4EL1.B | P4HB – ASTRID

4EL1.B | P4HB

General Structure Information

PDB ID	4el1
HGNC Gene Label(s)	P4HB
Structure Name	crystal structure of oxidized hpdi (abbxa)
Resolution	2.88Å
Reference	AUTH C.WANG,W.LI,J.REN,J.FANG,H.KE,W.GONG,W.FENG,C.-C.WANGTITL STRUCTURAL INSIGHTS INTO THE REDOX-REGULATED DYNAMICTITL 2 CONFORMATIONS OF HUMAN PROTEIN DISULFIDE ISOMERASEREF ANTIOXID REDOX SIGNAL V. 19 44 2013REFN ISSN 1557-7716PMID 22657537DOI 10.1089/ARS.2012.4630

Variant Set Distributions

ExAC Variants

Number Of Residues	452
Number Of SNVs	111
Number Of Permutations	28864
Optimal Distance Threshold	16.0
K Statistic	0.097
p-value	0.011

COSMIC

Number Of Residues	452
Number Of SNVs	4
Number Of Permutations	71
Optimal Distance Threshold	23.0
K Statistic	0.333
p-value	0.707

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	111
Number Of COSMIC SNVs	4
Optimal Distance Threshold	19.0
K Statistic	-0.145
p-value	0.896

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:79818290		P>A	B:20	(23.48, 0.05, 18.89)
17:79818244	rs376060719	A>V	B:35	(27.46, -5.50, 30.28)
17:79817215		K>I	B:65	(35.49, 14.43, 14.93)
17:79817183		E>K	B:76	(39.29, -3.34, 18.51)
17:79817175		R>S	B:78	(33.14, 1.09, 19.14)
17:79817176	rs377276762	R>T	B:78	(33.14, 1.09, 19.14)
17:79817159		A>T	B:84	(22.64, 10.39, 33.64)
17:79817156		T>A	B:85	(19.33, 12.23, 33.03)
17:79817142	rs148691482	D>E	B:89	(21.19, 4.00, 39.08)
17:79817131	rs371977426	Q>R	B:93	(26.98, 1.47, 40.06)
17:79817128	rs144034161	Y>C	B:94	(30.42, 2.81, 37.14)
17:79817119	COSM3717775	R>H	B:97	(33.90, 12.16, 41.05)
17:79817101		K>M	B:103	(35.51, 6.02, 33.18)
17:79817089	rs139540831	N>S	B:107	(39.71, -6.61, 29.09)
17:79817087	rs371866106	G>R	B:108	(35.58, -5.53, 31.04)
17:79817080		T>M	B:110	(34.13, -3.12, 36.28)
17:79817077		A>D	B:111	(37.42, -2.97, 38.86)
17:79813459	rs370896045	G>V	B:119	(41.76, 16.21, 26.07)
17:79813453		E>G	B:121	(40.37, 17.28, 19.70)
17:79813439	rs200582154	V>M	B:126	(42.67, 9.06, 19.09)
17:79813420	COSM283666	R>H	B:132	(46.28, 3.88, 27.15)
17:79813421		R>C	B:132	(46.28, 3.88, 27.15)
17:79813414	rs199978948	G>D	B:134	(46.73, -3.58, 22.68)
17:79813411	rs201906397	P>L	B:135	(49.25, -5.77, 22.69)
17:79813385	rs138621837	A>T	B:144	(67.71, -3.24, 22.94)
17:79813360		S>F	B:152	(61.15, 2.54, 30.73)
17:79813356		S>R	B:153	(60.18, 1.66, 34.41)
17:79813349	COSM3989429	A>T	B:156	(59.87, -4.45, 34.68)
17:79813337		F>V	B:160	(62.63, -14.67, 29.37)
17:79813331	rs150091072	K>E	B:162	(62.49, -21.05, 23.79)
17:79813152		V>M	B:164	(54.69, -18.06, 22.41)
17:79813145	rs146846893	S>L	B:166	(52.91, -22.05, 25.95)
17:79813133	rs532127753	K>M	B:170	(49.15, -17.98, 26.16)
17:79813104		D>H	B:180	(48.32, -0.67, 33.03)
17:79813095		P>S	B:183	(56.10, -2.43, 31.94)
17:79813074	rs202139152	S>C	B:190	(68.32, -17.34, 23.03)
17:79813045		D>E	B:199	(69.10, -21.92, 31.44)
17:79813047	rs199956742 COSM708626	D>N	B:199	(69.10, -21.92, 31.44)
17:79813043		K>R	B:200	(64.83, -22.68, 31.99)
17:79813034		V>A	B:203	(59.36, -14.68, 34.69)
17:79813026	rs143758998	F>V	B:206	(63.68, -6.64, 35.52)
17:79805218		D>E	B:210	(66.10, -2.96, 46.73)
17:79805210	rs140683347	R>Q	B:213	(67.56, -9.05, 38.34)
17:79805207		N>S	B:214	(62.93, -10.46, 41.51)
17:79805192	rs200521181	E>A	B:219	(52.60, -23.60, 37.82)
17:79805159		K>R	B:230	(50.87, -8.19, 43.91)
17:79805160		K>Q	B:230	(50.87, -8.19, 43.91)
17:79805156		H>R	B:231	(54.39, -10.28, 47.27)
17:79805142		L>F	B:236	(61.88, -3.06, 52.09)
17:79805139	rs145040305	V>I	B:237	(61.97, 1.35, 52.65)
17:79805124		E>K	B:242	(52.60, 15.72, 49.78)
17:79804936		I>V	B:248	(51.80, 5.10, 49.96)
17:79804893		P>L	B:262	(66.74, 13.38, 59.80)
17:79804891	rs145146947	K>Q	B:263	(68.92, 13.51, 55.02)
17:79804887		S>N	B:264	(71.22, 15.90, 59.63)
17:79804877		D>E	B:267	(74.49, 6.50, 61.59)
17:79804876	rs149995643	Y>D	B:268	(70.48, 8.61, 56.68)
17:79804870	rs202131545	G>S	B:270	(72.62, 3.00, 59.53)
17:79804856		N>K	B:274	(68.89, -0.74, 61.20)
17:79804840	rs201200527	E>K	B:280	(64.05, -8.00, 55.98)
17:79804837	rs201941827	S>R	B:281	(60.12, -9.12, 59.15)
17:79804489		I>T	B:291	(59.61, 11.03, 56.51)
17:79804487	rs145209834	D>N	B:292	(63.55, 14.21, 54.97)
17:79804474		T>N	B:296	(60.23, 21.74, 52.94)
17:79804470		D>E	B:297	(57.11, 18.91, 50.92)
17:79804472		D>N	B:297	(57.11, 18.91, 50.92)
17:79804465	rs201628945	Q>R	B:299	(56.86, 19.91, 57.50)
17:79804454		E>K	B:303	(52.40, 20.07, 61.15)
17:79804435		K>T	B:309	(62.69, 19.99, 62.22)
17:79804432		E>G	B:310	(63.08, 20.30, 66.87)
17:79804414		R>H	B:316	(55.10, 8.19, 65.39)
17:79804415		R>C	B:316	(55.10, 8.19, 65.39)
17:79804405		T>I	B:319	(46.20, 2.13, 61.45)
17:79804389		M>I	B:324	(43.29, 6.84, 61.96)
17:79804373		E>K	B:330	(58.23, 2.16, 73.84)
17:79804369	rs200205336	S>L	B:331	(62.44, 3.71, 72.51)
17:79804362	rs201332870	E>D	B:333	(67.13, 2.59, 71.13)
17:79804357	rs200458051	T>M	B:335	(67.88, -0.89, 66.78)
17:79804355		A>T	B:336	(66.42, -3.62, 64.25)
17:79804352	rs202226696	E>K	B:337	(67.00, -5.90, 67.83)
17:79804348		R>K	B:338	(64.31, -1.50, 70.73)
17:79804327	rs377551913	R>H	B:345	(55.37, -4.54, 72.38)
17:79804319		E>K	B:348	(51.27, -8.49, 70.64)
17:79804315	rs374995159	G>D	B:349	(48.54, -4.65, 72.15)
17:79804308		I>M	B:351	(51.53, -0.59, 71.76)
17:79803858		M>L	B:356	(47.31, 15.08, 70.21)
17:79803840	rs11558882	E>K	B:362	(51.73, 22.23, 87.57)
17:79803829	rs200719772	D>E	B:365	(43.52, 22.66, 89.29)
17:79803789		D>N	B:379	(39.90, 11.64, 85.42)
17:79803786		V>M	B:380	(37.68, 15.40, 84.69)
17:79803775	rs373333137	D>E	B:383	(33.58, 12.14, 87.60)
17:79803771		K>E	B:385	(31.89, 12.02, 91.99)
17:79803762		V>I	B:388	(31.71, 18.35, 83.59)
17:79803604		G>S	B:398	(36.09, 34.75, 67.88)
17:79803595		K>Q	B:401	(38.11, 35.88, 70.96)
17:79803582	rs374921280	P>L	B:405	(34.75, 36.68, 79.12)
17:79803583		P>S	B:405	(34.75, 36.68, 79.12)
17:79803579	rs200992601	I>T	B:406	(31.10, 34.94, 79.50)
17:79803558	rs148639349	T>M	B:413	(29.28, 31.27, 89.73)
17:79803552		K>R	B:415	(34.66, 29.28, 92.86)
17:79803553		K>E	B:415	(34.66, 29.28, 92.86)
17:79803535	rs573703484 COSM985937	V>I	B:421	(33.39, 21.20, 86.77)
17:79803529		A>T	B:423	(36.01, 23.32, 81.59)
17:79803521	rs149469078	M>I	B:425	(40.12, 21.07, 75.66)
17:79803516	rs371414493	S>L	B:427	(40.44, 20.77, 70.12)
17:79803514		T>A	B:428	(44.01, 21.96, 68.06)
17:79803493		V>I	B:435	(34.56, 13.76, 72.05)
17:79803490		K>E	B:436	(35.28, 13.41, 68.18)
17:79803454		A>T	B:448	(26.48, 12.73, 87.17)
17:79803450		S>N	B:449	(26.52, 9.61, 84.85)
17:79803441	rs138319633	R>K	B:452	(31.10, 7.63, 79.03)
17:79803438	rs201024339	T>M	B:453	(25.88, 10.94, 79.34)
17:79803091		G>R	B:459	(22.18, 27.84, 73.42)
17:79803087		E>A	B:460	(21.08, 31.63, 75.72)
17:79803084		R>H	B:461	(26.89, 30.46, 73.23)
17:79803081		T>M	B:462	(24.22, 33.79, 78.17)
17:79803079	COSM985936	L>M	B:463	(25.64, 33.92, 83.01)
17:79803046	rs200658612	G>S	B:474	(20.29, 19.47, 81.21)
17:79803042		Q>R	B:475	(16.31, 17.57, 81.19)

4EL1.B | P4HB.

4EL1.B | P4HB

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
17:79818257	COSM4170851	K>E	B:31	(21.36, -0.48, 33.54)
17:79817119	COSM3717775	R>H	B:97	(33.90, 12.16, 41.05)
17:79813041	COSM3712597	D>H	B:201	(61.65, -20.96, 29.76)
17:79804462	COSM1680156	R>H	B:300	(50.08, 17.36, 55.35)