2JKV.A | PGD – ASTRID

2JKV.A | PGD

General Structure Information

PDB ID	2jkv
HGNC Gene Label(s)	PGD
Structure Name	structure of human phosphogluconate dehydrogenase in complex with nadph at 2.53a
Resolution	2.53Å
Reference	AUTH S.S.NG,F.VON DELFT,E.S.PILKA,K.L.KAVANAGH,M.A.MCDONOUGH,AUTH 2 P.SAVITSKY,C.H.ARROWSMITH,J.WEIGELT,A.EDWARDS,M.SUNDSTROM,AUTH 3 C.J.SCHOFIELD,U.OPPERMANNTITL STRUCTURE OF HUMAN PHOSPHOGLUCONATE DEHYDROGENASE INTITL 2 COMPLEX WITH NADPH AT 2.53AREF TO BE PUBLISHEDREFN

Variant Set Distributions

ExAC Variants

Number Of Residues	482
Number Of SNVs	120
Number Of Permutations	30462
Optimal Distance Threshold	13.0
K Statistic	0.069
p-value	0.43

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:10459178		A>T	A:2	(23.03, 42.48, -17.56)
1:10459182	rs200854760	Q>R	A:3	(25.54, 43.30, -20.37)
1:10459694		I>S	A:6	(24.05, 34.03, -24.77)
1:10459696		A>S	A:7	(26.99, 32.43, -23.21)
1:10459712		A>G	A:12	(36.96, 26.36, -31.59)
1:10459736		L>Q	A:20	(30.59, 35.34, -35.27)
1:10459739	rs374270785	N>S	A:21	(25.49, 33.23, -36.36)
1:10459741		M>V	A:22	(24.73, 34.32, -31.97)
1:10459747		D>Y	A:24	(25.76, 38.51, -37.48)
1:10459749		D>E	A:24	(25.76, 38.51, -37.48)
1:10459753	rs372034488	G>R	A:26	(22.03, 40.77, -32.41)
1:10460481	rs150401113	V>A	A:39	(38.96, 35.14, -24.83)
1:10460486		D>H	A:41	(43.46, 35.84, -28.73)
1:10460499	rs201008071	N>S	A:45	(41.67, 38.65, -33.96)
1:10460502		E>A	A:46	(38.53, 36.09, -34.98)
1:10460552		S>P	A:63	(27.75, 38.60, -14.25)
1:10460556	rs529358008	K>M	A:64	(28.70, 39.91, -18.36)
1:10460567	rs199971575	P>A	A:68	(16.70, 33.51, -17.87)
1:10460570	rs142109660	R>G	A:69	(21.58, 33.71, -15.36)
1:10460574		R>Q	A:70	(20.16, 32.55, -22.27)
1:10460579		I>F	A:72	(26.13, 27.64, -25.16)
1:10460583		L>P	A:73	(28.60, 24.14, -23.28)
1:10460609	rs147995269	D>H	A:82	(30.59, 16.91, -16.38)
1:10460612		D>Y	A:83	(34.48, 19.72, -15.36)
1:10463141		D>G	A:93	(20.03, 31.57, -9.97)
1:10463146	rs145784341	G>C	A:95	(16.12, 28.78, -14.24)
1:10463155		I>V	A:98	(23.17, 24.74, -19.02)
1:10463159		I>T	A:99	(22.74, 24.87, -23.87)
1:10464221		R>W	A:112	(25.08, 15.72, -18.06)
1:10464228		R>Q	A:114	(17.27, 12.22, -15.19)
1:10464266	rs141190039	G>R	A:127	(22.53, 19.35, -31.75)
1:10464281		E>Q	A:132	(33.46, 26.24, -40.46)
1:10464293		R>W	A:136	(29.43, 32.52, -39.38)
1:10464306	COSM221894	S>L	A:140	(20.93, 21.86, -37.80)
1:10468135		I>V	A:153	(16.19, 28.58, -26.37)
1:10468144		I>V	A:156	(18.56, 32.63, -30.05)
1:10468165		K>E	A:163	(16.32, 29.64, -42.25)
1:10468167		K>N	A:163	(16.32, 29.64, -42.25)
1:10468169		V>A	A:164	(14.23, 26.13, -45.70)
1:10468192		D>N	A:172	(11.67, 22.15, -33.51)
1:10471481		D>N	A:176	(12.89, 14.37, -22.60)
1:10471523		I>V	A:190	(23.07, 8.44, -41.74)
1:10471541		Q>E	A:196	(32.57, 4.13, -46.90)
1:10471570	rs149480647	M>I	A:205	(34.86, 5.83, -60.33)
1:10471577		V>M	A:208	(36.97, -0.63, -62.51)
1:10471586	rs199961549	M>V	A:211	(37.66, 7.63, -64.12)
1:10471590		A>V	A:212	(40.36, 10.84, -63.90)
1:10473124		F>L	A:220	(30.65, 12.46, -57.68)
1:10473129		D>G	A:222	(26.81, 15.41, -63.36)
1:10473135	rs200926428	N>S	A:224	(24.49, 17.09, -57.15)
1:10473144		E>G	A:227	(18.00, 10.94, -58.03)
1:10473164	rs377265796	E>Q	A:234	(28.09, 19.80, -53.20)
1:10473177		N>S	A:238	(34.29, 20.52, -54.76)
1:10473194		D>Y	A:244	(48.13, 21.99, -53.75)
1:10473200	rs41289075	D>N	A:246	(51.67, 21.97, -56.74)
1:10473204	rs200998486	G>D	A:247	(48.77, 21.93, -59.29)
1:10473219	rs202134777	P>L	A:252	(46.20, 12.38, -54.19)
1:10473222	rs375996998	K>R	A:253	(49.22, 15.09, -51.89)
1:10473233		S>G	A:257	(43.98, 7.13, -41.80)
1:10473236		A>T	A:258	(40.36, 7.37, -40.72)
1:10473240		G>E	A:259	(38.97, 9.23, -38.28)
1:10473246		K>R	A:261	(35.99, 12.81, -32.98)
1:10473255		G>E	A:264	(29.46, 6.09, -34.72)
1:10473263	rs573041776	T>S	A:267	(25.28, 4.57, -33.61)
1:10473266	rs11547610	A>T	A:268	(26.68, 0.78, -33.42)
1:10473275	rs143540325	A>T	A:271	(22.23, -1.15, -32.32)
1:10473281		E>Q	A:273	(23.11, -2.06, -26.52)
1:10473287	rs199582637	G>S	A:275	(18.48, -5.00, -31.99)
1:10473290	COSM1262002	V>I	A:276	(18.64, -2.43, -34.44)
1:10473296		V>I	A:278	(22.23, -0.50, -38.09)
1:10473305		I>V	A:281	(27.18, 2.35, -38.90)
1:10477046		E>K	A:283	(30.75, -2.55, -42.19)
1:10477055	rs373599760	F>L	A:286	(34.30, -2.24, -37.89)
1:10477086		E>G	A:296	(48.76, -4.28, -40.47)
1:10477091		I>V	A:298	(51.97, -1.48, -46.31)
1:10477122		Q>R	A:308	(45.83, -12.27, -60.52)
1:10477131		Q>L	A:311	(39.39, -6.96, -67.33)
1:10477140	rs201224678	G>D	A:314	(32.70, -2.53, -71.05)
1:10477149		K>T	A:317	(28.72, 6.09, -70.33)
1:10477150		K>N	A:317	(28.72, 6.09, -70.33)
1:10477170		R>Q	A:324	(23.27, 7.16, -60.45)
1:10477172		K>E	A:325	(21.17, 3.28, -60.44)
1:10477434		A>V	A:326	(24.15, 1.74, -56.22)
1:10477440	rs370439682	Y>C	A:328	(19.18, 6.69, -54.86)
1:10477456	COSM3470569	I>M	A:333	(19.48, 1.04, -46.96)
1:10477460	rs559849952	Y>H	A:335	(19.15, 8.40, -44.91)
1:10477463		A>T	A:336	(16.29, 3.25, -43.19)
1:10477499	rs367589034	E>K	A:348	(13.68, 1.15, -25.28)
1:10477509		W>S	A:351	(13.24, 9.49, -26.18)
1:10477511		T>P	A:352	(7.51, 11.93, -28.39)
1:10477518		N>S	A:354	(8.35, 14.23, -35.58)
1:10477532	rs181999445	A>T	A:359	(13.66, 15.27, -41.85)
1:10477540		M>I	A:361	(15.58, 19.40, -38.39)
1:10477556		I>V	A:367	(26.49, 17.07, -43.26)
1:10478884	rs371087028	V>L	A:371	(16.54, 15.99, -52.56)
1:10478897	rs201124379	K>R	A:375	(9.64, 12.42, -50.57)
1:10478900		I>T	A:376	(11.50, 10.91, -45.30)
1:10478911		F>L	A:380	(7.29, 8.94, -41.38)
1:10478924		P>L	A:384	(2.58, 7.81, -38.71)
1:10478926	rs376709444	E>Q	A:385	(3.06, 4.24, -36.92)
1:10478944		L>V	A:391	(7.52, -0.46, -46.69)
1:10478952	rs572852737	D>E	A:393	(5.50, 3.64, -52.74)
1:10478965		A>P	A:398	(13.99, 3.51, -56.15)
1:10478982		Q>H	A:403	(17.50, -4.51, -57.76)
1:10479474		D>N	A:404	(19.72, -4.86, -62.29)
1:10479478	COSM3470570	S>F	A:405	(22.54, -1.51, -61.37)
1:10479484		R>Q	A:407	(21.87, -7.16, -57.36)
1:10479487		R>Q	A:408	(24.90, -4.57, -63.30)
1:10479492		V>I	A:410	(28.49, -5.57, -56.20)
1:10479498		T>A	A:412	(32.03, -5.93, -61.08)
1:10479522	rs185532565	M>V	A:420	(32.33, -3.25, -51.95)
1:10479529		C>Y	A:422	(28.84, -0.47, -47.29)
1:10479553	rs372240950	Y>C	A:430	(16.42, -5.29, -50.60)
1:10479558	rs533529724	G>R	A:432	(16.78, -10.12, -46.03)
1:10479720		E>Q	A:456	(10.09, -21.01, -31.90)
1:10479735		P>S	A:461	(4.66, -19.19, -32.34)
1:10479736		P>Q	A:461	(4.66, -19.19, -32.34)
1:10479763		T>I	A:470	(22.26, -36.92, -30.32)
1:10479765		G>S	A:471	(19.91, -39.57, -28.69)
1:10479768		H>Y	A:472	(22.77, -40.56, -27.38)
1:10479769		H>L	A:472	(22.77, -40.56, -27.38)
1:10479775		G>D	A:474	(18.98, -35.05, -22.14)
1:10479778		T>N	A:475	(15.69, -33.97, -20.36)
1:10479780		V>M	A:476	(17.89, -30.86, -18.51)
1:10479795		Y>D	A:481	(18.15, -16.57, -21.59)