1YG5.C | HBA1 – ASTRID

1YG5.C | HBA1

General Structure Information

PDB ID	1yg5
HGNC Gene Label(s)	HBA1
Structure Name	t-to-t(high) quaternary transitions in human hemoglobin: betaw37h oxy (2mm ihp, 20% peg) (10 test sets)
Resolution	2.7Å
Reference	AUTH J.S.KAVANAUGH,P.H.ROGERS,A.ARNONETITL CRYSTALLOGRAPHIC EVIDENCE FOR A NEW ENSEMBLE OFTITL 2 LIGAND-INDUCED ALLOSTERIC TRANSITIONS INTITL 3 HEMOGLOBIN: THE T-TO-T(HIGH) QUATERNARYTITL 4 TRANSITIONS.REF BIOCHEMISTRY V. 44 6101 2005REFN ISSN 0006-2960PMID 15835899DOI 10.1021/BI047813A

Variant Set Distributions

ExAC Variants

Number Of Residues	141
Number Of SNVs	11
Number Of Permutations	887
Optimal Distance Threshold	7.0
K Statistic	0.2
p-value	0.004

ClinVar

Number Of Residues	141
Number Of SNVs	102
Number Of Permutations	5388
Optimal Distance Threshold	13.0
K Statistic	0.215
p-value	0.281

Ripley’s K Analysis Plots

ExACClinVar

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	11
Number Of ClinVar SNVs	98
Optimal Distance Threshold	7.0
K Statistic	-0.148
p-value	0.003

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:223477	rs80132178	S>R	C:102	(16.94, 15.27, -22.87)
16:223484	rs41417548	C>Y	C:104	(21.30, 13.25, -25.50)
16:223489		L>M	C:106	(16.48, 14.71, -28.81)
16:223496	rs63750010 HbVar.2539 CM066095	T>N	C:108	(19.94, 9.33, -30.11)
16:223561	rs41529844	A>P	C:130	(10.40, 18.34, -19.92)
16:223579	rs41364652	L>M	C:136	(11.43, 12.89, -12.32)
16:223595	rs63751282	R>H	C:141	(12.25, 22.23, -1.71)
16:227313	rs63749948 HbVar.2749 CM810010	A>V	C:110	(17.75, 12.36, -34.29)
16:227318	rs34830032	H>D	C:112	(19.07, 6.00, -34.87)
16:227331	rs35932809	E>A	C:116	(10.11, 9.69, -38.15)
16:227373	rs63750613	A>V	C:130	(10.40, 18.34, -19.92)
16:227385	rs281864473 rs281864487 HbVar.2623	T>I	C:134	(9.06, 18.24, -13.99)

[+] ClinVar Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:222916	rs33981821	V>E	C:1	(1.14, 21.54, -21.20)
16:222933	rs34817956	K>Q	C:7	(-0.26, 13.78, -26.15)
16:222941	rs111033604	N>K	C:9	(3.74, 13.70, -32.66)
16:222958	rs34956202	G>D	C:15	(6.93, 3.58, -32.03)
16:222960	rs281865555	K>E	C:16	(8.24, 4.67, -35.77)
16:222972	rs281864814	H>Y	C:20	(15.51, -0.31, -31.70)
16:222981	rs281864819	E>K	C:23	(19.54, -0.82, -28.54)
16:222991	rs281864822	A>E	C:26	(22.45, 3.40, -24.16)
16:222994	rs281864823	E>V	C:27	(23.27, 5.83, -28.34)
16:223000	rs41341344	L>P	C:29	(23.20, 6.93, -20.99)
16:223002	rs111033605	E>K	C:30	(27.73, 6.33, -24.61)
16:223129	rs41430445	F>S	C:33	(27.97, 9.19, -19.05)
16:223141	rs281864826	P>L	C:37	(31.69, 14.94, -18.07)
16:223150	rs281864828	K>M	C:40	(30.78, 10.53, -15.05)
16:223170	rs281864834	D>N	C:47	(31.94, -0.08, -16.17)
16:223174	rs41392146	L>P	C:48	(31.06, 4.58, -17.23)
16:223179	rs41461652	H>Y	C:50	(32.23, 1.79, -25.84)
16:223195	rs63749934	V>A	C:55	(25.39, 1.48, -19.65)
16:223205	rs41378349	H>Q	C:58	(20.55, 2.30, -16.58)
16:223206	rs41328049	G>S	C:59	(19.05, 1.96, -20.73)
16:223214	rs33985574	K>N	C:61	(16.51, -0.06, -16.09)
16:223215	rs41515649	V>M	C:62	(15.90, 4.74, -19.08)
16:223224	rs41510746	A>T	C:65	(10.33, 4.50, -18.39)
16:223228	rs41323248	L>P	C:66	(10.59, 6.94, -21.37)
16:223236	rs63749997	A>T	C:69	(5.20, 7.69, -20.29)
16:223245	rs281864855	H>Y	C:72	(0.83, 5.60, -18.58)
16:223255	rs281864859	D>V	C:75	(-1.50, 10.17, -15.59)
16:223261	rs281864861	P>H	C:77	(2.24, 12.39, -12.30)
16:223263	rs111033602	N>H	C:78	(0.19, 8.99, -10.45)
16:223269	rs41466346	L>V	C:80	(6.56, 8.47, -13.15)
16:223272	rs41484451	S>P	C:81	(5.56, 8.10, -8.24)
16:223285	rs41331747	D>V	C:85	(10.21, 9.11, -4.58)
16:223294	rs33983416	A>E	C:88	(14.54, 13.44, -5.57)
16:223300	rs281864873	K>M	C:90	(17.95, 7.45, -2.96)
16:223314	rs281864881	P>T	C:95	(17.77, 19.67, -12.07)
16:223480	rs63750073	H>Y	C:103	(20.75, 17.30, -26.15)
16:223484	rs41417548	C>Y	C:104	(21.30, 13.25, -25.50)
16:223499	rs41479844	L>R	C:109	(15.61, 9.75, -31.11)
16:223502	rs28928889	A>D	C:110	(17.75, 12.36, -34.29)
16:223511	rs281860618	L>H	C:113	(14.32, 7.99, -36.27)
16:223519	rs33987053	E>K	C:116	(10.11, 9.69, -38.15)
16:223547	rs41397847	L>Q	C:125	(10.03, 14.74, -28.47)
16:223549	rs33933481	D>N	C:126	(11.90, 19.25, -25.91)
16:223561	rs41529844	A>P	C:130	(10.40, 18.34, -19.92)
16:223572	rs41514946	S>R	C:133	(12.13, 16.11, -16.13)
16:223580	rs41469945	L>P	C:136	(11.43, 12.89, -12.32)
16:223588	rs41361546	K>E	C:139	(8.17, 15.23, -5.01)
16:223590	rs41393644	K>N	C:139	(8.17, 15.23, -5.01)
16:226720	rs281864802	V>E	C:1	(1.14, 21.54, -21.20)
16:226723	rs36030576	L>R	C:2	(1.48, 17.53, -23.24)
16:226726	rs35850071	S>F	C:3	(-0.75, 18.78, -26.83)
16:226731	rs34751764	A>P	C:5	(-0.52, 17.06, -30.82)
16:226732	rs34090856	A>D	C:5	(-0.52, 17.06, -30.82)
16:226734	rs33961916	D>N	C:6	(2.45, 17.34, -28.38)
16:226735	rs33986902	D>V	C:6	(2.45, 17.34, -28.38)
16:226739	rs34410516	K>N	C:7	(-0.26, 13.78, -26.15)
16:226745	rs28928885	N>K	C:9	(3.74, 13.70, -32.66)
16:226749	rs33938574	K>Q	C:11	(1.71, 8.10, -28.72)
16:226751	rs281860646	K>N	C:11	(1.71, 8.10, -28.72)
16:226753	rs35615982	A>D	C:12	(4.72, 8.11, -33.16)
16:226761	rs35816645	G>C	C:15	(6.93, 3.58, -32.03)
16:226764	rs41407250	K>E	C:16	(8.24, 4.67, -35.77)
16:226765	rs35210126	K>M	C:16	(8.24, 4.67, -35.77)
16:226766	rs281860648	K>N	C:16	(8.24, 4.67, -35.77)
16:226770	rs34504387	G>C	C:18	(10.46, 0.48, -30.39)
16:226771	rs35993097	G>D	C:18	(10.46, 0.48, -30.39)
16:226774	rs35628685	A>E	C:19	(12.60, -2.46, -30.23)
16:226776	rs34708054	H>Y	C:20	(15.51, -0.31, -31.70)
16:226777	rs33943087	H>P	C:20	(15.51, -0.31, -31.70)
16:226779	rs34324664	A>P	C:21	(14.59, 1.70, -26.77)
16:226780	rs11548605	A>D	C:21	(14.59, 1.70, -26.77)
16:226783	rs34608326	G>D	C:22	(17.45, 0.71, -25.27)
16:226785	rs33939620	E>K	C:23	(19.54, -0.82, -28.54)
16:226786	rs33939421	E>V	C:23	(19.54, -0.82, -28.54)
16:226787	rs281860684	E>D	C:23	(19.54, -0.82, -28.54)
16:226788	rs34743106	Y>H	C:24	(17.64, 4.04, -29.95)
16:226789	rs28928880	Y>C	C:24	(17.64, 4.04, -29.95)
16:226795	rs35477770	A>E	C:26	(22.45, 3.40, -24.16)
16:226797	rs34776279	E>K	C:27	(23.27, 5.83, -28.34)
16:226798	rs33964507	E>V	C:27	(23.27, 5.83, -28.34)
16:226806	rs33993166	E>K	C:30	(27.73, 6.33, -24.61)
16:226936	rs35203445	L>R	C:34	(31.62, 11.20, -23.61)
16:226945	rs35776155	P>L	C:37	(31.69, 14.94, -18.07)
16:226953	rs34492931	K>E	C:40	(30.78, 10.53, -15.05)
16:226955	rs28928886	K>N	C:40	(30.78, 10.53, -15.05)
16:226956	rs34890875	T>S	C:41	(29.14, 12.30, -10.37)
16:226962	rs35511459	F>V	C:43	(25.95, 6.98, -12.68)
16:226966	rs33978134	P>L	C:44	(30.09, 5.84, -8.85)
16:226968	rs33931984	H>Y	C:45	(27.50, 2.46, -9.05)
16:226969	rs28928883	H>P	C:45	(27.50, 2.46, -9.05)
16:226970	rs281860685	H>Q	C:45	(27.50, 2.46, -9.05)
16:226974	rs34269448	D>N	C:47	(31.94, -0.08, -16.17)
16:226975	rs33944368	D>A	C:47	(31.94, -0.08, -16.17)
16:226984	rs33967561	H>L	C:50	(32.23, 1.79, -25.84)
16:226986	rs33960522	G>S	C:51	(30.06, -0.57, -24.13)
16:226987	rs35934411	G>D	C:51	(30.06, -0.57, -24.13)
16:226993	rs34574239	A>D	C:53	(26.70, -3.86, -19.20)
16:226995	rs35317336	Q>E	C:54	(26.87, -1.29, -15.56)
16:226996	rs36024711	Q>R	C:54	(26.87, -1.29, -15.56)
16:226998	rs34068598	V>L	C:55	(25.39, 1.48, -19.65)
16:227001	rs34182019	K>E	C:56	(23.75, -2.72, -22.82)
16:227002	rs33949106	K>T	C:56	(23.75, -2.72, -22.82)
16:227003	rs281860657	K>N	C:56	(23.75, -2.72, -22.82)
16:227004	rs35252931	G>R	C:57	(21.10, -1.87, -18.81)
16:227005	rs36062788	G>D	C:57	(21.10, -1.87, -18.81)
16:227007	rs35213748	H>Y	C:58	(20.55, 2.30, -16.58)
16:227011	rs28928878	G>D	C:59	(19.05, 1.96, -20.73)
16:227013	rs34259907	K>E	C:60	(15.99, -2.03, -20.85)
16:227017	rs41381645	K>T	C:61	(16.51, -0.06, -16.09)
16:227023	rs34502246	A>D	C:63	(13.57, 3.36, -22.09)
16:227025	rs33984024	D>N	C:64	(11.45, 0.33, -20.39)
16:227026	rs35873730	D>G	C:64	(11.45, 0.33, -20.39)
16:227029	rs34733452	A>V	C:65	(10.33, 4.50, -18.39)
16:227037	rs34823698	N>Y	C:68	(5.14, 3.91, -18.43)
16:227047	rs3180281	A>E	C:71	(1.33, 5.10, -22.26)
16:227049	rs36104787	H>Y	C:72	(0.83, 5.60, -18.58)
16:227050	rs35859529	H>R	C:72	(0.83, 5.60, -18.58)
16:227055	rs28928875	D>N	C:74	(-3.17, 11.73, -20.55)
16:227056	rs33921047	D>V	C:74	(-3.17, 11.73, -20.55)
16:227058	rs33977363	D>N	C:75	(-1.50, 10.17, -15.59)
16:227059	rs33991223	D>A	C:75	(-1.50, 10.17, -15.59)
16:227062	rs33969953	M>K	C:76	(3.18, 11.85, -16.57)
16:227065	rs34019158	P>H	C:77	(2.24, 12.39, -12.30)
16:227067	rs33964623	N>H	C:78	(0.19, 8.99, -10.45)
16:227069	rs34440919	N>K	C:78	(0.19, 8.99, -10.45)
16:227070	rs34586189	A>T	C:79	(2.94, 6.85, -13.47)
16:227071	rs387906544	A>G	C:79	(2.94, 6.85, -13.47)
16:227074	rs34071856	L>R	C:80	(6.56, 8.47, -13.15)
16:227077	rs34936612	S>C	C:81	(5.56, 8.10, -8.24)
16:227080	rs34879587	A>D	C:82	(8.56, 6.23, -8.13)
16:227085	rs33926206	S>R	C:84	(9.84, 10.81, -8.23)
16:227088	rs33915947	D>N	C:85	(10.21, 9.11, -4.58)
16:227092	rs35548338	L>R	C:86	(14.98, 7.06, -6.77)
16:227094	rs28928876	H>N	C:87	(15.79, 10.21, -9.86)
16:227095	rs33976776	H>P	C:87	(15.79, 10.21, -9.86)
16:227097	rs35239527	A>S	C:88	(14.54, 13.44, -5.57)
16:227100	rs34988734	H>Y	C:89	(13.22, 12.52, -1.89)
16:227101	rs33944813	H>L	C:89	(13.22, 12.52, -1.89)
16:227102	rs1061009	H>Q	C:89	(13.22, 12.52, -1.89)
16:227104	rs33911106	K>M	C:90	(17.95, 7.45, -2.96)
16:227105	rs33914470	K>N	C:90	(17.95, 7.45, -2.96)
16:227107	rs34684963	L>P	C:91	(19.53, 9.28, -6.37)
16:227109	rs34868036	R>W	C:92	(19.97, 12.31, -3.26)
16:227110	rs33991779	R>Q	C:92	(19.97, 12.31, -3.26)
16:227113	rs34769782	V>A	C:93	(19.70, 14.28, -9.55)
16:227115	rs34102339	D>N	C:94	(20.70, 19.00, -10.35)
16:227116	rs28928879	D>A	C:94	(20.70, 19.00, -10.35)
16:227117	rs34814612	D>E	C:94	(20.70, 19.00, -10.35)
16:227118	rs33984621	P>T	C:95	(17.77, 19.67, -12.07)
16:227119	rs33931314	P>Q	C:95	(17.77, 19.67, -12.07)
16:227124	rs41322954	N>H	C:97	(21.99, 16.55, -14.86)
16:227130	rs34806456	K>E	C:99	(17.83, 20.68, -19.48)
16:227132	rs34273731	K>N	C:99	(17.83, 20.68, -19.48)
16:227291	rs28928884	H>Y	C:103	(20.75, 17.30, -26.15)
16:227292	rs35329201	H>R	C:103	(20.75, 17.30, -26.15)
16:227294	rs35059618	C>S	C:104	(21.30, 13.25, -25.50)
16:227312	rs34629158	A>T	C:110	(17.75, 12.36, -34.29)
16:227313	rs63749948	A>D	C:110	(17.75, 12.36, -34.29)
16:227315	rs34863047	A>T	C:111	(20.11, 9.67, -35.48)
16:227318	rs34830032	H>D	C:112	(19.07, 6.00, -34.87)
16:227319	rs34713708	H>R	C:112	(19.07, 6.00, -34.87)
16:227322	rs35654345	L>H	C:113	(14.32, 7.99, -36.27)
16:227324	rs34472107	P>S	C:114	(15.84, 10.04, -40.07)
16:227325	rs33910377	P>L	C:114	(15.84, 10.04, -40.07)
16:227328	rs34204059	A>D	C:115	(11.85, 10.71, -41.09)
16:227330	rs63749882	E>K	C:116	(10.11, 9.69, -38.15)
16:227331	rs35932809	E>A	C:116	(10.11, 9.69, -38.15)
16:227343	rs63749927	A>E	C:120	(7.11, 18.82, -34.67)
16:227345	rs63751008	V>M	C:121	(8.41, 15.49, -33.80)
16:227351	rs28928881	A>T	C:123	(9.04, 19.86, -30.40)
16:227360	rs63750950	D>N	C:126	(11.90, 19.25, -25.91)
16:227361	rs63750467	D>V	C:126	(11.90, 19.25, -25.91)
16:227364	rs63751308	K>T	C:127	(6.69, 20.18, -24.95)
16:227365	rs63749865	K>N	C:127	(6.69, 20.18, -24.95)
16:227370	rs35993655	L>P	C:129	(11.82, 14.75, -22.48)
16:227373	rs63750613	A>D	C:130	(10.40, 18.34, -19.92)
16:227375	rs35974739	S>P	C:131	(7.37, 16.94, -18.64)
16:227379	rs35166834	V>G	C:132	(9.55, 13.46, -17.67)
16:227388	rs35994191	V>E	C:135	(7.52, 14.40, -12.71)
16:227390	rs121913127	L>M	C:136	(11.43, 12.89, -12.32)
16:227396	rs34011123	S>P	C:138	(8.95, 17.52, -8.35)
16:227400	rs34849179	K>T	C:139	(8.17, 15.23, -5.01)
16:227402	rs35723200	Y>H	C:140	(15.02, 18.89, -4.91)
16:227405	rs33991910	R>S	C:141	(12.25, 22.23, -1.71)
16:227406	rs33935328	R>H	C:141	(12.25, 22.23, -1.71)