1KHB.A | PCK1 – ASTRID

1KHB.A | PCK1

General Structure Information

PDB ID	1khb
HGNC Gene Label(s)	PCK1
Structure Name	pepck complex with nonhydrolyzable gtp analog, native data
Resolution	1.85Å
Reference	AUTH P.DUNTEN,C.BELUNIS,R.CROWTHER,K.HOLLFELDER,AUTH 2 U.KAMMLOTT,W.LEVIN,H.MICHEL,G.B.RAMSEY,A.SWAIN,AUTH 3 D.WEBER,S.J.WERTHEIMERTITL CRYSTAL STRUCTURE OF HUMAN CYTOSOLICTITL 2 PHOSPHOENOLPYRUVATE CARBOXYKINASE REVEALS A NEWTITL 3 GTP-BINDING SITE.REF J.MOL.BIOL. V. 316 257 2002REFN ISSN 0022-2836PMID 11851336DOI 10.1006/JMBI.2001.5364

Variant Set Distributions

ExAC Variants

Number Of Residues	603
Number Of SNVs	199
Number Of Permutations	74589
Optimal Distance Threshold	6.0
K Statistic	0.009
p-value	0.672

COSMIC

Number Of Residues	603
Number Of SNVs	15
Number Of Permutations	11869
Optimal Distance Threshold	8.0
K Statistic	0.038
p-value	0.984

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	199
Number Of COSMIC SNVs	14
Optimal Distance Threshold	29.0
K Statistic	0.178
p-value	0.144

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:56136498	rs146652385	L>F	A:11	(44.96, -5.96, 49.44)
20:56136499		L>H	A:11	(44.96, -5.96, 49.44)
20:56136501		S>P	A:12	(41.83, -7.51, 52.10)
20:56136502	rs548898026 COSM4099731	S>L	A:12	(41.83, -7.51, 52.10)
20:56136510	rs61749691	V>F	A:15	(40.33, -2.48, 52.92)
20:56136531	rs140235265	S>G	A:22	(32.85, -4.34, 44.63)
20:56136535		L>P	A:23	(35.95, -3.43, 42.57)
20:56136538		P>L	A:24	(35.08, -3.76, 38.62)
20:56136559		L>R	A:31	(43.96, -1.28, 43.40)
20:56136561		E>K	A:32	(45.46, -5.69, 42.93)
20:56136562	rs557851089	E>G	A:32	(45.46, -5.69, 42.93)
20:56136566		N>K	A:33	(48.96, -3.77, 39.95)
20:56136570		A>S	A:35	(49.37, -1.14, 45.87)
20:56136573		E>K	A:36	(51.76, -4.62, 45.40)
20:56136588	rs148380007	D>N	A:41	(49.72, 1.72, 55.32)
20:56136591		H>N	A:42	(45.46, 1.49, 55.38)
20:56136594		I>V	A:43	(43.07, 0.77, 50.51)
20:56136598	rs144360449	H>R	A:44	(38.85, 4.95, 51.22)
20:56136601	rs202197769	I>T	A:45	(36.97, 1.96, 48.09)
20:56136604		C>S	A:46	(35.59, 6.23, 47.29)
20:56136609	rs542465770	G>S	A:48	(30.54, 9.88, 47.54)
20:56136630	rs373529977 COSM1028388	R>W	A:55	(33.73, 10.01, 57.08)
20:56136631	rs28383585	R>Q	A:55	(33.73, 10.01, 57.08)
20:56136646	rs28383586	M>T	A:60	(41.36, 17.16, 55.98)
20:56136653		E>D	A:62	(41.91, 16.89, 63.53)
20:56136658		G>A	A:64	(45.84, 20.85, 58.96)
20:56136660	rs200152114	I>V	A:65	(44.92, 19.49, 55.57)
20:56136669	rs369101907 COSM3799694	R>W	A:68	(34.56, 24.93, 59.36)
20:56136670	rs147273759	R>Q	A:68	(34.56, 24.93, 59.36)
20:56136680		K>N	A:71	(31.40, 34.41, 57.39)
20:56136691	COSM1681789	C>Y	A:75	(33.27, 26.44, 53.88)
20:56137150	rs376452415	R>T	A:83	(57.99, 24.27, 47.47)
20:56137151		R>S	A:83	(57.99, 24.27, 47.47)
20:56137167	rs267606015 COSM3911653	E>K	A:89	(53.82, 24.44, 31.43)
20:56137179		V>I	A:93	(55.02, 15.07, 29.94)
20:56137185	rs536299130 COSM4099732	V>I	A:95	(54.63, 9.50, 26.68)
20:56137189		T>I	A:96	(54.70, 9.16, 22.44)
20:56137212		P>S	A:104	(55.52, 19.86, 16.38)
20:56137221		K>E	A:107	(61.89, 25.43, 11.17)
20:56137227		G>S	A:109	(64.23, 25.60, 18.87)
20:56137242		G>S	A:114	(54.99, 20.96, 24.34)
20:56137246	rs184086519	R>H	A:115	(58.45, 18.04, 27.74)
20:56137253		M>I	A:117	(59.18, 11.99, 28.17)
20:56137258		E>V	A:119	(58.26, 4.71, 25.69)
20:56137275	rs373113903	A>T	A:125	(60.99, 8.43, 36.16)
20:56137276		A>V	A:125	(60.99, 8.43, 36.16)
20:56137281		N>D	A:127	(61.11, 3.24, 38.23)
20:56137303		M>T	A:134	(51.44, 5.72, 48.92)
20:56137754	rs141813623	R>C	A:137	(50.58, 8.79, 53.24)
20:56137755	rs150560473	R>H	A:137	(50.58, 8.79, 53.24)
20:56137758	rs28359542	T>I	A:138	(45.48, 6.09, 52.70)
20:56137761		M>T	A:139	(45.53, 4.12, 47.92)
20:56137762		M>I	A:139	(45.53, 4.12, 47.92)
20:56137766		V>I	A:141	(39.72, 4.40, 45.06)
20:56137788		P>L	A:148	(26.71, 13.37, 32.39)
20:56137796		S>T	A:151	(26.37, 10.68, 28.27)
20:56137797		S>L	A:151	(26.37, 10.68, 28.27)
20:56137806		S>L	A:154	(30.55, 10.29, 29.20)
20:56137808		K>E	A:155	(34.56, 9.32, 28.54)
20:56137809		K>R	A:155	(34.56, 9.32, 28.54)
20:56137811	rs149873355	I>F	A:156	(34.61, 6.55, 33.48)
20:56137812	rs145580276	I>N	A:156	(34.61, 6.55, 33.48)
20:56137814	COSM1028390	G>S	A:157	(37.70, 7.04, 35.92)
20:56137817		I>V	A:158	(39.75, 4.98, 38.41)
20:56137841	rs368269624 COSM2153160 COSM3405225	V>M	A:166	(42.37, 15.03, 45.62)
20:56137842		V>E	A:166	(42.37, 15.03, 45.62)
20:56137844		V>M	A:167	(38.98, 12.99, 47.44)
20:56137857	rs375564832	R>Q	A:171	(31.78, 15.04, 46.47)
20:56137866	rs199822253 COSM253800 COSM3933887	T>M	A:174	(33.86, 14.99, 39.35)
20:56137868		R>W	A:175	(29.58, 14.08, 37.58)
20:56137878		T>M	A:178	(29.30, 3.86, 44.17)
20:56137880	rs373884006 COSM355156	P>T	A:179	(27.34, 5.76, 41.47)
20:56137883	rs367998997 COSM3799695 COSM3799696	V>I	A:180	(30.70, 5.88, 38.64)
20:56137895	rs707555	V>L	A:184	(32.34, 1.35, 34.59)
20:56137898	rs371728787	G>S	A:185	(31.53, -1.80, 34.98)
20:56137901	rs11552146	D>N	A:186	(33.15, -4.76, 32.94)
20:56137902		D>G	A:186	(33.15, -4.76, 32.94)
20:56137916		K>Q	A:191	(44.71, 3.33, 33.97)
20:56137927	rs141485103	H>Q	A:194	(48.36, 11.73, 42.84)
20:56137931	rs374694652	V>M	A:196	(52.09, 13.75, 47.33)
20:56137938		C>Y	A:198	(55.76, 12.42, 50.78)
20:56137940		P>S	A:199	(56.96, 8.89, 51.80)
20:56138097		N>K	A:208	(51.18, 24.78, 55.77)
20:56138098		N>Y	A:209	(50.25, 20.06, 57.46)
20:56138104		P>T	A:211	(52.11, 17.13, 51.21)
20:56138113		P>S	A:214	(58.92, 20.06, 44.46)
20:56138114		P>L	A:214	(58.92, 20.06, 44.46)
20:56138123	rs377150721 COSM444094	T>M	A:217	(57.10, 17.35, 40.10)
20:56138131		A>T	A:220	(52.22, 12.14, 32.85)
20:56138138		L>R	A:222	(50.83, 7.38, 29.00)
20:56138146		R>C	A:225	(50.55, 2.88, 28.34)
20:56138147	rs369153854	R>H	A:225	(50.55, 2.88, 28.34)
20:56138152	COSM262831	E>K	A:227	(48.20, 5.12, 31.77)
20:56138171		S>N	A:233	(51.57, 18.05, 43.15)
20:56138197	rs373906233	G>R	A:242	(40.13, 14.97, 34.85)
20:56138218		R>W	A:249	(46.71, 17.56, 28.56)
20:56138223		M>I	A:250	(44.11, 11.95, 27.14)
20:56138227		S>G	A:252	(42.47, 16.05, 22.55)
20:56138230	rs201972484	R>W	A:253	(45.96, 11.62, 21.03)
20:56138231		R>Q	A:253	(45.96, 11.62, 21.03)
20:56138248		G>R	A:259	(35.22, 13.18, 15.80)
20:56138266	rs200745451	M>V	A:265	(35.98, 26.31, 25.06)
20:56138267	rs141761035	M>T	A:265	(35.98, 26.31, 25.06)
20:56138268		M>I	A:265	(35.98, 26.31, 25.06)
20:56138621	rs8192708	I>V	A:267	(29.54, 26.90, 27.45)
20:56138625		L>R	A:268	(27.21, 31.02, 27.25)
20:56138630		I>V	A:270	(22.59, 34.50, 25.22)
20:56138637	rs558731216	N>S	A:272	(16.67, 37.78, 23.09)
20:56138638		N>K	A:272	(16.67, 37.78, 23.09)
20:56138648	rs11552145	E>K	A:276	(16.47, 34.08, 20.08)
20:56138660		L>V	A:280	(27.99, 31.21, 22.75)
20:56138664	rs200991428 COSM1261522 COSM4099733	A>V	A:281	(31.95, 29.11, 22.90)
20:56138667	COSM578042	A>V	A:282	(34.96, 30.53, 24.87)
20:56138669	rs574265290	A>T	A:283	(38.75, 30.50, 24.21)
20:56138670		A>V	A:283	(38.75, 30.50, 24.21)
20:56138687	COSM578040 COSM3548146 COSM3548147	G>R	A:289	(37.62, 35.64, 31.70)
20:56138703		A>D	A:294	(30.14, 32.21, 32.01)
20:56138707	rs545773547	M>I	A:295	(29.10, 33.09, 35.79)
20:56138709	rs147749756	M>R	A:296	(27.61, 37.69, 32.17)
20:56138720	rs61760967	L>F	A:300	(21.83, 44.78, 28.02)
20:56138732		K>E	A:304	(18.84, 35.02, 30.82)
20:56138735		V>F	A:305	(23.57, 34.80, 30.82)
20:56138738	rs201677393	E>K	A:306	(21.69, 30.66, 31.39)
20:56138741		C>R	A:307	(26.41, 28.52, 33.00)
20:56138744	rs45603039	V>I	A:308	(27.00, 25.19, 30.58)
20:56138747	rs201186470 COSM1261521	G>R	A:309	(30.57, 26.30, 31.55)
20:56138759		A>S	A:313	(34.44, 21.63, 26.06)
20:56138765		M>V	A:315	(32.59, 20.21, 20.98)
20:56138777	COSM4099736 COSM4099737	A>T	A:319	(22.67, 14.28, 12.79)
20:56138783		G>C	A:321	(25.33, 19.40, 12.18)
20:56139260	COSM724064	F>L	A:333	(39.70, 25.01, 40.33)
20:56139263		G>S	A:334	(38.48, 29.37, 40.59)
20:56139269	rs574426927 COSM2764408 COSM3405227	A>T	A:336	(39.69, 34.26, 43.63)
20:56139272	rs148953365	P>S	A:337	(41.78, 36.55, 43.02)
20:56139279		T>I	A:339	(35.99, 37.54, 42.73)
20:56139294	rs533717610	N>S	A:344	(31.34, 37.28, 39.21)
20:56139295	rs553589410	N>K	A:344	(31.34, 37.28, 39.21)
20:56139299		N>D	A:346	(26.42, 35.01, 39.67)
20:56139302		A>T	A:347	(30.42, 33.65, 41.88)
20:56139305		I>F	A:348	(30.19, 35.81, 45.25)
20:56139310	rs576636213	K>N	A:349	(25.27, 34.67, 44.62)
20:56139326	rs143715557	T>A	A:355	(33.28, 25.95, 48.94)
20:56139329		I>V	A:356	(37.20, 23.72, 49.02)
20:56139335	rs545533074	T>A	A:358	(43.19, 26.97, 47.92)
20:56139356	COSM1713716	D>N	A:365	(34.97, 36.60, 60.66)
20:56139359	rs148075029	G>R	A:366	(35.89, 33.24, 58.98)
20:56139360		G>V	A:366	(35.89, 33.24, 58.98)
20:56139362		G>C	A:367	(36.48, 34.48, 56.23)
20:56139363		G>D	A:367	(36.48, 34.48, 56.23)
20:56139365	rs1804160	V>I	A:368	(37.23, 34.62, 52.60)
20:56139369		Y>C	A:369	(39.59, 39.71, 52.06)
20:56139390	rs144845374	P>L	A:376	(34.63, 46.70, 53.16)
20:56139402	rs376361752	G>D	A:380	(38.18, 44.47, 64.08)
20:56139404	COSM1028402	V>I	A:381	(38.00, 42.45, 61.13)
20:56139410	rs369625007	I>F	A:383	(43.61, 40.02, 57.17)
20:56139419		W>R	A:386	(49.55, 32.55, 50.65)
20:56139431		E>K	A:390	(48.38, 39.66, 60.85)
20:56139434		W>R	A:391	(47.62, 41.69, 54.59)
20:56139447		D>G	A:395	(52.85, 44.01, 54.34)
20:56139543	rs376297762	P>T	A:398	(49.66, 39.48, 48.17)
20:56139561		S>A	A:404	(43.97, 31.57, 44.56)
20:56139562	rs149472972	S>L	A:404	(43.97, 31.57, 44.56)
20:56139577		P>L	A:409	(29.32, 23.27, 43.64)
20:56139584		S>R	A:411	(24.57, 23.09, 41.43)
20:56139598	rs569350822	I>T	A:416	(23.24, 26.58, 36.16)
20:56139601	rs143952631	D>V	A:417	(21.69, 26.04, 31.56)
20:56139619	rs148603002	P>L	A:423	(22.64, 13.96, 27.58)
20:56139630	rs28359550	P>S	A:427	(23.44, 23.94, 20.32)
20:56139655	rs141020523	G>D	A:435	(42.78, 38.24, 25.05)
20:56139657	rs200480357	R>C	A:436	(44.82, 40.24, 29.38)
20:56139658	rs112632361	R>H	A:436	(44.82, 40.24, 29.38)
20:56139666		A>S	A:439	(47.43, 46.97, 21.60)
20:56139667		A>V	A:439	(47.43, 46.97, 21.60)
20:56140107		V>L	A:444	(34.81, 42.71, 18.22)
20:56140120		L>P	A:448	(36.36, 36.47, 6.63)
20:56140132	rs150001707	H>R	A:452	(40.11, 33.96, 9.05)
20:56140135		G>A	A:453	(39.16, 31.11, 12.17)
20:56140143	rs368610566	V>M	A:456	(41.89, 33.66, 14.52)
20:56140147		G>E	A:457	(43.25, 30.80, 16.84)
20:56140149	rs372883844	A>T	A:458	(46.26, 30.06, 15.67)
20:56140150	rs370747699	A>V	A:458	(46.26, 30.06, 15.67)
20:56140152		A>T	A:459	(47.02, 33.64, 16.28)
20:56140155		M>L	A:460	(45.32, 33.26, 20.27)
20:56140165	rs376043660	E>A	A:463	(49.74, 40.90, 28.55)
20:56140411		I>V	A:474	(55.76, 39.22, 28.18)
20:56140427		P>L	A:479	(47.27, 28.52, 20.48)
20:56140438		R>W	A:483	(50.65, 27.40, 25.61)
20:56140439	rs41302559	R>Q	A:483	(50.65, 27.40, 25.61)
20:56140441		P>T	A:484	(49.13, 24.38, 27.96)
20:56140444	rs377174792	F>I	A:485	(46.19, 22.60, 28.21)
20:56140457	rs555506747	N>S	A:489	(50.84, 17.62, 16.31)
20:56140462	rs374878290	G>S	A:491	(48.89, 20.53, 13.26)
20:56140475	rs144962331	A>D	A:495	(43.65, 19.68, 10.50)
20:56140478		H>R	A:496	(40.25, 17.65, 13.81)
20:56140496		Q>R	A:502	(35.37, 19.35, 4.73)
20:56140498		H>Y	A:503	(30.74, 17.01, 8.75)
20:56140530		H>Q	A:513	(39.44, 37.83, 18.66)
20:56140535		N>T	A:515	(40.42, 42.83, 23.43)
20:56140543		R>W	A:518	(42.70, 48.51, 22.50)
20:56140544		R>Q	A:518	(42.70, 48.51, 22.50)
20:56140567	rs546079074	L>F	A:526	(39.45, 51.82, 25.80)
20:56140574	rs145570510	P>L	A:528	(33.96, 48.75, 30.54)
20:56140581	rs200656485	F>L	A:530	(33.73, 42.98, 33.88)
20:56140583		G>E	A:531	(28.56, 43.13, 31.77)
20:56140609	rs377429546	M>V	A:540	(28.43, 37.96, 18.66)
20:56140616		N>S	A:542	(22.04, 39.98, 16.04)
20:56140618	COSM1028408	R>W	A:543	(26.49, 38.90, 11.91)
20:56140619	rs373324803	R>Q	A:543	(26.49, 38.90, 11.91)
20:56140624	rs202078062 COSM3548162	D>N	A:545	(20.32, 35.70, 13.37)
20:56140628		G>A	A:546	(21.98, 38.30, 9.80)
20:56140640	rs141743884	T>I	A:550	(29.30, 44.07, 8.58)
20:56140649		T>M	A:553	(38.39, 44.82, 8.11)
20:56140667		P>L	A:559	(31.22, 46.70, 14.40)
20:56140669	rs200640038	K>Q	A:560	(27.94, 49.17, 10.49)
20:56140675		D>N	A:562	(26.24, 53.74, 15.41)
20:56140699		G>R	A:570	(29.55, 56.22, 28.95)
20:56140711	rs199728493	M>V	A:574	(34.16, 53.32, 19.63)
20:56140714	rs138431434	M>V	A:575	(38.21, 56.22, 16.69)
20:56140726	rs34103538	S>R	A:579	(41.99, 51.17, 15.69)
20:56140729	rs371783318	I>V	A:580	(42.66, 48.58, 12.29)
20:56140736		K>R	A:582	(49.45, 49.18, 7.34)
20:56140755	rs367756890	E>D	A:588	(50.51, 40.87, 14.78)
20:56140768	rs201175342	E>K	A:593	(54.55, 34.05, 8.88)
20:56140770		E>D	A:593	(54.55, 34.05, 8.88)
20:56140793		N>S	A:601	(57.75, 23.03, 10.29)
20:56140798	rs375658003	D>N	A:603	(53.00, 19.33, 10.81)
20:56140807	rs200272426	C>G	A:606	(47.70, 24.42, 3.36)
20:56140814		I>T	A:608	(46.81, 27.96, 8.02)
20:56140816	rs17847705	E>K	A:609	(50.54, 27.97, 4.33)
20:56140820	rs373831494	R>K	A:610	(46.04, 28.55, 1.34)
20:56140822	rs200805749	E>Q	A:611	(44.23, 32.34, 5.68)

1KHB.A | PCK1.

1KHB.A | PCK1

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
20:56136647	COSM1713714	M>I	A:60	(41.36, 17.16, 55.98)
20:56136651	COSM3548126	E>K	A:62	(41.91, 16.89, 63.53)
20:56137185	COSM4099732	V>I	A:95	(54.63, 9.50, 26.68)
20:56137841	COSM3405225	V>M	A:166	(42.37, 15.03, 45.62)
20:56137866	COSM3933887	T>M	A:174	(33.86, 14.99, 39.35)
20:56137883	COSM3799695	V>I	A:180	(30.70, 5.88, 38.64)
20:56137895	COSM3736801	V>L	A:184	(32.34, 1.35, 34.59)
20:56138123	COSM444094	T>K	A:217	(57.10, 17.35, 40.10)
20:56138621	COSM4987731	I>V	A:267	(29.54, 26.90, 27.45)
20:56138664	COSM1261522	A>V	A:281	(31.95, 29.11, 22.90)
20:56138777	COSM4099737	A>T	A:319	(22.67, 14.28, 12.79)
20:56139236	COSM257682	A>T	A:325	(28.25, 20.88, 23.96)
20:56139255	COSM3379095	G>D	A:331	(32.48, 22.38, 38.60)
20:56139347	COSM1028400	E>K	A:362	(41.02, 33.36, 57.49)
20:56139383	COSM1533929	D>Y	A:374	(35.10, 45.56, 46.58)
20:56140168	COSM218632	A>V	A:464	(51.32, 37.89, 30.89)
20:56140528	COSM254889	H>Y	A:513	(39.44, 37.83, 18.66)
20:56140824	COSM1681792	E>D	A:611	(44.23, 32.34, 5.68)