1X5Z.A | PTPRD

General Structure Information

PDB ID	1x5z
HGNC Gene Label(s)	PTPRD
Structure Name	solution structure of the fibronectin type-iii domain of human protein tyrosine phosphatase, receptor type, d isoform 4 variant
Resolution	-1.0Å
Reference	AUTH M.YONEYAMA,K.SAITO,N.TOCHIO,S.KOSHIBA,M.INOUE,AUTH 2 T.KIGAWA,S.YOKOYAMATITL SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-IIITITL 2 DOMAIN OF HUMAN PROTEIN TYROSINE PHOSPHATASE,TITL 3 RECEPTOR TYPE, D ISOFORM 4 VARIANTREF TO BE PUBLISHEDREFN

Variant Set Distributions

ExAC Variants

Number Of Residues	102
Number Of SNVs	42
Number Of Permutations	17069
Optimal Distance Threshold	7.0
K Statistic	0.046
p-value	0.079

COSMIC

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:8517874	COSM1110530 COSM1110531 COSM1598518 COSM1598517	D>G	A:8	(7.44, 2.92, 24.03)
9:8517872		I>V	A:9	(10.02, 2.47, 19.28)
9:8517869		Q>E	A:10	(9.02, 8.01, 20.09)
9:8517866		V>I	A:11	(5.83, 4.61, 15.87)
9:8517863		I>V	A:12	(8.77, 7.65, 12.39)
9:8517857		Q>E	A:14	(5.67, 10.06, 6.95)
9:8517854		T>A	A:15	(0.75, 11.35, 6.74)
9:8507429		G>R	A:19	(-4.60, 0.98, 3.21)
9:8507415		N>K	A:23	(-12.47, -9.08, 2.12)
9:8507386		S>I	A:33	(0.07, -24.63, -4.64)
9:8507380		L>W	A:35	(-5.17, -18.95, -4.78)
9:8507381		L>V	A:35	(-5.17, -18.95, -4.78)
9:8507374		S>C	A:37	(-8.33, -14.14, -1.81)
9:8507372		W>R	A:38	(-5.10, -9.59, -2.47)
9:8507362		P>Q	A:41	(-6.92, -0.43, -1.07)
9:8507359	rs371642520	R>H	A:42	(-9.62, 5.64, -1.50)
9:8507360		R>C	A:42	(-9.62, 5.64, -1.50)
9:8507348	rs200427689	I>V	A:46	(-1.13, -0.63, -5.52)
9:8507344	rs573381420	A>V	A:47	(3.97, -1.02, -6.32)
9:8507341		N>S	A:48	(4.54, -4.35, -5.08)
9:8507323		K>R	A:54	(6.61, -17.35, 10.12)
9:8507320		D>G	A:55	(8.36, -22.89, 8.24)
9:8507321		D>H	A:55	(8.36, -22.89, 8.24)
9:8507310		H>Q	A:58	(10.52, -22.26, 15.60)
9:8504405		Q>E	A:62	(11.56, -15.17, 3.84)
9:8504401	COSM1110524 COSM1110525 COSM1598522 COSM1598521 COSM3659000 COSM3219791	R>Q	A:63	(10.12, -9.55, 3.26)
9:8504402		R>G	A:63	(10.12, -9.55, 3.26)
9:8504398		I>N	A:64	(6.96, -13.67, -2.00)
9:8504392		I>T	A:66	(2.76, -10.53, -4.30)
9:8504393	rs368781521	I>L	A:66	(2.76, -10.53, -4.30)
9:8504386		P>L	A:68	(0.47, -4.55, -8.46)
9:8504387		P>A	A:68	(0.47, -4.55, -8.46)
9:8504384		G>R	A:69	(-3.54, -6.72, -7.67)
9:8504372		R>G	A:73	(-0.69, -19.69, -9.38)
9:8504363	COSM3927098 COSM456150 COSM456151 COSM3927101 COSM1134323 COSM3927097 COSM1134322 COSM3927096 COSM39	G>R	A:76	(6.46, -24.22, -3.89)
9:8504356	rs372682523	K>I	A:78	(7.73, -29.18, 1.89)
9:8504353		P>L	A:79	(3.35, -31.79, 1.36)
9:8504338	rs147427272	Y>C	A:84	(2.15, -18.87, 10.35)
9:8504334	rs149726933	F>L	A:85	(0.73, -17.46, 4.55)
9:8504333	COSM48722 COSM1463271 COSM1463270 COSM1463269	R>C	A:86	(2.13, -10.93, 8.60)
9:8504330		L>M	A:87	(-1.22, -9.39, 1.80)
9:8504320	rs150553394	R>H	A:90	(6.34, -2.77, -0.63)
9:8504321	rs200847027 COSM3996646 COSM3996649 COSM3996645 COSM3996644 COSM3996647 COSM3996648	R>C	A:90	(6.34, -2.77, -0.63)
9:8504315		P>S	A:92	(5.76, 4.01, -4.50)
9:8504306		L>V	A:95	(5.45, -0.81, 4.17)
9:8504297		S>P	A:98	(0.04, -5.59, 8.12)
9:8504290		A>V	A:100	(-4.80, -10.42, 9.94)
9:8504283	rs560653184	I>M	A:102	(-4.15, -15.34, 7.15)
9:8504284		I>T	A:102	(-4.15, -15.34, 7.15)
9:8504279		A>T	A:104	(-2.99, -22.01, 5.00)

1X5Z.A | PTPRD.

1X5Z.A | PTPRD

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
9:8507350	COSM1110527	T>I	A:45	(-1.24, 4.65, -7.29)
9:8504401	COSM1110525	R>Q	A:63	(10.12, -9.55, 3.26)
9:8504333	COSM1463270	R>S	A:86	(2.13, -10.93, 8.60)