General Structure Information
| PDB ID | 3ou5 |
| HGNC Gene Label(s) | SHMT2 |
| Structure Name | human mitochondrial serine hydroxymethyltransferase 2 |
| Resolution | 2.04Å |
| Reference | AUTH H.WU,A.DONG,H.ZENG,P.LOPPNAU,M.SUNDSTROM,C.H.ARROWSMITH,AUTH 2 A.M.EDWARDS,A.BOCHKAREV,A.N.PLOTNIKOV,AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC)TITL CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL SERINETITL 2 HYDROXYMETHYLTRANSFERASE 2REF TO BE PUBLISHEDREFN |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 422 |
| Number Of SNVs | 97 |
| Number Of Permutations | 57570 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.009 |
| p-value | 0.634 |
COSMIC
| Number Of Residues | 422 |
| Number Of SNVs | 4 |
| Number Of Permutations | 76 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.5 |
| p-value | 0.114 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 97 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.236 |
| p-value | 0.649 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:57624696 | rs183592454 | S>R | A:32 | (-10.58, 60.58, 45.00) |
| 12:57624703 | D>H | A:35 | (-8.05, 62.59, 47.95) | |
| 12:57624712 | P>S | A:38 | (-2.58, 58.31, 49.24) | |
| 12:57624735 | Q>H | A:45 | (1.65, 58.45, 40.01) | |
| 12:57624737 | R>K | A:46 | (5.60, 54.55, 40.74) | |
| 12:57624745 | D>H | A:49 | (7.14, 56.87, 35.12) | |
| 12:57624754 | rs568519647 | C>R | A:52 | (6.08, 56.34, 29.99) |
| 12:57624756 | rs141369249 | C>W | A:52 | (6.08, 56.34, 29.99) |
| 12:57624757 | rs373440935 | R>S | A:53 | (10.61, 54.85, 32.77) |
| 12:57625271 | C>Y | A:64 | (-5.70, 50.58, 27.08) | |
| 12:57625273 | S>C | A:65 | (-8.15, 53.05, 25.78) | |
| 12:57625283 | rs554585552 | A>V | A:68 | (-12.17, 51.07, 27.79) |
| 12:57625291 | rs373156028 COSM1363269 |
A>T | A:71 | (-16.28, 51.04, 31.01) |
| 12:57625304 | C>Y | A:75 | (-22.22, 51.35, 36.99) | |
| 12:57625539 | C>G | A:103 | (-20.68, 43.22, 22.13) | |
| 12:57625540 | C>Y | A:103 | (-20.68, 43.22, 22.13) | |
| 12:57625545 | rs375584473 | R>C | A:105 | (-25.12, 44.40, 17.84) |
| 12:57625546 | R>H | A:105 | (-25.12, 44.40, 17.84) | |
| 12:57625559 | E>D | A:109 | (-19.36, 45.85, 12.83) | |
| 12:57625570 | L>R | A:113 | (-18.79, 38.52, 10.31) | |
| 12:57625576 | P>L | A:115 | (-25.32, 37.61, 11.06) | |
| 12:57625611 | rs527594157 | G>R | A:127 | (-8.47, 33.61, 26.48) |
| 12:57625632 | rs143872444 | V>I | A:134 | (-13.56, 25.23, 22.04) |
| 12:57625656 | rs370853912 | H>Y | A:142 | (-9.89, 11.30, 24.10) |
| 12:57626071 | L>R | A:181 | (8.28, 25.38, 12.19) | |
| 12:57626248 | L>F | A:187 | (7.81, 28.71, 6.85) | |
| 12:57626261 | N>S | A:191 | (4.22, 18.24, 3.62) | |
| 12:57626262 | N>K | A:191 | (4.22, 18.24, 3.62) | |
| 12:57626269 | A>T | A:194 | (-0.80, 16.52, 5.87) | |
| 12:57626270 | A>V | A:194 | (-0.80, 16.52, 5.87) | |
| 12:57626282 | rs199498720 | R>Q | A:198 | (-3.02, 12.39, 5.06) |
| 12:57626290 | R>W | A:201 | (-7.22, 10.62, 10.53) | |
| 12:57626291 | R>Q | A:201 | (-7.22, 10.62, 10.53) | |
| 12:57626297 | rs184950916 | R>Q | A:203 | (-12.97, 15.95, 15.09) |
| 12:57626305 | I>V | A:206 | (-5.04, 24.76, 16.85) | |
| 12:57626329 | R>C | A:214 | (6.26, 35.59, 7.34) | |
| 12:57626330 | R>H | A:214 | (6.26, 35.59, 7.34) | |
| 12:57626345 | A>V | A:219 | (-6.51, 27.38, 2.98) | |
| 12:57626347 | rs143192247 | R>C | A:220 | (-1.57, 24.10, 2.52) |
| 12:57626348 | rs201088482 COSM247313 |
R>H | A:220 | (-1.57, 24.10, 2.52) |
| 12:57626495 | D>E | A:226 | (-12.09, 19.58, 4.16) | |
| 12:57626506 | A>G | A:230 | (-11.37, 18.30, 11.07) | |
| 12:57626531 | H>Q | A:238 | (-0.95, 37.26, 19.26) | |
| 12:57626566 | S>L | A:250 | (-9.36, 36.41, 7.26) | |
| 12:57626574 | rs148573932 | K>E | A:253 | (-12.60, 33.80, 4.14) |
| 12:57626580 | A>T | A:255 | (-12.71, 28.75, 9.86) | |
| 12:57626588 | I>M | A:257 | (-14.13, 27.92, 15.47) | |
| 12:57626589 | rs151127748 | V>I | A:258 | (-12.27, 32.26, 15.49) |
| 12:57626592 | T>A | A:259 | (-10.31, 32.27, 19.25) | |
| 12:57626617 | COSM1194251 | R>P | A:267 | (-5.39, 49.70, 20.74) |
| 12:57626623 | A>V | A:269 | (-9.26, 44.62, 27.68) | |
| 12:57626982 | R>W | A:277 | (-19.92, 29.02, 10.31) | |
| 12:57626989 | G>E | A:279 | (-26.23, 27.53, 9.71) | |
| 12:57627018 | rs530949491 | R>W | A:289 | (-31.40, 19.34, 2.66) |
| 12:57627019 | rs139092594 | R>Q | A:289 | (-31.40, 19.34, 2.66) |
| 12:57627046 | R>Q | A:298 | (-21.47, 21.65, 20.88) | |
| 12:57627060 | rs144005044 | V>L | A:303 | (-19.56, 28.96, 28.86) |
| 12:57627082 | G>V | A:310 | (-21.26, 35.59, 35.09) | |
| 12:57627109 | rs371269540 | V>A | A:319 | (-15.05, 44.40, 24.67) |
| 12:57627115 | V>A | A:321 | (-15.41, 50.37, 23.47) | |
| 12:57627355 | P>A | A:329 | (-10.80, 54.95, 9.83) | |
| 12:57627358 | rs371588002 | M>V | A:330 | (-8.84, 56.14, 13.01) |
| 12:57627359 | M>T | A:330 | (-8.84, 56.14, 13.01) | |
| 12:57627364 | R>W | A:332 | (-6.82, 50.03, 7.42) | |
| 12:57627365 | rs201473547 | R>Q | A:332 | (-6.82, 50.03, 7.42) |
| 12:57627369 | E>D | A:333 | (-4.22, 54.42, 8.99) | |
| 12:57627406 | A>T | A:346 | (13.61, 44.21, 10.03) | |
| 12:57627425 | R>Q | A:352 | (22.05, 47.44, 12.19) | |
| 12:57627431 | rs372801976 | Y>S | A:354 | (21.26, 41.55, 14.22) |
| 12:57627436 | L>M | A:356 | (15.49, 37.73, 10.76) | |
| 12:57627540 | D>H | A:362 | (4.51, 39.52, 6.30) | |
| 12:57627541 | D>G | A:362 | (4.51, 39.52, 6.30) | |
| 12:57627552 | rs576397341 | V>L | A:366 | (10.53, 40.50, 14.52) |
| 12:57627558 | V>M | A:368 | (16.03, 37.81, 16.37) | |
| 12:57627567 | R>W | A:371 | (21.36, 30.65, 17.13) | |
| 12:57627568 | R>Q | A:371 | (21.36, 30.65, 17.13) | |
| 12:57627576 | G>S | A:374 | (26.63, 34.79, 20.38) | |
| 12:57627589 | A>D | A:378 | (18.14, 35.09, 28.03) | |
| 12:57627591 | rs369332082 COSM4043820 COSM4043821 |
R>W | A:379 | (22.83, 35.34, 28.38) |
| 12:57627598 | E>G | A:381 | (15.08, 38.85, 28.19) | |
| 12:57627600 | rs145565217 | R>W | A:382 | (18.02, 41.02, 33.00) |
| 12:57627601 | rs543789322 | R>Q | A:382 | (18.02, 41.02, 33.00) |
| 12:57627615 | V>I | A:387 | (18.17, 49.33, 29.33) | |
| 12:57627623 | I>M | A:389 | (14.44, 47.62, 26.28) | |
| 12:57627625 | T>I | A:390 | (10.42, 45.20, 27.37) | |
| 12:57627633 | K>E | A:393 | (12.98, 34.19, 26.33) | |
| 12:57627651 | rs373701336 | D>N | A:399 | (16.83, 25.83, 19.91) |
| 12:57627655 | rs199818914 | R>Q | A:400 | (19.96, 21.44, 21.32) |
| 12:57627675 | COSM941999 COSM4043822 |
G>S | A:407 | (15.81, 34.27, 20.67) |
| 12:57627681 | R>W | A:409 | (8.37, 37.84, 20.88) | |
| 12:57627682 | R>Q | A:409 | (8.37, 37.84, 20.88) | |
| 12:57627788 | rs75878068 | A>T | A:412 | (5.13, 47.06, 16.87) |
| 12:57627789 | A>D | A:412 | (5.13, 47.06, 16.87) | |
| 12:57627804 | rs560987048 | S>F | A:417 | (0.09, 53.07, 20.18) |
| 12:57627815 | rs371444119 COSM192281 |
R>C | A:421 | (5.30, 57.03, 13.07) |
| 12:57627816 | rs189439132 | R>H | A:421 | (5.30, 57.03, 13.07) |
| 12:57627830 | rs143597171 | R>W | A:426 | (15.55, 52.25, 11.13) |
| 12:57627843 | D>G | A:430 | (20.42, 51.88, 17.03) | |
| 12:57627852 | D>V | A:433 | (23.14, 46.91, 18.58) | |
| 12:57627856 | E>D | A:434 | (24.07, 50.15, 22.43) | |
| 12:57627860 | rs202118297 | V>L | A:436 | (23.44, 42.86, 22.14) |
| 12:57627866 | I>V | A:438 | (26.61, 45.39, 26.93) | |
| 12:57627874 | L>F | A:440 | (28.37, 39.94, 23.32) | |
| 12:57628035 | rs376786689 | K>R | A:453 | (21.37, 37.02, 35.36) |
| 12:57628041 | F>S | A:455 | (29.33, 40.91, 35.70) | |
| 12:57628046 | rs143811737 | L>F | A:457 | (23.45, 43.95, 39.14) |
| 12:57628051 | rs369976295 | K>N | A:458 | (28.18, 43.87, 40.40) |
| 12:57628059 | rs182091061 | E>G | A:461 | (32.81, 48.73, 33.10) |
| 12:57628070 | COSM942001 COSM3376324 |
R>C | A:465 | (28.65, 49.84, 29.37) |
| 12:57628071 | rs536394351 COSM3812648 COSM4043825 COSM3812649 COSM4043826 |
R>H | A:465 | (28.65, 49.84, 29.37) |
| 12:57628080 | N>S | A:468 | (24.56, 55.80, 29.59) | |
| 12:57628092 | rs200906224 | R>Q | A:472 | (21.20, 56.93, 25.89) |
| 12:57628113 | A>V | A:479 | (8.52, 62.07, 24.25) | |
| 12:57628121 | M>V | A:482 | (0.75, 56.64, 27.01) | |
| 12:57628137 | E>G | A:487 | (-2.07, 61.38, 36.72) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 12:57625269 | COSM3359863 | F>L | A:63 | (0.24, 50.80, 25.83) |
| 12:57626237 | COSM3463729 | P>L | A:183 | (14.12, 24.33, 9.83) |
| 12:57627363 | COSM3734308 | F>L | A:331 | (-7.65, 50.04, 14.29) |
| 12:57627675 | COSM4043822 | G>S | A:407 | (15.81, 34.27, 20.67) |
| 12:57627816 | COSM147554 | R>H | A:421 | (5.30, 57.03, 13.07) |
| 12:57628070 | COSM3376324 | R>C | A:465 | (28.65, 49.84, 29.37) |