3FF3.A | NAALAD2

General Structure Information

PDB ID	3ff3
HGNC Gene Label(s)	NAALAD2
Structure Name	the high resolution structure of human glutamate carboxypeptidase iii (gcpiii/naaladase ii) in complex with l-glutamate
Resolution	1.37Å
Reference	AUTH K.HLOUCHOVA,C.BARINKA,J.KONVALINKA,J.LUBKOWSKITITL STRUCTURAL INSIGHT INTO THE EVOLUTIONARY AND PHARMACOLOGICTITL 2 HOMOLOGY OF GLUTAMATE CARBOXYPEPTIDASES II AND IIIREF FEBS J. V. 276 4448 2009REFN ISSN 1742-464XPMID 19678840DOI 10.1111/J.1742-4658.2009.07152.X

Variant Set Distributions

ExAC Variants

Number Of Residues	689
Number Of SNVs	163
Number Of Permutations	43316
Optimal Distance Threshold	13.0
K Statistic	0.064
p-value	0.344

COSMIC

Number Of Residues	689
Number Of SNVs	20
Number Of Permutations	18784
Optimal Distance Threshold	10.0
K Statistic	0.016
p-value	0.716

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	163
Number Of COSMIC SNVs	18
Optimal Distance Threshold	23.0
K Statistic	-0.057
p-value	0.291

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:89868787		R>Q	A:48	(22.26, 73.24, 12.32)
11:89868802	rs139378419	S>F	A:53	(25.56, 73.88, 21.35)
11:89868817	rs149998034	E>G	A:58	(27.95, 65.46, 32.42)
11:89868818		E>D	A:58	(27.95, 65.46, 32.42)
11:89868822		I>V	A:60	(24.74, 62.06, 27.71)
11:89868829		S>L	A:62	(23.81, 61.91, 34.02)
11:89868838		R>H	A:65	(24.57, 55.46, 36.45)
11:89880499		S>T	A:66	(19.81, 57.24, 35.57)
11:89880508	rs534567554	K>E	A:69	(21.36, 52.56, 39.03)
11:89880511		L>F	A:70	(18.10, 48.65, 38.15)
11:89880514		P>A	A:71	(17.47, 45.63, 35.61)
11:89880517	COSM3454253	H>Y	A:72	(16.19, 48.17, 31.34)
11:89880530	rs201217402	T>I	A:76	(9.60, 44.28, 33.54)
11:89880547		L>V	A:82	(12.52, 53.79, 32.19)
11:89880553	rs375279849	K>E	A:84	(6.32, 56.11, 34.42)
11:89880604	rs11018879	V>I	A:101	(1.36, 53.52, 23.56)
11:89880613	COSM1470531	D>H	A:104	(-1.03, 43.10, 24.89)
11:89880615		D>E	A:104	(-1.03, 43.10, 24.89)
11:89880649		N>D	A:116	(17.26, 26.48, 31.36)
11:89880659		S>L	A:119	(23.96, 17.75, 29.92)
11:89880667		D>N	A:122	(27.03, 8.00, 31.17)
11:89880677		E>G	A:125	(20.84, 7.70, 31.67)
11:89882181		K>R	A:130	(24.48, 20.61, 34.91)
11:89882211	rs374082301	G>D	A:140	(28.09, 46.73, 42.64)
11:89882262		Q>R	A:157	(9.33, 23.85, 25.85)
11:89882267	rs144605402	M>V	A:159	(13.91, 16.68, 27.22)
11:89883653		D>H	A:163	(25.32, 12.41, 18.98)
11:89883672		Y>C	A:169	(30.65, 31.36, 12.84)
11:89883677	rs147884512	R>C	A:171	(28.23, 30.80, 8.33)
11:89883689		F>V	A:175	(24.69, 24.04, 8.06)
11:89883708	rs76577722	E>G	A:181	(32.64, 20.08, 1.13)
11:89883711		M>R	A:182	(32.47, 17.99, 5.77)
11:89883714		G>D	A:183	(29.76, 14.17, 5.39)
11:89883726	rs77745866	T>I	A:187	(19.54, 14.49, 10.84)
11:89883753		G>E	A:196	(28.48, 35.31, 14.92)
11:89885466		V>I	A:204	(18.01, 28.49, 14.75)
11:89885467	rs73543373	V>A	A:204	(18.01, 28.49, 14.75)
11:89885479	rs563183977	M>T	A:208	(15.23, 24.15, 12.06)
11:89885514		D>H	A:220	(34.81, 31.57, 20.63)
11:89885521		A>D	A:222	(37.65, 34.52, 18.51)
11:89885527		Y>C	A:224	(32.18, 37.57, 21.06)
11:89885560		G>E	A:235	(38.20, 45.03, 31.31)
11:89885564		W>C	A:236	(37.33, 46.07, 25.99)
11:89885565		N>Y	A:237	(37.21, 41.27, 27.12)
11:89885578		T>N	A:241	(31.30, 33.04, 33.20)
11:89885593	rs540889664 COSM3454257	G>V	A:246	(18.55, 36.34, 22.66)
11:89885614		G>D	A:253	(8.75, 41.82, 10.06)
11:89891318	rs200875869 COSM369830	T>A	A:268	(-6.62, 41.79, 18.46)
11:89891343		G>V	A:276	(3.62, 31.73, 15.47)
11:89891354	rs200163147	P>S	A:280	(11.54, 28.33, 17.15)
11:89891358	COSM3870383	R>Q	A:281	(8.75, 25.25, 16.29)
11:89891363	COSM1676369	P>S	A:283	(15.61, 23.35, 21.56)
11:89891366	rs201924685	V>I	A:284	(17.87, 27.45, 21.69)
11:89891369		H>Y	A:285	(20.62, 27.70, 26.38)
11:89891382		Y>C	A:289	(34.88, 31.50, 27.19)
11:89891391		A>V	A:292	(32.12, 25.15, 25.58)
11:89891396	rs199949872	I>L	A:294	(33.91, 21.03, 28.87)
11:89891399	rs370946523	L>I	A:295	(30.55, 20.56, 25.48)
11:89891405	rs138601382	R>C	A:297	(38.00, 19.27, 26.21)
11:89891406	COSM138008	R>L	A:297	(38.00, 19.27, 26.21)
11:89892418		G>V	A:301	(36.02, 12.66, 14.07)
11:89892423		A>S	A:303	(38.90, 17.33, 11.37)
11:89892432	COSM3454264	D>N	A:306	(39.38, 25.16, 7.41)
11:89892437		K>N	A:307	(43.09, 27.97, 9.74)
11:89892440	rs571722338	S>R	A:308	(37.62, 28.89, 9.21)
11:89892469		S>N	A:318	(36.63, 18.29, 15.96)
11:89892474	COSM1739830	G>R	A:320	(31.85, 15.06, 14.62)
11:89896121		V>I	A:332	(24.51, 16.03, 24.71)
11:89896125		R>T	A:333	(20.70, 14.78, 28.40)
11:89896155		T>I	A:343	(3.32, 40.65, 28.07)
11:89896167		N>S	A:347	(5.66, 52.46, 23.26)
11:89896169		V>I	A:348	(7.03, 56.75, 25.18)
11:89896178		T>A	A:351	(4.63, 65.54, 20.00)
11:89896181		I>V	A:352	(7.31, 69.06, 18.78)
11:89896182		I>T	A:352	(7.31, 69.06, 18.78)
11:89896190		S>P	A:355	(4.01, 75.74, 12.32)
11:89896202		D>H	A:359	(0.48, 67.04, 7.60)
11:89896486		V>I	A:362	(10.43, 63.67, 11.63)
11:89896498		G>S	A:366	(14.16, 54.26, 20.57)
11:89896504	COSM198041 COSM1510108	R>W	A:368	(12.42, 51.52, 27.09)
11:89896505	rs148133568	R>Q	A:368	(12.42, 51.52, 27.09)
11:89896511		S>F	A:370	(17.31, 45.61, 28.39)
11:89896537	rs80078229	T>A	A:379	(20.77, 52.85, 27.71)
11:89896538	rs557102428	T>I	A:379	(20.77, 52.85, 27.71)
11:89896546		V>I	A:382	(17.99, 56.17, 26.12)
11:89896549	rs142435532	A>P	A:383	(20.63, 59.19, 26.75)
11:89896567	rs546019162	A>S	A:389	(14.65, 66.46, 23.78)
11:89896570	rs147308857	R>W	A:390	(17.95, 69.45, 27.17)
11:89896571	rs372632658	R>Q	A:390	(17.95, 69.45, 27.17)
11:89896584		K>N	A:394	(16.68, 75.50, 25.83)
11:89896712	rs140795220	P>R	A:402	(8.73, 73.02, 14.34)
11:89896733		A>V	A:409	(10.06, 57.27, 20.38)
11:89896738	rs143159839	W>G	A:411	(9.90, 52.55, 19.78)
11:89896744		A>T	A:413	(10.34, 44.94, 22.87)
11:89896747		E>Q	A:414	(14.47, 45.62, 20.10)
11:89896760		L>R	A:418	(11.72, 44.86, 16.26)
11:89896763		L>P	A:419	(7.72, 43.63, 19.23)
11:89896777	rs149945009	W>R	A:424	(3.39, 53.89, 16.51)
11:89896783	COSM3935664	E>Q	A:426	(1.14, 47.09, 12.50)
11:89902097		E>Q	A:427	(-2.02, 51.54, 15.75)
11:89902107	rs542826169	K>R	A:430	(-3.24, 53.96, 7.03)
11:89902143		S>L	A:442	(18.23, 56.23, 19.22)
11:89902146		D>G	A:443	(19.96, 51.84, 19.42)
11:89902151		S>P	A:445	(25.90, 55.45, 20.82)
11:89902154	rs10830430	I>V	A:446	(29.37, 53.75, 22.28)
11:89903254	rs544891300	V>I	A:454	(26.25, 55.90, 8.71)
11:89903260	rs200506248	C>R	A:456	(21.38, 55.50, 4.97)
11:89903267		P>R	A:458	(20.37, 56.81, -0.77)
11:89903273		L>P	A:460	(19.60, 60.82, 4.05)
11:89903287	rs200072686	Y>D	A:465	(28.39, 62.84, 3.49)
11:89903302		E>Q	A:470	(28.20, 71.92, 10.42)
11:89907044		L>W	A:488	(37.21, 60.75, 5.16)
11:89907059		S>L	A:493	(34.22, 55.01, 0.24)
11:89909145		N>S	A:503	(26.63, 51.30, 5.42)
11:89909174	COSM198043	A>T	A:513	(9.05, 48.85, 9.59)
11:89909181	rs145386660	F>Y	A:515	(13.52, 51.42, 4.67)
11:89909193	COSM3454272	G>A	A:519	(9.03, 53.63, 2.95)
11:89909210		A>S	A:525	(24.24, 56.75, 13.86)
11:89909213		R>C	A:526	(26.54, 52.61, 15.50)
11:89909214		R>H	A:526	(26.54, 52.61, 15.50)
11:89911027		D>N	A:534	(38.99, 45.74, 15.52)
11:89911028		D>V	A:534	(38.99, 45.74, 15.52)
11:89911030		K>E	A:535	(38.77, 41.32, 13.09)
11:89911036		S>G	A:537	(31.75, 40.17, 16.78)
11:89911042		Y>H	A:539	(29.34, 45.03, 22.18)
11:89911057		T>A	A:544	(26.26, 40.45, 28.81)
11:89911069	rs576502653	T>A	A:548	(28.15, 48.35, 32.94)
11:89911082		V>A	A:552	(30.80, 53.13, 28.98)
11:89911112		K>R	A:562	(33.41, 59.65, 21.24)
11:89911117		L>V	A:564	(28.06, 64.87, 22.30)
11:89911118	rs140733929	L>R	A:564	(28.06, 64.87, 22.30)
11:89911148		V>A	A:574	(15.53, 65.60, 13.25)
11:89911160		V>A	A:578	(11.46, 69.17, 10.80)
11:89911162		D>H	A:579	(12.75, 73.54, 10.09)
11:89911191		Q>H	A:588	(20.97, 62.94, -8.94)
11:89911196	rs201787529	Y>C	A:590	(17.95, 55.90, -4.34)
11:89911198		A>T	A:591	(20.57, 56.96, -9.24)
11:89911216		Y>D	A:597	(22.63, 48.92, -5.60)
11:89911217		Y>S	A:597	(22.63, 48.92, -5.60)
11:89911226		S>N	A:600	(26.33, 44.08, -8.52)
11:89911228		I>V	A:601	(22.76, 41.50, -9.58)
11:89911231	rs139287840	Y>H	A:602	(25.26, 41.66, -15.46)
11:89911240		S>P	A:605	(25.01, 36.66, -13.51)
11:89911250		H>L	A:608	(24.98, 31.52, -13.62)
11:89911259	rs189428951	Q>L	A:611	(22.69, 28.72, -17.78)
11:89911267		D>N	A:614	(20.04, 28.22, -22.45)
11:89911276		V>L	A:617	(17.53, 35.43, -18.61)
11:89911282	rs143067326	F>L	A:619	(19.78, 41.37, -15.90)
11:89914790	COSM1605341	S>T	A:621	(14.69, 45.69, -17.99)
11:89914823		A>S	A:632	(14.08, 61.66, -13.71)
11:89914826		A>S	A:633	(16.41, 62.66, -11.19)
11:89914838		H>Y	A:637	(17.08, 67.61, -8.24)
11:89914845		R>Q	A:639	(11.54, 70.07, -12.41)
11:89914851	rs141848412	I>T	A:641	(16.74, 74.82, -8.86)
11:89916104		M>T	A:654	(8.42, 69.60, -5.69)
11:89916107		N>S	A:655	(8.22, 68.68, -0.48)
11:89916121		L>I	A:660	(5.88, 59.92, -1.84)
11:89916130		R>G	A:663	(6.71, 56.05, 0.60)
11:89916146		P>L	A:668	(1.99, 45.41, -1.92)
11:89924728		H>R	A:679	(12.29, 48.44, -0.42)
11:89924733		I>V	A:681	(15.92, 48.34, -3.86)
11:89924752	rs563266116	H>R	A:687	(21.47, 34.05, 4.06)
11:89924754		N>D	A:688	(22.46, 38.29, 8.29)
11:89924755		N>S	A:688	(22.46, 38.29, 8.29)
11:89924781		G>R	A:697	(14.75, 38.99, -5.39)
11:89924788	rs373596183	Y>C	A:699	(21.23, 37.39, -3.60)
11:89924796		I>V	A:702	(20.77, 33.72, -8.53)
11:89924801		F>L	A:703	(21.93, 31.70, -3.02)
11:89924806	rs146722371	I>T	A:705	(20.39, 28.56, -9.38)
11:89924817		A>T	A:709	(15.84, 20.64, -9.00)
11:89924826		R>C	A:712	(12.97, 24.35, -17.95)
11:89924854		H>R	A:721	(11.78, 38.47, -8.75)
11:89924866		A>E	A:725	(12.67, 45.64, -10.51)
11:89924874		T>A	A:728	(9.59, 49.24, -9.08)
11:89924889		A>T	A:733	(10.43, 57.63, -12.18)
11:89924890		A>V	A:733	(10.43, 57.63, -12.18)
11:89924892		G>R	A:734	(7.16, 58.67, -12.47)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:89868837	COSM932955	R>C	A:65	(24.57, 55.46, 36.45)
11:89880527	COSM226266	G>E	A:75	(7.66, 43.50, 30.88)
11:89880599	COSM1258658	K>T	A:99	(0.78, 60.26, 25.22)
11:89883650	COSM3454255	G>R	A:162	(22.61, 13.30, 21.61)
11:89883723	COSM545721	C>S	A:186	(22.89, 17.35, 11.26)
11:89885520	COSM3703734	A>T	A:222	(37.65, 34.52, 18.51)
11:89891342	COSM4560001	G>R	A:276	(3.62, 31.73, 15.47)
11:89891358	COSM3870383	R>Q	A:281	(8.75, 25.25, 16.29)
11:89891367	COSM3810621	V>A	A:284	(17.87, 27.45, 21.69)
11:89891372	COSM3454263	P>S	A:286	(22.83, 30.37, 25.84)
11:89892456	COSM84103	N>D	A:314	(43.00, 24.19, 24.42)
11:89892490	COSM4563457	G>E	A:325	(38.70, 10.07, 25.12)
11:89902152	COSM2150136	S>C	A:445	(25.90, 55.45, 20.82)
11:89911121	COSM932962	S>F	A:565	(28.91, 63.20, 18.33)
11:89911136	COSM3454274	R>Q	A:570	(21.31, 60.09, 16.68)
11:89911166	COSM1676370	S>Y	A:580	(13.77, 72.41, 5.86)
11:89911178	COSM3454275	P>L	A:584	(16.75, 67.49, 2.97)
11:89911237	COSM932964	L>I	A:604	(26.43, 37.90, -8.81)
11:89914790	COSM1605341	S>P	A:621	(14.69, 45.69, -17.99)
11:89916133	COSM430017	A>T	A:664	(7.80, 53.58, -4.84)
11:89924775	COSM1605342	F>L	A:695	(18.09, 44.77, -6.79)
11:89924790	COSM198049	D>N	A:700	(17.05, 35.33, -2.79)
11:89924849	COSM932967	K>N	A:719	(12.56, 35.80, -16.30)

3FF3.A | NAALAD2.

3FF3.A | NAALAD2

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