2QQK.A | NRP2 – ASTRID

2QQK.A | NRP2

General Structure Information

PDB ID	2qqk
HGNC Gene Label(s)	NRP2
Structure Name	neuropilin-2 a1a2b1b2 domains in complex with a semaphorin-blocking fab
Resolution	2.75Å
Reference	AUTH B.A.APPLETON,P.WU,J.MALONEY,J.YIN,W.C.LIANG,S.STAWICKI,AUTH 2 K.MORTARA,K.K.BOWMAN,J.M.ELLIOTT,W.DESMARAIS,J.F.BAZAN,AUTH 3 A.BAGRI,M.TESSIER-LAVIGNE,A.W.KOCH,Y.WU,R.J.WATTS,C.WIESMANNTITL STRUCTURAL STUDIES OF NEUROPILIN/ANTIBODY COMPLEXES PROVIDETITL 2 INSIGHTS INTO SEMAPHORIN AND VEGF BINDINGREF EMBO J. V. 26 4902 2007REFN ISSN 0261-4189PMID 17989695DOI 10.1038/SJ.EMBOJ.7601906

Variant Set Distributions

ExAC Variants

Number Of Residues	541
Number Of SNVs	140
Number Of Permutations	68248
Optimal Distance Threshold	27.0
K Statistic	0.378
p-value	0.029

COSMIC

Number Of Residues	541
Number Of SNVs	4
Number Of Permutations	574
Optimal Distance Threshold	8.0
K Statistic	0.167
p-value	0.425

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	140
Number Of COSMIC SNVs	6
Optimal Distance Threshold	42.0
K Statistic	0.183
p-value	0.828

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:206562283		G>D	A:30	(-15.21, -47.20, -41.73)
2:206562286	COSM209704	R>H	A:31	(-17.61, -47.61, -45.81)
2:206562324		G>S	A:44	(-6.98, -44.40, -28.00)
2:206562336		D>H	A:48	(-0.78, -47.31, -25.52)
2:206562345	rs200272716	S>A	A:51	(-3.52, -55.98, -28.32)
2:206562346		S>F	A:51	(-3.52, -55.98, -28.32)
2:206562360		E>K	A:56	(-10.96, -52.24, -42.17)
2:206562376		A>V	A:61	(-15.29, -38.87, -52.62)
2:206562381	COSM3682516 COSM3682517	E>K	A:63	(-17.03, -36.67, -57.17)
2:206562402	rs545784428	L>V	A:70	(-4.10, -38.87, -46.12)
2:206562412		N>S	A:73	(0.45, -36.24, -36.15)
2:206580962		D>E	A:99	(-2.01, -50.41, -55.52)
2:206581002		I>V	A:113	(-0.73, -40.31, -48.89)
2:206581033	rs849541	R>K	A:123	(-5.09, -52.77, -42.41)
2:206581038		T>S	A:125	(-2.40, -54.37, -37.88)
2:206581077		R>C	A:138	(-4.96, -33.43, -40.36)
2:206581083	rs150835990	E>Q	A:140	(-8.65, -32.82, -46.93)
2:206587207		E>K	A:147	(-12.93, -29.86, -66.68)
2:206587210		D>Y	A:148	(-16.83, -29.93, -63.04)
2:206587238	rs547293929	N>I	A:157	(-34.30, -32.93, -79.31)
2:206587246		I>V	A:160	(-24.11, -36.96, -75.40)
2:206587249		E>K	A:161	(-20.31, -35.14, -77.64)
2:206587252		S>T	A:162	(-16.58, -36.75, -76.08)
2:206587277		P>R	A:170	(-9.13, -35.07, -73.20)
2:206587294		T>A	A:176	(-21.12, -37.46, -65.01)
2:206587322		M>K	A:185	(-41.44, -39.94, -70.95)
2:206587323	rs372681346	M>I	A:185	(-41.44, -39.94, -70.95)
2:206587327	rs150011205	I>V	A:187	(-34.52, -42.47, -71.77)
2:206587405		L>M	A:213	(-18.59, -45.46, -71.31)
2:206587432		V>I	A:222	(-25.97, -45.92, -56.60)
2:206588511		G>C	A:223	(-26.98, -47.83, -59.48)
2:206588518		L>P	A:225	(-23.55, -51.43, -64.25)
2:206588523		G>S	A:227	(-22.20, -51.12, -68.80)
2:206588551		S>F	A:236	(-26.50, -51.21, -78.00)
2:206588559	COSM1691852 COSM3576603 COSM3576604 COSM1691853	R>C	A:239	(-35.66, -48.36, -76.06)
2:206588560	rs201324375	R>H	A:239	(-35.66, -48.36, -76.06)
2:206588566	rs563060469	S>L	A:241	(-38.70, -46.87, -67.57)
2:206588569	rs138033888	T>M	A:242	(-36.00, -45.49, -64.44)
2:206588577		L>F	A:245	(-29.72, -43.19, -68.12)
2:206588596	rs113330212	T>M	A:251	(-9.76, -40.55, -69.49)
2:206588605		A>V	A:254	(-2.31, -42.58, -72.94)
2:206588629	rs370384347	A>V	A:262	(-24.41, -39.75, -78.83)
2:206588631		R>C	A:263	(-29.14, -39.70, -81.24)
2:206588632	rs199881632	R>H	A:263	(-29.14, -39.70, -81.24)
2:206588634		Y>H	A:264	(-31.39, -37.28, -75.31)
2:206588640		L>M	A:266	(-37.34, -38.06, -74.00)
2:206588644		V>A	A:267	(-40.80, -41.13, -75.97)
2:206590645		C>G	A:277	(-47.71, -58.94, -69.36)
2:206590648		N>Y	A:278	(-48.45, -60.81, -73.43)
2:206590649		N>S	A:278	(-48.45, -60.81, -73.43)
2:206590651		V>I	A:279	(-45.01, -58.21, -74.92)
2:206590654	rs79750907	P>S	A:280	(-42.74, -59.51, -77.28)
2:206590663		M>V	A:283	(-34.68, -62.34, -79.15)
2:206590666	rs377035589	E>K	A:284	(-38.38, -62.07, -83.88)
2:206590676	rs114305456	R>Q	A:287	(-36.50, -53.16, -79.36)
2:206590679		I>T	A:288	(-32.82, -58.23, -77.12)
2:206590681		A>T	A:289	(-28.94, -56.86, -78.53)
2:206590696		S>G	A:294	(-24.74, -64.98, -73.64)
2:206590715		S>C	A:300	(-16.01, -75.03, -82.99)
2:206590720	rs368857132	G>R	A:302	(-18.99, -70.44, -85.56)
2:206590721	rs369347008	G>E	A:302	(-18.99, -70.44, -85.56)
2:206590732		P>S	A:306	(-25.18, -66.81, -79.17)
2:206590744		R>W	A:310	(-32.36, -63.31, -82.36)
2:206590745	rs372080377 COSM124852	R>Q	A:310	(-32.36, -63.31, -82.36)
2:206590751		H>P	A:312	(-39.08, -67.54, -86.34)
2:206590754		G>D	A:313	(-34.04, -67.71, -87.75)
2:206590780	rs200002477	L>M	A:322	(-19.97, -80.50, -74.95)
2:206590784		D>G	A:323	(-23.99, -81.68, -76.08)
2:206590787	rs371668549	S>C	A:324	(-24.44, -80.88, -71.23)
2:206592615		V>L	A:331	(-30.67, -63.01, -71.84)
2:206592625	COSM4090461 COSM4090462 COSM4090463	R>H	A:334	(-28.94, -54.34, -70.35)
2:206592643	rs150064130	T>M	A:340	(-44.81, -64.01, -68.56)
2:206592645		A>T	A:341	(-43.05, -66.33, -71.32)
2:206592661		G>E	A:346	(-34.98, -75.32, -83.12)
2:206592664		A>V	A:347	(-32.50, -76.09, -85.70)
2:206592673		R>K	A:350	(-28.19, -72.07, -94.11)
2:206592683	rs376340891	Q>H	A:353	(-30.19, -80.62, -94.96)
2:206592686	rs149039089	N>K	A:354	(-29.39, -82.48, -90.08)
2:206592694		Y>S	A:357	(-35.47, -81.66, -81.15)
2:206592696		V>I	A:358	(-34.27, -78.73, -76.61)
2:206592702		S>T	A:360	(-35.97, -80.32, -71.71)
2:206592730		G>E	A:369	(-25.37, -62.39, -62.43)
2:206592732		E>K	A:370	(-22.92, -62.92, -58.86)
2:206592741		M>V	A:373	(-33.96, -68.62, -58.89)
2:206592744		V>L	A:374	(-33.81, -72.74, -60.23)
2:206592751		R>Q	A:376	(-37.98, -74.49, -57.21)
2:206592757		G>V	A:378	(-42.70, -76.37, -55.51)
2:206605262	rs201603089	D>A	A:389	(-39.97, -80.40, -84.37)
2:206605288		L>I	A:398	(-44.14, -68.70, -66.23)
2:206605292		H>R	A:399	(-46.71, -70.94, -62.28)
2:206605294	rs367956491 COSM3838378 COSM3838379 COSM3838380	A>T	A:400	(-45.13, -67.68, -61.85)
2:206605307		T>I	A:404	(-35.74, -60.74, -63.81)
2:206605325	rs138662221	R>H	A:410	(-29.30, -74.66, -67.38)
2:206605339		H>Y	A:415	(-33.19, -85.37, -81.51)
2:206605351	rs146073574	A>T	A:419	(-30.51, -76.26, -80.62)
2:206605358		R>Q	A:421	(-34.55, -70.95, -83.19)
2:206605366		L>F	A:424	(-38.15, -63.93, -73.79)
2:206605378	rs139711818	R>W	A:428	(-40.09, -52.44, -68.99)
2:206607956	rs551278469	L>F	A:441	(-33.08, -49.15, -58.19)
2:206607965		L>V	A:444	(-34.16, -40.20, -57.20)
2:206607968	rs201900948	I>L	A:445	(-34.76, -42.11, -52.58)
2:206607984		I>T	A:450	(-33.16, -44.68, -46.22)
2:206607992		S>P	A:453	(-35.26, -49.56, -36.40)
2:206608017	rs530582033	S>I	A:461	(-24.92, -47.99, -45.62)
2:206608020		P>R	A:462	(-28.11, -46.29, -46.16)
2:206608023		S>N	A:463	(-27.17, -47.81, -49.96)
2:206608025		A>T	A:464	(-27.90, -51.56, -48.32)
2:206608031	COSM1217852 COSM1217853	R>C	A:466	(-30.56, -48.45, -52.42)
2:206608045		S>R	A:470	(-27.48, -53.66, -52.66)
2:206608046		R>C	A:471	(-24.31, -56.27, -54.14)
2:206608047	rs149849497	R>H	A:471	(-24.31, -56.27, -54.14)
2:206608050	rs200906927	S>L	A:472	(-26.21, -56.34, -48.81)
2:206608060		F>L	A:475	(-29.03, -57.57, -42.14)
2:206608061	rs546952277	P>S	A:476	(-31.58, -56.19, -37.97)
2:206608062		P>R	A:476	(-31.58, -56.19, -37.97)
2:206608065		R>Q	A:477	(-28.64, -54.99, -32.13)
2:206608085		G>S	A:484	(-43.69, -55.88, -35.17)
2:206608086	rs147580347	G>A	A:484	(-43.69, -55.88, -35.17)
2:206608103	rs375155400	V>I	A:490	(-38.84, -44.63, -47.22)
2:206608109		L>M	A:492	(-41.03, -40.67, -50.67)
2:206608121		K>Q	A:496	(-45.66, -39.39, -53.58)
2:206608125		T>I	A:497	(-49.96, -42.02, -54.90)
2:206608133	COSM269737 COSM3576611 COSM3576612	G>S	A:500	(-46.50, -50.35, -53.74)
2:206608151		A>T	A:506	(-30.12, -60.59, -48.59)
2:206608152		A>V	A:506	(-30.12, -60.59, -48.59)
2:206608154		R>C	A:507	(-24.95, -61.41, -51.15)
2:206608155	rs537993529	R>H	A:507	(-24.95, -61.41, -51.15)
2:206608190		A>T	A:519	(-31.86, -63.87, -45.74)
2:206608196		V>L	A:521	(-38.94, -61.33, -45.39)
2:206608200	COSM442161 COSM1482675	R>H	A:522	(-41.01, -66.81, -45.44)
2:206608217	rs373407554	Y>H	A:528	(-50.24, -45.41, -44.53)
2:206608229		G>S	A:532	(-43.92, -39.35, -38.82)
2:206608233		K>R	A:533	(-44.71, -38.90, -34.59)
2:206608241		E>Q	A:536	(-53.23, -45.58, -41.16)
2:206608242		E>G	A:536	(-53.23, -45.58, -41.16)
2:206608248		I>T	A:538	(-52.48, -51.62, -45.27)
2:206608251		Q>R	A:539	(-56.49, -52.58, -42.52)
2:206608266		Q>R	A:544	(-61.62, -55.44, -39.69)
2:206610485		M>L	A:553	(-39.88, -68.40, -51.74)
2:206610501		P>L	A:558	(-37.64, -60.01, -56.69)
2:206610510		R>Q	A:561	(-46.38, -58.43, -53.23)
2:206610513		R>K	A:562	(-49.37, -54.23, -57.38)
2:206610519	rs368539545	D>G	A:564	(-55.79, -50.34, -52.47)
2:206610526		I>M	A:566	(-52.13, -45.00, -50.09)
2:206610535		Q>H	A:569	(-43.55, -37.98, -47.42)
2:206610536		Y>H	A:570	(-42.48, -40.02, -44.25)
2:206610543	COSM442162 COSM1134140	R>Q	A:572	(-42.52, -47.39, -40.93)
2:206610570		A>V	A:581	(-30.63, -66.20, -40.80)
2:206610576		I>T	A:583	(-34.68, -59.77, -40.82)
2:206610579		G>A	A:584	(-33.52, -59.63, -44.80)
2:206610584	COSM2713322 COSM2713323 COSM3933513	R>W	A:586	(-32.15, -56.37, -51.20)
2:206610585	rs371257328	R>Q	A:586	(-32.15, -56.37, -51.20)
2:206610602		C>S	A:592	(-47.53, -41.55, -58.29)
2:206610608	rs145001167	W>R	A:594	(-51.48, -36.11, -54.37)

2QQK.A | NRP2.

2QQK.A | NRP2

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants