1BJ4.A | SHMT1

General Structure Information

PDB ID	1bj4
HGNC Gene Label(s)	SHMT1
Structure Name	recombinant serine hydroxymethyltransferase (human)
Resolution	2.65Å
Reference	AUTH S.B.RENWICK,K.SNELL,U.BAUMANNTITL THE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC SERINETITL 2 HYDROXYMETHYLTRANSFERASE: A TARGET FOR CANCER CHEMOTHERAPYREF STRUCTURE V. 6 1105 1998REFN ISSN 0969-2126PMID 9753690DOI 10.1016/S0969-2126(98)00112-9

Variant Set Distributions

ExAC Variants

Number Of Residues	470
Number Of SNVs	115
Number Of Permutations	32909
Optimal Distance Threshold	26.0
K Statistic	0.331
p-value	0.036

COSMIC

Number Of Residues	470
Number Of SNVs	6
Number Of Permutations	2956
Optimal Distance Threshold	18.0
K Statistic	0.267
p-value	0.555

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	115
Number Of COSMIC SNVs	4
Optimal Distance Threshold	35.0
K Statistic	-0.403
p-value	0.296

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:18259262		A>T	A:12	(78.87, 33.77, 224.28)
17:18259243		H>R	A:18	(74.83, 38.28, 215.98)
17:18259239		D>E	A:19	(78.92, 38.73, 215.47)
17:18259237		K>R	A:20	(78.79, 35.42, 212.04)
17:18259235		M>V	A:21	(74.28, 36.38, 211.11)
17:18259209	rs542325188	S>R	A:29	(73.10, 32.99, 204.74)
17:18257130		V>A	A:33	(68.27, 33.86, 197.59)
17:18257125		N>D	A:35	(70.52, 29.28, 194.04)
17:18257119		I>V	A:37	(70.67, 35.54, 192.16)
17:18257115		K>R	A:38	(73.85, 32.29, 190.13)
17:18257104	rs201557147	N>D	A:42	(71.77, 31.41, 183.21)
17:18257100		R>Q	A:43	(66.79, 34.84, 182.32)
17:18257101		R>W	A:43	(66.79, 34.84, 182.32)
17:18257073		A>D	A:52	(62.90, 48.69, 175.73)
17:18257053	rs570376791 COSM1381352	R>G	A:59	(81.98, 45.57, 188.72)
17:18257032	rs142011814	G>S	A:66	(76.45, 47.55, 198.93)
17:18257026		C>G	A:68	(77.78, 51.92, 203.98)
17:18257017		N>D	A:71	(73.29, 52.02, 207.04)
17:18257013	rs371956910	K>R	A:72	(72.83, 57.86, 207.40)
17:18257004		E>A	A:75	(64.95, 62.56, 206.68)
17:18256995	COSM3672376	P>L	A:78	(72.02, 69.21, 201.13)
17:18256986		R>K	A:81	(70.20, 66.79, 205.52)
17:18251744	rs373431106	G>R	A:85	(76.14, 63.18, 210.01)
17:18251731		I>T	A:89	(75.52, 61.67, 202.67)
17:18251732		I>V	A:89	(75.52, 61.67, 202.67)
17:18251667		C>W	A:110	(68.98, 77.96, 184.51)
17:18251660		V>F	A:113	(68.40, 68.28, 190.34)
17:18251650		Q>R	A:116	(65.90, 62.26, 197.20)
17:18251642	rs575084452	S>T	A:119	(61.68, 55.40, 190.77)
17:18250968		S>P	A:121	(56.71, 56.64, 189.20)
17:18250964		P>L	A:122	(58.07, 58.14, 192.27)
17:18250962		A>T	A:123	(59.11, 61.40, 190.13)
17:18250946	rs145196297	Y>C	A:128	(52.28, 64.86, 188.54)
17:18250934		V>A	A:132	(49.07, 70.01, 189.59)
17:18250919		R>H	A:137	(41.89, 69.69, 184.55)
17:18250920	rs375177539 COSM1225661	R>C	A:137	(41.89, 69.69, 184.55)
17:18250917		I>V	A:138	(47.31, 66.06, 184.01)
17:18250913		M>R	A:139	(46.81, 66.57, 178.88)
17:18250895		D>V	A:145	(48.42, 55.63, 171.81)
17:18250896		D>H	A:145	(48.42, 55.63, 171.81)
17:18250889	rs563467894 COSM293680	G>D	A:147	(51.95, 55.62, 177.30)
17:18250881		T>A	A:150	(52.64, 58.00, 185.36)
17:18250861	rs558723951	D>E	A:156	(33.77, 54.83, 181.54)
17:18250858	rs142211553	K>N	A:157	(33.76, 51.28, 184.87)
17:18250860		K>Q	A:157	(33.76, 51.28, 184.87)
17:18250833		F>I	A:166	(45.23, 61.24, 194.13)
17:18250823		S>F	A:169	(43.42, 62.82, 183.52)
17:18250821		M>V	A:170	(42.26, 64.47, 178.92)
17:18244115		T>A	A:178	(50.47, 58.54, 160.74)
17:18244102		N>S	A:182	(47.16, 64.69, 166.60)
17:18244075	rs144654081	R>H	A:191	(42.24, 75.67, 172.63)
17:18244076	rs148701087	R>C	A:191	(42.24, 75.67, 172.63)
17:18244073		L>F	A:192	(37.97, 72.50, 175.66)
17:18244063		P>L	A:195	(45.78, 71.95, 180.87)
17:18244060		K>T	A:196	(47.03, 73.60, 185.43)
17:18244057	rs73291881	L>P	A:197	(51.07, 69.43, 183.53)
17:18244049	rs149605287	A>T	A:200	(56.54, 65.10, 177.24)
17:18243555	rs532563885	S>P	A:206	(59.66, 55.64, 167.40)
17:18243534	rs115185998	R>W	A:213	(53.03, 72.40, 168.30)
17:18243528		R>W	A:215	(56.98, 75.93, 176.03)
17:18243524	rs78909145	K>R	A:216	(52.79, 77.05, 170.78)
17:18243525		K>E	A:216	(52.79, 77.05, 170.78)
17:18243511		E>D	A:220	(47.50, 78.72, 174.14)
17:18243506	rs376383952	G>E	A:222	(49.24, 78.04, 181.31)
17:18243500		Y>C	A:224	(53.83, 74.30, 184.80)
17:18243491		A>V	A:227	(59.38, 65.88, 180.43)
17:18243473		S>T	A:233	(67.90, 59.21, 179.21)
17:18243453	rs150889470	V>M	A:240	(71.67, 60.54, 169.76)
17:18243430		H>Q	A:247	(61.78, 73.48, 174.11)
17:18243422	rs545559384	V>A	A:250	(59.92, 69.94, 184.36)
17:18243383		R>Q	A:263	(65.33, 49.89, 188.77)
17:18243365		Y>C	A:269	(64.55, 71.97, 189.47)
17:18243360		K>E	A:271	(67.01, 77.66, 188.78)
17:18238983		K>T	A:274	(58.61, 82.63, 184.95)
17:18238980		S>N	A:275	(58.88, 86.68, 183.88)
17:18238968		K>T	A:279	(57.24, 98.70, 182.44)
17:18238948		Y>D	A:286	(61.07, 79.78, 186.99)
17:18238937		E>D	A:289	(64.44, 74.67, 193.84)
17:18238935	rs141973751	S>C	A:290	(60.59, 74.95, 196.73)
17:18238926		N>I	A:293	(62.68, 70.06, 196.84)
17:18238908	rs202224272	G>V	A:299	(55.74, 64.85, 201.58)
17:18238900		G>R	A:302	(61.83, 59.72, 203.32)
17:18238897		G>R	A:303	(64.56, 58.27, 203.40)
17:18238879		I>V	A:309	(72.03, 58.67, 195.47)
17:18236600	rs185437646	V>I	A:312	(72.79, 57.65, 190.05)
17:18236576	rs532183764	M>V	A:320	(79.69, 62.39, 181.18)
17:18236573	rs370650805	T>A	A:321	(81.95, 58.65, 178.71)
17:18236547		H>Q	A:329	(75.54, 57.29, 168.23)
17:18236548		H>L	A:329	(75.54, 57.29, 168.23)
17:18236540	rs137980761	V>M	A:332	(70.17, 54.30, 166.89)
17:18236516	rs7215148	E>Q	A:340	(66.54, 48.11, 157.37)
17:18236506	rs371534658	T>M	A:343	(60.79, 46.43, 156.48)
17:18236507		T>S	A:343	(60.79, 46.43, 156.48)
17:18236491	rs147504483	K>R	A:348	(53.38, 47.85, 159.44)
17:18236488		I>T	A:349	(57.56, 49.26, 161.31)
17:18236482		T>I	A:351	(56.37, 55.45, 161.86)
17:18233972		N>K	A:356	(64.45, 55.74, 169.05)
17:18233950		R>C	A:364	(47.49, 44.45, 162.02)
17:18233943	rs200618764	K>T	A:366	(53.32, 38.72, 158.63)
17:18233928		G>E	A:371	(50.35, 38.02, 172.33)
17:18233918		E>D	A:374	(54.52, 38.08, 174.38)
17:18233896		I>V	A:382	(63.14, 35.85, 172.15)
17:18233871		P>R	A:390	(48.09, 52.70, 165.88)
17:18233872		P>T	A:390	(48.09, 52.70, 165.88)
17:18232700		D>N	A:392	(44.33, 48.36, 167.83)
17:18232693	rs139056136	S>N	A:394	(41.14, 45.60, 171.45)
17:18232691		A>T	A:395	(43.58, 46.02, 174.40)
17:18232688	COSM460403	L>V	A:396	(42.20, 41.84, 175.14)
17:18232684	rs368256562 COSM1225662	R>Q	A:397	(43.49, 39.89, 169.45)
17:18232685	rs140862126	R>W	A:397	(43.49, 39.89, 169.45)
17:18232651		L>P	A:408	(71.29, 42.96, 173.02)
17:18232648	rs150725254	T>M	A:409	(73.87, 47.24, 172.35)
17:18232615	rs377430870	K>R	A:420	(71.64, 36.27, 163.54)
17:18232598		H>Y	A:426	(60.31, 35.36, 160.59)
17:18232200		T>I	A:439	(44.08, 26.27, 167.23)
17:18232201		T>S	A:439	(44.08, 26.27, 167.23)
17:18232179		K>R	A:446	(43.07, 29.12, 177.59)
17:18232153	rs546838005	D>Y	A:455	(53.71, 17.15, 173.26)
17:18232143		Q>L	A:458	(58.25, 19.59, 173.05)
17:18232140	rs151014481	A>V	A:459	(60.74, 20.30, 169.26)
17:18232138		A>T	A:460	(60.30, 23.43, 167.67)
17:18232135		V>M	A:461	(60.24, 25.48, 170.96)
17:18232122	rs375373531	R>Q	A:465	(65.08, 27.55, 174.57)
17:18232123	rs551074461	R>W	A:465	(65.08, 27.55, 174.57)
17:18232116		E>G	A:467	(69.75, 28.34, 166.94)
17:18232102		A>T	A:472	(73.69, 34.77, 173.44)
17:18232098		S>F	A:473	(76.12, 32.50, 175.00)
17:18232095		L>P	A:474	(78.58, 34.01, 171.64)
17:18232096	rs1979277	L>F	A:474	(78.58, 34.01, 171.64)

1BJ4.A | SHMT1.

1BJ4.A | SHMT1

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:18243507	COSM1381350	G>R	A:222	(49.24, 78.04, 181.31)
17:18236563	COSM1679638	F>C	A:324	(77.01, 56.44, 177.27)
17:18232688	COSM460403	L>V	A:396	(42.20, 41.84, 175.14)
17:18232670	COSM1381349	R>W	A:402	(58.23, 47.63, 173.56)
17:18232648	COSM1381348	T>M	A:409	(73.87, 47.24, 172.35)
17:18232096	COSM1381346	L>F	A:474	(78.58, 34.01, 171.64)