4A5T.S | PLG – ASTRID

4A5T.S | PLG

General Structure Information

PDB ID	4a5t
HGNC Gene Label(s)	PLG
Structure Name	structural basis for the conformational modulation
Resolution	3.49Å
Reference	AUTH Y.XUE,C.BODIN,K.OLSSONTITL CRYSTAL STRUCTURE OF THE NATIVE PLASMINOGEN REVEALS ANTITL 2 ACTIVATION-RESISTANT COMPACT CONFORMATION.REF J. THROMB. HAEMOST. V. 10 1385 2012REFN ISSN 1538-7933PMID 22540246DOI 10.1111/J.1538-7836.2012.04765.X

Variant Set Distributions

ExAC Variants

Number Of Residues	767
Number Of SNVs	176
Number Of Permutations	81331
Optimal Distance Threshold	19.0
K Statistic	0.103
p-value	0.023

ClinVar

Number Of Residues	767
Number Of SNVs	6
Number Of Permutations	3293
Optimal Distance Threshold	27.0
K Statistic	0.133
p-value	0.931

COSMIC

Number Of Residues	767
Number Of SNVs	26
Number Of Permutations	35657
Optimal Distance Threshold	8.0
K Statistic	0.018
p-value	0.853

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	176
Number Of ClinVar SNVs	6
Optimal Distance Threshold	11.0
K Statistic	0.038
p-value	1.0

Cosmic vs. ExAC

Number Of ExAC SNVs	176
Number Of COSMIC SNVs	20
Optimal Distance Threshold	8.0
K Statistic	0.01
p-value	0.68

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:161127450		P>S	S:2	(6.28, 42.71, 11.00)
6:161127456		D>N	S:4	(4.85, 42.34, 5.98)
6:161127457		D>V	S:4	(4.85, 42.34, 5.98)
6:161127462		Y>H	S:6	(9.93, 37.21, 6.00)
6:161127466		V>E	S:7	(6.55, 34.16, 1.92)
6:161127492		S>G	S:16	(19.77, 23.16, 3.87)
6:161127501	rs73015965	K>E	S:19	(21.88, 24.84, 8.05)
6:161127504	rs138353396	K>Q	S:20	(23.05, 27.78, 12.76)
6:161127526		I>T	S:27	(7.94, 32.97, 14.90)
6:161127547		C>Y	S:34	(17.47, 36.09, 10.27)
6:161127549		E>K	S:35	(16.92, 40.32, 9.96)
6:161127555		D>N	S:37	(22.89, 38.41, 8.64)
6:161128772		M>L	S:57	(18.13, 28.49, 5.80)
6:161128775		A>T	S:58	(20.92, 30.63, 2.58)
6:161128778		E>K	S:59	(19.43, 27.80, 1.42)
6:161128801		I>M	S:66	(10.24, 22.88, -0.61)
6:161132112		Y>F	S:80	(16.95, 37.48, -1.24)
6:161132129	rs148659959	T>A	S:86	(12.17, 49.05, -7.86)
6:161132130		T>I	S:86	(12.17, 49.05, -7.86)
6:161132133		G>A	S:87	(14.17, 51.67, -9.25)
6:161132157	rs139357983	T>M	S:95	(18.57, 35.51, -11.21)
6:161132163		S>Y	S:97	(22.70, 36.53, -16.25)
6:161132173	rs377275189	K>N	S:100	(20.94, 46.09, -22.56)
6:161132177		G>S	S:102	(22.70, 39.45, -23.92)
6:161132184	rs370856655	T>I	S:104	(27.01, 36.36, -20.25)
6:161132211		P>H	S:113	(37.23, 38.75, -18.54)
6:161132215	rs4252186	H>Q	S:114	(36.77, 42.18, -17.21)
6:161132219	rs199833895	P>S	S:116	(36.66, 43.30, -10.44)
6:161134036	COSM293668	H>Q	S:123	(31.46, 46.31, -2.13)
6:161134037		P>S	S:124	(30.28, 42.90, 1.75)
6:161134045		E>D	S:126	(26.23, 45.57, -1.85)
6:161134058		N>Y	S:131	(26.48, 36.11, -13.08)
6:161134076		D>N	S:137	(27.05, 52.21, -7.88)
6:161134078	rs146415258	D>E	S:137	(27.05, 52.21, -7.88)
6:161134082	rs141045811	D>N	S:139	(23.75, 53.79, -11.64)
6:161134086	rs201792453	P>L	S:140	(20.99, 56.23, -12.16)
6:161134094		P>T	S:143	(20.82, 46.75, -12.71)
6:161134103	rs139828885	Y>H	S:146	(32.00, 43.75, -13.95)
6:161134115	rs143256245	P>T	S:150	(36.60, 40.80, -23.75)
6:161134118		E>K	S:151	(35.91, 44.29, -26.99)
6:161134123	rs374619723	K>N	S:152	(31.69, 45.53, -23.00)
6:161134124	rs145535174	R>G	S:153	(35.16, 46.49, -16.86)
6:161134139	rs374903528 COSM1221187	D>N	S:158	(16.52, 44.66, -19.36)
6:161134148	rs369353385	E>K	S:161	(9.57, 48.17, -12.81)
6:161134149		E>G	S:161	(9.57, 48.17, -12.81)
6:161135838	rs377016135	H>R	S:168	(2.86, 46.60, -15.74)
6:161135850		E>G	S:172	(-3.70, 41.89, -15.00)
6:161135859	rs150072546	D>V	S:175	(1.77, 43.90, -6.03)
6:161135876	rs149145958	T>A	S:181	(-10.62, 55.46, -4.38)
6:161135880		M>T	S:182	(-11.07, 57.58, -8.64)
6:161135881		M>I	S:182	(-11.07, 57.58, -8.64)
6:161135900	rs201014517	A>S	S:189	(-10.95, 44.92, 3.68)
6:161135906	COSM1545406	D>N	S:191	(-10.77, 40.15, 5.69)
6:161135910	COSM1075696	S>Y	S:192	(-14.34, 42.72, 5.59)
6:161135924	rs374234922 COSM3860174	A>T	S:197	(-21.15, 42.33, 1.33)
6:161135931		G>V	S:199	(-17.19, 37.49, -2.83)
6:161135933	rs151092364	Y>H	S:200	(-14.60, 39.79, -4.98)
6:161135940		P>L	S:202	(-9.58, 36.22, 0.53)
6:161135943	rs566440089	S>F	S:203	(-10.16, 32.20, 1.46)
6:161137693		L>V	S:210	(-7.47, 39.77, -2.29)
6:161137720		D>N	S:219	(-12.40, 41.04, -12.08)
6:161137733	COSM207452	R>Q	S:223	(-8.78, 51.45, -13.62)
6:161137746	rs146910079	F>L	S:227	(-15.47, 46.23, -2.34)
6:161137751	rs139012522	T>I	S:229	(-15.48, 52.76, 4.12)
6:161137757	rs372026592	P>L	S:231	(-21.78, 53.08, 3.35)
6:161137759		N>H	S:232	(-23.59, 55.35, 0.31)
6:161137760		N>S	S:232	(-23.59, 55.35, 0.31)
6:161137765		R>C	S:234	(-20.51, 47.22, -3.12)
6:161137766	rs143034754	R>H	S:234	(-20.51, 47.22, -3.12)
6:161137780	rs138242513	D>N	S:239	(-6.26, 56.73, -9.26)
6:161137789		R>C	S:242	(-1.00, 53.86, -16.99)
6:161137790	rs4252187	R>H	S:242	(-1.00, 53.86, -16.99)
6:161139352		T>P	S:253	(1.38, 37.12, -31.98)
6:161139361		C>R	S:256	(-4.11, 33.65, -37.80)
6:161139376		G>S	S:261	(-8.29, 35.47, -30.55)
6:161139389	rs371746732 COSM1131986	R>H	S:265	(-1.48, 42.83, -33.95)
6:161139391	COSM1292237	G>W	S:266	(-4.14, 41.66, -37.43)
6:161139394		N>D	S:267	(-4.63, 44.07, -40.31)
6:161139395		N>S	S:267	(-4.63, 44.07, -40.31)
6:161139409	rs564003153	V>M	S:272	(-19.46, 37.98, -40.33)
6:161139415		G>R	S:274	(-20.01, 43.33, -43.32)
6:161139464		R>T	S:290	(-13.72, 47.34, -24.42)
6:161139481		P>S	S:296	(-2.50, 48.91, -23.18)
6:161139488		K>I	S:298	(-5.29, 44.06, -24.88)
6:161139732		D>H	S:301	(-4.37, 49.16, -32.95)
6:161139781		H>L	S:317	(-17.42, 48.47, -31.19)
6:161139789	rs200604924	N>D	S:320	(-24.24, 50.26, -38.32)
6:161139793	rs549550780	S>T	S:321	(-26.24, 53.03, -36.03)
6:161139797	rs138051887	Q>H	S:322	(-29.15, 50.13, -36.47)
6:161139801	rs142647215	R>W	S:324	(-22.50, 48.76, -29.21)
6:161139802		R>Q	S:324	(-22.50, 48.76, -29.21)
6:161139821	rs535713437	I>M	S:330	(-10.56, 35.64, -38.31)
6:161139822		P>S	S:331	(-8.70, 33.27, -40.93)
6:161139828		C>R	S:333	(-4.20, 29.02, -38.26)
6:161139837		S>P	S:336	(0.98, 23.56, -34.47)
6:161139838		S>Y	S:336	(0.98, 23.56, -34.47)
6:161139849	rs201973253	T>A	S:340	(-3.44, 21.76, -30.43)
6:161139864	rs369616186	P>S	S:345	(-6.04, 25.32, -15.98)
6:161143450		E>D	S:350	(-16.49, 20.08, -5.59)
6:161143457		P>A	S:353	(-18.31, 12.89, -1.11)
6:161143463	rs121918028	V>F	S:355	(-22.39, 10.81, 2.07)
6:161143467	rs142086839	Q>R	S:356	(-17.96, 11.82, 5.60)
6:161143481		G>S	S:361	(-6.52, 2.60, 7.98)
6:161143484	rs376572197	D>Y	S:362	(-3.13, 4.07, 6.02)
6:161143491	rs370326625	Q>R	S:364	(-1.78, 3.63, 1.45)
6:161143493		S>G	S:365	(-6.74, 2.06, -0.25)
6:161143500	COSM207455	R>Q	S:367	(-7.99, 4.88, -4.66)
6:161143514		T>A	S:372	(-12.12, 18.86, 1.01)
6:161143547		S>P	S:383	(-0.63, 17.46, -12.22)
6:161143553		M>V	S:385	(3.78, 21.87, -9.91)
6:161143555		M>I	S:385	(3.78, 21.87, -9.91)
6:161143565	rs4252119	R>W	S:389	(7.53, 22.19, -7.70)
6:161143566		R>Q	S:389	(7.53, 22.19, -7.70)
6:161143572		Q>R	S:391	(8.86, 15.11, -6.38)
6:161143575		K>T	S:392	(4.31, 13.50, -4.15)
6:161143596		N>T	S:399	(0.44, 1.93, -8.08)
6:161152085	rs139071351	G>D	S:401	(-4.09, 7.33, -7.51)
6:161152095	COSM3622604	M>I	S:404	(-8.04, 14.82, -11.05)
6:161152111		P>S	S:410	(1.33, 8.89, -1.59)
6:161152118	COSM3024006	A>D	S:412	(2.61, 6.34, 4.06)
6:161152134	rs370807852	W>C	S:417	(-1.39, 13.93, 1.49)
6:161152145		T>I	S:421	(-5.44, 25.76, -3.38)
6:161152147	COSM3622607	D>N	S:422	(-3.56, 28.41, 0.58)
6:161152154		S>N	S:424	(-0.12, 29.65, 3.10)
6:161152156	rs574500945 COSM673693	V>I	S:425	(-1.27, 25.90, 3.51)
6:161152160		R>T	S:426	(3.40, 22.16, 0.57)
6:161152183		K>E	S:434	(-10.58, 5.61, 10.46)
6:161152784		M>I	S:463	(-12.92, 15.20, 18.43)
6:161152807	rs140537724	R>Q	S:471	(-10.04, 18.04, 27.77)
6:161152837	rs140970354	T>M	S:481	(2.88, 3.82, 20.75)
6:161152848		D>H	S:485	(2.87, 10.71, 31.50)
6:161152857	rs138011858	A>S	S:488	(7.15, 13.21, 32.02)
6:161152858	rs372603134	A>V	S:488	(7.15, 13.21, 32.02)
6:161152865		E>D	S:490	(12.27, 10.07, 31.53)
6:161152876		H>L	S:494	(8.46, 17.92, 27.76)
6:161152888	rs377265821	T>I	S:498	(4.32, 21.11, 30.87)
6:161152905	rs4252129	R>W	S:504	(-6.96, 26.90, 31.00)
6:161155054		G>R	S:520	(-4.29, 16.99, 13.36)
6:161155060		P>T	S:522	(-5.46, 15.01, 19.05)
6:161155066		C>R	S:524	(1.23, 12.39, 22.35)
6:161155079		N>S	S:528	(9.16, 5.17, 20.65)
6:161155106		D>G	S:537	(-7.84, 7.78, 16.11)
6:161157933	rs569278081	D>H	S:547	(-27.72, 17.11, 10.00)
6:161157949		Q>R	S:552	(-28.65, 10.37, 3.64)
6:161157952		V>E	S:553	(-28.82, 10.00, -1.65)
6:161157961		K>R	S:556	(-25.91, 12.76, -10.60)
6:161157972	rs138728014	G>R	S:560	(-22.54, 21.79, -16.79)
6:161157981		V>L	S:563	(-28.72, 20.95, -22.35)
6:161157988		G>E	S:565	(-29.57, 18.53, -17.34)
6:161158000	rs202141531	H>R	S:569	(-29.06, 10.17, -8.12)
6:161158024	rs372520102	V>G	S:577	(-41.03, 21.00, -1.94)
6:161159574		G>R	S:584	(-52.42, 17.38, -7.96)
6:161159601		I>L	S:593	(-36.22, 25.67, 5.95)
6:161159604		S>T	S:594	(-38.22, 23.31, 8.99)
6:161159615	rs121918031 CM971219	W>C	S:597	(-42.36, 27.39, 8.79)
6:161159617		V>E	S:598	(-41.68, 25.72, 2.99)
6:161159625	rs121918027	A>T	S:601	(-42.07, 32.08, -4.46)
6:161160104		P>S	S:609	(-55.32, 33.85, -0.82)
6:161160120		Y>C	S:614	(-51.54, 26.72, -1.70)
6:161160125		V>I	S:616	(-46.49, 20.51, 0.69)
6:161160128		I>V	S:617	(-45.68, 16.71, -1.91)
6:161160158	rs369196761 COSM3860183	E>K	S:627	(-42.53, 7.45, -4.55)
6:161160161		P>S	S:628	(-45.37, 4.86, -1.42)
6:161160162	rs187157735	P>L	S:628	(-45.37, 4.86, -1.42)
6:161160180		E>G	S:634	(-53.13, 21.69, 4.11)
6:161160200		E>Q	S:641	(-40.73, 39.65, 2.37)
6:161160207		T>I	S:643	(-39.32, 44.26, 2.12)
6:161160219		I>T	S:647	(-39.80, 35.39, -0.66)
6:161162348	COSM595135	A>V	S:656	(-42.43, 16.98, 8.77)
6:161162350	rs142551860	V>I	S:657	(-41.65, 13.03, 9.05)
6:161162355		I>M	S:658	(-37.27, 13.93, 9.86)
6:161162369	rs147175166	I>N	S:663	(-33.51, 16.22, 4.92)
6:161162386		S>T	S:669	(-25.14, 33.53, 7.19)
6:161162392		N>D	S:671	(-25.94, 39.46, 4.75)
6:161162407	rs181030365	D>N	S:676	(-17.38, 34.37, -8.48)
6:161162411	rs147930532	R>Q	S:677	(-17.32, 30.16, -11.66)
6:161162416	rs201323384	E>K	S:679	(-20.35, 25.35, -9.02)
6:161162419		C>R	S:680	(-24.62, 25.85, -7.50)
6:161162446		Q>E	S:689	(-42.43, 19.04, -24.84)
6:161162448		Q>H	S:689	(-42.43, 19.04, -24.84)
6:161173155	rs202074006 CM034888	G>R	S:693	(-37.32, 13.45, -17.75)
6:161173159		A>V	S:694	(-40.54, 13.65, -17.78)
6:161173165		L>P	S:696	(-38.25, 12.82, -13.51)
6:161173189		V>A	S:704	(-22.23, 32.16, -8.63)
6:161173212	COSM3024040	R>C	S:712	(-19.58, 44.07, -15.85)
6:161173213	rs150065136	R>H	S:712	(-19.58, 44.07, -15.85)
6:161173215	rs145177652	Y>H	S:713	(-23.93, 47.37, -21.70)
6:161173216	rs149148300	Y>C	S:713	(-23.93, 47.37, -21.70)
6:161173251		L>V	S:725	(-27.99, 35.48, -6.60)
6:161173272	rs121918033	G>R	S:732	(-24.04, 30.07, -24.47)
6:161173278		T>A	S:734	(-29.20, 28.23, -21.54)
6:161173962	rs199619244	E>K	S:749	(-20.54, 25.46, 2.67)
6:161173968		D>Y	S:751	(-19.94, 18.74, 5.42)
6:161174001		G>S	S:762	(-39.65, 36.77, -13.51)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:161127528	COSM225865	E>K	S:28	(8.46, 36.63, 17.07)
6:161127532	COSM2151443	E>G	S:29	(13.19, 34.40, 19.39)
6:161127561	COSM3622592	E>K	S:39	(28.15, 33.33, 9.88)
6:161132151	COSM1634613	R>I	S:93	(19.42, 41.44, -4.34)
6:161134082	COSM276811	D>N	S:139	(23.75, 53.79, -11.64)
6:161134139	COSM1221187	D>N	S:158	(16.52, 44.66, -19.36)
6:161135861	COSM216743	G>S	S:176	(0.39, 47.29, -4.32)
6:161135906	COSM1545406	D>Y	S:191	(-10.77, 40.15, 5.69)
6:161137712	COSM246667	R>H	S:216	(-5.08, 44.45, -5.64)
6:161137733	COSM207452	R>Q	S:223	(-8.78, 51.45, -13.62)
6:161137766	COSM1158341	R>H	S:234	(-20.51, 47.22, -3.12)
6:161139389	COSM1131986	R>H	S:265	(-1.48, 42.83, -33.95)
6:161139760	COSM3622601	G>E	S:310	(-14.00, 36.88, -23.22)
6:161143500	COSM207455	R>Q	S:367	(-7.99, 4.88, -4.66)
6:161143527	COSM1722523	G>E	S:376	(-12.07, 23.52, 3.55)
6:161143599	COSM1075699	A>V	S:400	(-1.46, 5.99, -5.67)
6:161152118	COSM3024006	A>V	S:412	(2.61, 6.34, 4.06)
6:161152120	COSM3622605	D>N	S:413	(0.88, 9.70, 6.53)
6:161152156	COSM673693	V>I	S:425	(-1.27, 25.90, 3.51)
6:161155096	COSM304319	D>N	S:534	(2.21, 10.51, 16.93)
6:161160173	COSM3622612	E>K	S:632	(-50.22, 15.22, 0.91)
6:161160179	COSM1722524	E>K	S:634	(-53.13, 21.69, 4.11)
6:161160198	COSM1720066	LE>LK	S:640	(-45.97, 37.46, 1.84)
6:161160210	COSM207457	R>Q	S:644	(-37.83, 42.88, -2.92)
6:161173177	COSM2148977	A>V	S:700	(-28.62, 22.18, -12.67)
6:161173248	COSM3622617	E>K	S:724	(-31.33, 40.24, -6.16)

4A5T.S | PLG.

4A5T.S | PLG

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