General Structure Information
| PDB ID | 1xnj |
| HGNC Gene Label(s) | PAPSS1 |
| Structure Name | aps complex of human paps synthetase 1 |
| Resolution | 1.98Å |
| Reference | AUTH S.HARJES,P.BAYER,A.J.SCHEIDIGTITL THE CRYSTAL STRUCTURE OF HUMAN PAPS SYNTHETASE 1 REVEALSTITL 2 ASYMMETRY IN SUBSTRATE BINDINGREF J.MOL.BIOL. V. 347 623 2005REFN ISSN 0022-2836PMID 15755455DOI 10.1016/J.JMB.2005.01.005 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 562 |
| Number Of SNVs | 123 |
| Number Of Permutations | 37445 |
| Optimal Distance Threshold | 19.0 |
| K Statistic | 0.152 |
| p-value | 0.608 |
COSMIC
| Number Of Residues | 562 |
| Number Of SNVs | 6 |
| Number Of Permutations | 2396 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.467 |
| p-value | 0.064 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 123 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.332 |
| p-value | 0.174 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:108622372 | V>M | A:44 | (30.67, 45.19, 51.75) | |
| 4:108622351 | COSM3380749 | R>C | A:51 | (38.62, 45.26, 52.85) |
| 4:108615109 | rs374094277 | V>I | A:77 | (34.98, 54.93, 45.79) |
| 4:108615105 | C>F | A:78 | (37.57, 54.86, 42.52) | |
| 4:108615102 | H>R | A:79 | (40.24, 52.07, 43.38) | |
| 4:108615103 | H>Y | A:79 | (40.24, 52.07, 43.38) | |
| 4:108615018 | E>G | A:107 | (36.71, 63.00, 77.18) | |
| 4:108615006 | R>Q | A:111 | (32.79, 57.74, 74.04) | |
| 4:108615003 | COSM1049869 | R>L | A:112 | (29.36, 60.34, 71.68) |
| 4:108614986 | K>E | A:118 | (33.54, 49.73, 66.79) | |
| 4:108614963 | L>F | A:125 | (32.94, 50.26, 55.92) | |
| 4:108614928 | Q>R | A:137 | (44.06, 59.35, 77.37) | |
| 4:108608327 | N>H | A:140 | (45.73, 56.06, 72.94) | |
| 4:108608318 | R>G | A:143 | (45.01, 52.64, 68.68) | |
| 4:108608312 | I>V | A:145 | (37.48, 51.09, 71.24) | |
| 4:108608302 | G>V | A:148 | (39.62, 44.97, 71.22) | |
| 4:108608272 | V>D | A:158 | (47.84, 65.83, 59.61) | |
| 4:108608264 | COSM1694793 | P>S | A:161 | (53.75, 73.64, 60.89) |
| 4:108603267 | E>D | A:191 | (46.71, 71.92, 74.78) | |
| 4:108603251 | A>T | A:197 | (53.32, 55.94, 67.39) | |
| 4:108603220 | C>Y | A:207 | (53.17, 67.23, 50.18) | |
| 4:108603221 | C>R | A:207 | (53.17, 67.23, 50.18) | |
| 4:108603217 | D>G | A:208 | (50.74, 66.57, 46.84) | |
| 4:108581225 | I>V | A:225 | (42.78, 47.14, 53.97) | |
| 4:108581195 | K>E | A:235 | (46.95, 29.81, 35.34) | |
| 4:108581179 | P>L | A:240 | (59.29, 27.29, 36.15) | |
| 4:108581180 | P>T | A:240 | (59.29, 27.29, 36.15) | |
| 4:108581159 | A>T | A:247 | (61.84, 19.90, 30.72) | |
| 4:108581140 | T>I | A:253 | (61.80, 11.35, 26.10) | |
| 4:108581128 | L>P | A:257 | (52.45, 17.11, 17.42) | |
| 4:108581123 | I>V | A:259 | (52.93, 22.93, 15.99) | |
| 4:108578160 | D>Y | A:263 | (49.10, 26.10, 16.46) | |
| 4:108578149 | W>C | A:266 | (45.61, 30.39, 19.91) | |
| 4:108578150 | W>L | A:266 | (45.61, 30.39, 19.91) | |
| 4:108578126 | W>L | A:274 | (46.94, 37.14, 27.52) | |
| 4:108578093 | R>K | A:285 | (33.32, 20.00, 31.22) | |
| 4:108578083 | L>F | A:288 | (30.94, 21.84, 25.19) | |
| 4:108578080 | rs370930280 | Q>H | A:289 | (31.58, 25.17, 29.35) |
| 4:108578069 | COSM1538872 | F>C | A:293 | (26.93, 27.91, 28.05) |
| 4:108576030 | rs376322060 | I>V | A:308 | (41.75, 27.85, 23.30) |
| 4:108576020 | T>I | A:311 | (44.11, 20.32, 15.80) | |
| 4:108576017 | rs372068591 | A>V | A:312 | (44.41, 16.36, 14.96) |
| 4:108576015 | rs141549597 | T>A | A:313 | (45.26, 13.95, 12.13) |
| 4:108576011 | rs368478142 | H>R | A:314 | (42.34, 9.30, 12.38) |
| 4:108576012 | rs200480398 | H>Y | A:314 | (42.34, 9.30, 12.38) |
| 4:108576009 | E>Q | A:315 | (46.57, 9.83, 10.69) | |
| 4:108575999 | E>G | A:318 | (45.62, 6.20, 15.20) | |
| 4:108575994 | L>V | A:320 | (49.63, 10.54, 20.15) | |
| 4:108575973 | A>T | A:327 | (55.74, 17.13, 22.32) | |
| 4:108575954 | rs377296602 COSM1219261 |
R>H | A:333 | (62.06, 25.15, 18.01) |
| 4:108575955 | rs35176475 | R>C | A:333 | (62.06, 25.15, 18.01) |
| 4:108575952 | R>C | A:334 | (60.87, 18.68, 21.41) | |
| 4:108575936 | rs570454399 | R>H | A:339 | (51.98, 16.02, 30.84) |
| 4:108575937 | rs148756122 | R>C | A:339 | (51.98, 16.02, 30.84) |
| 4:108575933 | N>S | A:340 | (47.20, 14.02, 31.05) | |
| 4:108575924 | F>C | A:343 | (42.63, 12.63, 21.83) | |
| 4:108575921 | F>S | A:344 | (37.79, 16.55, 21.87) | |
| 4:108575901 | R>C | A:351 | (34.78, 25.56, 15.85) | |
| 4:108575891 | R>I | A:354 | (27.21, 26.67, 18.03) | |
| 4:108575879 | T>M | A:358 | (28.90, 31.63, 9.55) | |
| 4:108575862 | P>A | A:364 | (39.52, 33.89, 6.66) | |
| 4:108574781 | M>T | A:368 | (42.58, 28.16, 8.83) | |
| 4:108574779 | V>L | A:369 | (39.05, 25.37, 10.88) | |
| 4:108574776 | M>L | A:370 | (37.31, 23.41, 7.52) | |
| 4:108574709 | G>V | A:392 | (61.64, 43.44, 16.12) | |
| 4:108574710 | rs200600274 | G>S | A:392 | (61.64, 43.44, 16.12) |
| 4:108574701 | COSM88491 | Q>E | A:395 | (60.36, 45.17, 21.64) |
| 4:108574694 | R>H | A:397 | (55.85, 40.53, 21.15) | |
| 4:108574695 | COSM1049862 | R>C | A:397 | (55.85, 40.53, 21.15) |
| 4:108574685 | P>L | A:400 | (50.01, 39.58, 31.35) | |
| 4:108574683 | T>A | A:401 | (52.92, 39.76, 34.50) | |
| 4:108574676 | COSM1196712 | L>R | A:403 | (51.24, 44.69, 30.95) |
| 4:108574652 | N>S | A:411 | (52.09, 55.02, 39.66) | |
| 4:108574649 | A>D | A:412 | (48.31, 53.65, 37.59) | |
| 4:108566203 | R>C | A:421 | (41.65, 44.55, 12.81) | |
| 4:108566166 | Q>R | A:433 | (40.99, 61.38, 23.14) | |
| 4:108566160 | COSM363382 | T>N | A:435 | (37.94, 57.05, 27.94) |
| 4:108566137 | G>S | A:443 | (38.95, 60.64, 39.87) | |
| 4:108566130 | rs369956234 | R>Q | A:445 | (43.12, 62.34, 39.91) |
| 4:108566127 | rs574210354 COSM4121203 |
R>H | A:446 | (47.64, 58.30, 38.59) |
| 4:108566128 | rs146467824 | R>C | A:446 | (47.64, 58.30, 38.59) |
| 4:108566095 | rs201166328 | W>R | A:457 | (45.76, 34.79, 10.88) |
| 4:108566082 | rs549473406 | D>G | A:461 | (43.36, 42.32, 3.37) |
| 4:108566083 | D>N | A:461 | (43.36, 42.32, 3.37) | |
| 4:108566074 | rs544807411 | P>S | A:464 | (51.15, 44.36, 8.03) |
| 4:108566062 | rs139739500 | R>C | A:468 | (49.56, 47.17, 12.59) |
| 4:108566029 | G>R | A:479 | (50.08, 63.54, 20.12) | |
| 4:108566016 | rs142297947 | P>L | A:483 | (53.67, 59.06, 24.94) |
| 4:108566010 | T>M | A:485 | (49.83, 58.27, 29.43) | |
| 4:108566001 | V>A | A:488 | (52.56, 50.25, 23.04) | |
| 4:108565989 | P>L | A:492 | (49.41, 37.43, 21.43) | |
| 4:108565986 | S>C | A:493 | (45.82, 36.50, 19.43) | |
| 4:108565963 | T>A | A:501 | (32.03, 35.83, 19.91) | |
| 4:108565960 | E>K | A:502 | (36.75, 37.86, 18.61) | |
| 4:108552997 | A>V | A:509 | (42.38, 39.37, 27.87) | |
| 4:108552994 | R>Q | A:510 | (42.88, 42.97, 26.55) | |
| 4:108552971 | Y>D | A:518 | (37.47, 46.68, 26.34) | |
| 4:108552968 | rs183618664 | I>V | A:519 | (37.47, 50.95, 24.71) |
| 4:108552958 | R>Q | A:522 | (32.66, 49.92, 14.26) | |
| 4:108552932 | rs35758879 | E>Q | A:531 | (29.91, 35.26, -0.23) |
| 4:108552901 | H>R | A:541 | (24.77, 42.94, 17.88) | |
| 4:108552896 | A>S | A:543 | (28.49, 46.39, 22.47) | |
| 4:108552890 | V>L | A:545 | (26.94, 41.32, 23.69) | |
| 4:108552883 | rs145511221 | T>M | A:547 | (27.48, 45.58, 27.90) |
| 4:108552872 | G>S | A:551 | (32.47, 37.09, 33.28) | |
| 4:108552854 | I>V | A:557 | (32.35, 47.72, 29.18) | |
| 4:108552851 | rs551936839 | V>I | A:558 | (33.53, 52.07, 27.62) |
| 4:108552848 | rs72673574 | P>S | A:559 | (30.30, 52.03, 25.39) |
| 4:108552841 | R>Q | A:561 | (27.36, 57.27, 18.96) | |
| 4:108552826 | N>S | A:566 | (32.59, 66.75, 10.61) | |
| 4:108552824 | rs376989490 | K>E | A:567 | (32.87, 67.28, 5.56) |
| 4:108552820 | rs141193464 | K>R | A:568 | (30.33, 71.58, 9.00) |
| 4:108552815 | K>E | A:570 | (37.30, 70.86, 9.55) | |
| 4:108552811 | R>H | A:571 | (36.02, 67.53, 15.04) | |
| 4:108552809 | M>V | A:572 | (37.05, 62.46, 13.56) | |
| 4:108552802 | Y>C | A:574 | (31.24, 60.57, 18.60) | |
| 4:108552796 | D>G | A:576 | (23.96, 62.95, 13.80) | |
| 4:108552787 | H>R | A:579 | (24.01, 66.83, 10.84) | |
| 4:108535541 | H>R | A:580 | (24.35, 61.26, 6.10) | |
| 4:108535533 | F>L | A:583 | (29.45, 63.06, 9.42) | |
| 4:108535511 | COSM1426271 | R>Q | A:590 | (38.85, 56.66, -0.13) |
| 4:108535506 | rs374190069 COSM447204 |
R>C | A:592 | (43.90, 50.46, -0.82) |
| 4:108535502 | K>R | A:593 | (41.30, 53.49, -3.77) | |
| 4:108535499 | L>R | A:594 | (43.41, 58.23, -1.20) | |
| 4:108535493 | rs370009530 | R>Q | A:596 | (46.61, 53.24, -6.10) |
| 4:108535490 | rs542008559 | E>G | A:597 | (44.82, 58.65, -6.55) |
| 4:108535478 | rs148229699 | P>R | A:601 | (43.47, 61.88, 4.06) |
| 4:108535476 | P>S | A:602 | (40.86, 64.51, 5.23) | |
| 4:108535464 | rs531796367 | M>V | A:606 | (45.58, 59.95, 9.92) |
| 4:108535454 | K>R | A:609 | (54.50, 62.14, 11.00) | |
| 4:108535443 | rs373727276 | V>M | A:613 | (53.77, 55.09, 7.50) |
| 4:108535427 | rs545915930 | Y>C | A:618 | (48.96, 51.50, 1.14) |
| 4:108535416 | rs142192388 | E>K | A:622 | (52.33, 48.94, -6.57) |
| 4:108535409 | A>V | A:624 | (54.75, 43.63, -5.59) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:108615079 | COSM1618240 | D>Y | A:87 | (33.11, 65.06, 59.45) |
| 4:108615003 | COSM1049869 | R>H | A:112 | (29.36, 60.34, 71.68) |
| 4:108614998 | COSM1671193 | A>T | A:114 | (35.35, 55.96, 68.38) |
| 4:108608287 | COSM1158882 | F>S | A:153 | (43.26, 52.91, 64.98) |
| 4:108603176 | COSM1618239 | E>K | A:222 | (52.10, 47.53, 53.94) |
| 4:108575925 | COSM307520 | F>V | A:343 | (42.63, 12.63, 21.83) |
| 4:108574727 | COSM1260892 | R>L | A:386 | (59.67, 33.91, 26.83) |