68, -51.41, 8.73)
11:66616557		P>L	A:1117	(1.53, -53.83, 5.82)
11:66616542		D>G	A:1122	(-5.06, -63.83, 15.41)
11:66616543	COSM3452213	D>H	A:1122	(-5.06, -63.83, 15.41)
11:66616536		K>T	A:1124	(-9.95, -61.71, 17.61)
11:66616537		K>Q	A:1124	(-9.95, -61.71, 17.61)
11:66616531	rs182440197	V>M	A:1126	(-17.49, -64.65, 15.02)
11:66616527	rs200217380	A>V	A:1127	(-18.50, -64.27, 11.13)
11:66616528		A>P	A:1127	(-18.50, -64.27, 11.13)
11:66616524	rs138990904	G>A	A:1128	(-20.97, -61.83, 12.33)
11:66616521	rs141118314	A>V	A:1129	(-20.53, -60.32, 15.36)
11:66616519		K>E	A:1130	(-22.35, -57.10, 18.50)
11:66616516	rs116518022	V>M	A:1131	(-18.49, -54.85, 18.16)
11:66616498		L>V	A:1137	(-11.27, -56.87, 15.39)
11:66616491		V>A	A:1139	(-3.57, -59.97, 15.19)
11:66616479		M>T	A:1143	(9.60, -58.08, 10.42)
11:66616472	rs201796252 COSM2041137	M>I	A:1145	(5.48, -53.86, 13.12)
11:66616450	rs199640363	M>V	A:1153	(-18.19, -48.40, 14.56)
11:66616438		V>L	A:1157	(-20.17, -57.41, 11.75)
11:66616434	rs149054698	R>H	A:1158	(-22.68, -57.30, 6.72)
11:66616432		K>E	A:1159	(-18.41, -61.61, 4.80)
11:66616414	COSM3676279	D>Y	A:1165	(-1.89, -67.42, 6.58)
11:66616410	rs147594996	M>T	A:1166	(-1.38, -64.90, 2.06)
11:66616391		D>E	A:1172	(-6.35, -54.43, 2.17)
11:66616393	rs568925019	D>N	A:1172	(-6.35, -54.43, 2.17)
11:66616373		E>D	A:1178	(-24.10, -51.94, 10.54)
11:66616375	rs141139690	E>K	A:1178	(-24.10, -51.94, 10.54)

3BG3.A | PC.

3BG3.A | PC

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:66620030	rs113994144	T>A	A:569	(-9.41, -74.60, -59.83)
11:66620018	rs796052029	A>T	A:573	(-10.49, -77.33, -55.40)
11:66619987	rs119103242	R>L	A:583	(-8.04, -63.00, -51.78)
11:66619415	rs28940589	A>T	A:610	(-18.46, -72.33, -49.58)
11:66619351	rs113994145	R>Q	A:631	(-18.50, -62.95, -67.01)
11:66618710	rs375528540	R>H	A:675	(-23.68, -78.70, -60.66)
11:66618389	rs28940590	M>I	A:743	(-19.85, -86.55, -52.98)
11:66617884	rs774897991	R>Q	A:842	(-1.66, -75.09, -52.97)
11:66617869	rs113994147	A>V	A:847	(-2.28, -71.67, -43.46)
11:66617583	rs796052032	T>M	A:908	(-24.04, -80.34, -47.98)