General Structure Information
| PDB ID | 3ctz |
| HGNC Gene Label(s) | XPNPEP1 |
| Structure Name | structure of human cytosolic x-prolyl aminopeptidase |
| Resolution | 1.6Å |
| Reference | AUTH X.LI,Z.LOU,X.LI,W.ZHOU,M.MA,Y.CAO,Y.GENG,M.BARTLAM,AUTH 2 X.C.ZHANG,Z.RAOTITL STRUCTURE OF HUMAN CYTOSOLIC X-PROLYL AMINOPEPTIDASE: ATITL 2 DOUBLE MN(II)-DEPENDENT DIMERIC ENZYME WITH A NOVELTITL 3 THREE-DOMAIN SUBUNITREF J.BIOL.CHEM. V. 283 22858 2008REFN ISSN 0021-9258PMID 18515364DOI 10.1074/JBC.M710274200 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 617 |
| Number Of SNVs | 117 |
| Number Of Permutations | 53029 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | 0.036 |
| p-value | 0.187 |
COSMIC
| Number Of Residues | 617 |
| Number Of SNVs | 5 |
| Number Of Permutations | 748 |
| Optimal Distance Threshold | 28.0 |
| K Statistic | 0.5 |
| p-value | 0.766 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 117 |
| Number Of COSMIC SNVs | 4 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | -0.184 |
| p-value | 0.729 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:111667556 | K>Q | A:4 | (25.72, 44.48, 74.25) | |
| 10:111667552 | V>A | A:5 | (29.31, 41.92, 75.05) | |
| 10:111667546 | S>L | A:7 | (29.71, 36.86, 72.14) | |
| 10:111667534 | rs373235364 | R>Q | A:11 | (26.91, 30.02, 72.65) |
| 10:111667535 | rs139653703 | R>W | A:11 | (26.91, 30.02, 72.65) |
| 10:111667513 | R>K | A:18 | (21.74, 23.21, 64.90) | |
| 10:111667510 | rs115088881 | N>S | A:19 | (16.83, 23.00, 69.67) |
| 10:111667502 | Y>D | A:22 | (13.21, 25.60, 69.78) | |
| 10:111667495 | rs186071811 | T>S | A:24 | (12.46, 20.06, 62.29) |
| 10:111667489 | COSM375379 | P>L | A:26 | (18.97, 22.41, 61.54) |
| 10:111667480 | rs532031977 | A>G | A:29 | (19.77, 31.44, 59.18) |
| 10:111667465 | S>L | A:34 | (12.33, 45.82, 64.21) | |
| 10:111667462 | rs548510533 | G>A | A:35 | (8.95, 44.23, 64.52) |
| 10:111667453 | H>L | A:38 | (-0.04, 43.91, 66.04) | |
| 10:111652821 | A>S | A:44 | (7.67, 47.02, 72.98) | |
| 10:111651555 | rs139006104 | A>T | A:71 | (24.16, 41.23, 60.11) |
| 10:111651536 | R>H | A:77 | (17.62, 57.33, 61.07) | |
| 10:111651518 | A>D | A:83 | (29.00, 51.04, 65.12) | |
| 10:111651488 | M>K | A:93 | (25.03, 45.90, 56.15) | |
| 10:111651482 | rs374096637 | M>T | A:95 | (20.08, 50.75, 54.33) |
| 10:111648346 | rs138153964 | K>N | A:98 | (26.31, 52.79, 46.21) |
| 10:111648336 | T>A | A:102 | (20.28, 42.79, 49.48) | |
| 10:111648322 | W>C | A:106 | (24.76, 38.38, 53.79) | |
| 10:111648267 | P>S | A:125 | (5.04, 41.10, 56.24) | |
| 10:111648261 | D>N | A:127 | (4.90, 41.75, 51.76) | |
| 10:111647948 | Y>H | A:128 | (10.63, 40.13, 54.29) | |
| 10:111647912 | G>S | A:140 | (18.33, 26.29, 47.11) | |
| 10:111647883 | N>K | A:149 | (11.19, 33.97, 69.09) | |
| 10:111647863 | T>I | A:156 | (16.55, 35.42, 80.91) | |
| 10:111647857 | rs201637073 COSM914695 COSM1152137 |
R>H | A:158 | (10.78, 39.03, 76.92) |
| 10:111647858 | R>C | A:158 | (10.78, 39.03, 76.92) | |
| 10:111647848 | R>H | A:161 | (3.56, 42.03, 75.63) | |
| 10:111647849 | rs368651568 | R>C | A:161 | (3.56, 42.03, 75.63) |
| 10:111647839 | rs370932957 | K>R | A:164 | (-0.96, 49.30, 80.84) |
| 10:111647831 | L>F | A:167 | (-10.39, 54.42, 78.27) | |
| 10:111647821 | COSM201213 | G>A | A:170 | (-18.54, 57.80, 74.34) |
| 10:111646097 | I>F | A:176 | (-21.10, 55.55, 66.13) | |
| 10:111646091 | W>R | A:178 | (-20.01, 47.76, 70.23) | |
| 10:111646084 | rs377362084 | D>G | A:180 | (-24.05, 50.99, 65.08) |
| 10:111646079 | rs150417519 | V>I | A:182 | (-20.20, 45.76, 63.98) |
| 10:111646072 | COSM136798 | D>A | A:184 | (-21.91, 49.60, 59.47) |
| 10:111646061 | COSM1504037 COSM1504036 |
K>E | A:188 | (-19.26, 47.00, 54.04) |
| 10:111646043 | rs560427557 | V>I | A:194 | (-16.90, 38.12, 53.72) |
| 10:111646038 | rs150580047 | M>I | A:195 | (-18.35, 34.77, 56.10) |
| 10:111646031 | rs530030165 | V>L | A:198 | (-8.96, 39.25, 60.67) |
| 10:111643847 | rs141671804 | I>V | A:227 | (-12.28, 37.43, 64.55) |
| 10:111643843 | I>T | A:228 | (-15.67, 40.43, 62.99) | |
| 10:111643840 | rs138082398 | G>A | A:229 | (-18.73, 38.04, 62.13) |
| 10:111643831 | T>M | A:232 | (-19.86, 36.03, 65.89) | |
| 10:111643829 | I>V | A:233 | (-17.86, 39.40, 68.13) | |
| 10:111643826 | M>L | A:234 | (-13.79, 36.31, 68.25) | |
| 10:111642399 | L>I | A:235 | (-11.73, 40.45, 71.84) | |
| 10:111642392 | I>T | A:237 | (-7.74, 40.83, 75.35) | |
| 10:111642375 | D>N | A:243 | (-13.13, 41.98, 84.09) | |
| 10:111642371 | rs368063298 | A>V | A:244 | (-13.72, 46.54, 84.37) |
| 10:111642372 | rs571518575 | A>T | A:244 | (-13.72, 46.54, 84.37) |
| 10:111642330 | E>Q | A:258 | (-28.88, 41.20, 70.56) | |
| 10:111642326 | rs182746342 | A>V | A:259 | (-26.13, 36.92, 69.85) |
| 10:111642302 | P>L | A:267 | (-6.95, 34.09, 74.93) | |
| 10:111642282 | E>K | A:274 | (-9.86, 30.03, 67.66) | |
| 10:111642258 | L>V | A:282 | (-14.38, 27.76, 55.41) | |
| 10:111642251 | P>L | A:284 | (-16.25, 26.39, 48.97) | |
| 10:111642240 | V>M | A:288 | (-11.31, 35.48, 55.24) | |
| 10:111642210 | V>M | A:298 | (-2.48, 35.76, 60.34) | |
| 10:111642204 | COSM3434072 COSM3434071 |
E>K | A:300 | (-0.36, 31.09, 55.19) |
| 10:111640683 | rs535955770 | R>C | A:307 | (-5.54, 34.10, 51.59) |
| 10:111640676 | C>Y | A:309 | (-6.27, 40.31, 50.61) | |
| 10:111640670 | P>L | A:311 | (-5.25, 47.33, 50.67) | |
| 10:111640656 | C>S | A:316 | (-9.25, 52.44, 57.44) | |
| 10:111640643 | A>G | A:320 | (-11.01, 58.59, 57.92) | |
| 10:111640641 | rs369826207 | V>M | A:321 | (-14.52, 60.06, 57.85) |
| 10:111640607 | R>Q | A:332 | (-13.27, 69.59, 72.37) | |
| 10:111640608 | rs565503742 | R>W | A:332 | (-13.27, 69.59, 72.37) |
| 10:111639996 | I>V | A:335 | (-8.95, 75.17, 71.78) | |
| 10:111639978 | L>V | A:341 | (1.58, 76.31, 72.67) | |
| 10:111639975 | C>S | A:342 | (0.25, 80.65, 74.31) | |
| 10:111639958 | W>C | A:347 | (9.21, 79.82, 79.57) | |
| 10:111639948 | E>K | A:351 | (12.91, 82.95, 80.60) | |
| 10:111637807 | rs369697114 | G>S | A:355 | (20.30, 81.66, 79.07) |
| 10:111637770 | E>G | A:367 | (5.04, 67.63, 79.09) | |
| 10:111637768 | E>K | A:368 | (4.74, 72.26, 82.73) | |
| 10:111637578 | rs149021633 | T>M | A:387 | (18.57, 75.49, 68.26) |
| 10:111637567 | G>S | A:391 | (16.92, 71.74, 62.68) | |
| 10:111637563 | A>V | A:392 | (18.32, 70.42, 59.88) | |
| 10:111637564 | A>T | A:392 | (18.32, 70.42, 59.88) | |
| 10:111637551 | rs374290930 | Y>C | A:396 | (17.96, 65.77, 67.36) |
| 10:111637548 | A>V | A:397 | (16.55, 63.28, 69.39) | |
| 10:111637549 | A>T | A:397 | (16.55, 63.28, 69.39) | |
| 10:111635352 | rs61736592 | V>G | A:399 | (21.29, 63.59, 73.69) |
| 10:111635343 | T>M | A:402 | (23.85, 67.28, 71.96) | |
| 10:111635338 | R>G | A:404 | (22.47, 73.76, 70.73) | |
| 10:111635320 | E>K | A:410 | (20.27, 79.88, 66.93) | |
| 10:111635301 | S>L | A:416 | (4.43, 69.42, 69.53) | |
| 10:111633175 | T>A | A:425 | (-2.35, 67.40, 68.65) | |
| 10:111633165 | T>M | A:428 | (5.49, 72.78, 63.76) | |
| 10:111633136 | rs544413007 | A>T | A:438 | (17.42, 87.11, 54.92) |
| 10:111631582 | V>A | A:454 | (-2.35, 73.51, 50.97) | |
| 10:111631577 | A>T | A:456 | (-6.43, 77.78, 50.46) | |
| 10:111631564 | P>L | A:460 | (-12.71, 68.79, 43.55) | |
| 10:111630651 | D>N | A:469 | (2.60, 67.71, 47.49) | |
| 10:111630638 | R>H | A:473 | (6.98, 70.67, 47.50) | |
| 10:111630572 | L>W | A:495 | (-6.15, 57.12, 67.53) | |
| 10:111630570 | rs556970182 | N>Y | A:496 | (-2.59, 56.65, 65.64) |
| 10:111630563 | H>R | A:498 | (1.62, 59.46, 62.41) | |
| 10:111629778 | Y>F | A:526 | (14.92, 74.44, 53.62) | |
| 10:111629749 | rs550675188 | I>V | A:536 | (4.93, 75.98, 58.95) |
| 10:111629722 | rs142238416 | V>L | A:545 | (-16.50, 75.33, 49.72) |
| 10:111628460 | N>S | A:552 | (-20.05, 66.95, 37.07) | |
| 10:111628454 | R>Q | A:554 | (-19.80, 64.73, 42.22) | |
| 10:111628439 | F>S | A:559 | (-8.33, 72.70, 54.01) | |
| 10:111628424 | L>W | A:564 | (-5.79, 78.07, 66.41) | |
| 10:111628421 | rs376462927 | V>A | A:565 | (-0.71, 78.67, 66.85) |
| 10:111628399 | I>M | A:572 | (7.29, 86.89, 57.17) | |
| 10:111628395 | V>M | A:574 | (5.60, 90.95, 54.22) | |
| 10:111625067 | D>N | A:583 | (-5.80, 88.62, 53.31) | |
| 10:111625054 | N>S | A:587 | (-8.43, 85.54, 58.98) | |
| 10:111625035 | R>S | A:593 | (-6.93, 88.21, 68.47) | |
| 10:111625036 | rs142010880 | R>K | A:593 | (-6.93, 88.21, 68.47) |
| 10:111625027 | I>T | A:596 | (-7.41, 80.62, 71.68) | |
| 10:111625019 | rs148080323 | E>K | A:599 | (-10.49, 79.09, 76.56) |
| 10:111625011 | rs200865221 | Q>H | A:601 | (-11.17, 85.41, 79.79) |
| 10:111625003 | G>V | A:604 | (-7.22, 83.29, 83.52) | |
| 10:111625000 | R>H | A:605 | (-4.22, 80.81, 81.45) | |
| 10:111625001 | R>C | A:605 | (-4.22, 80.81, 81.45) | |
| 10:111624986 | E>Q | A:610 | (-1.34, 90.27, 77.57) | |
| 10:111624976 | I>N | A:613 | (-3.45, 90.26, 71.60) | |
| 10:111624977 | rs567637506 | I>L | A:613 | (-3.45, 90.26, 71.60) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 10:111667493 | COSM171637 | E>K | A:25 | (15.52, 20.26, 59.71) |
| 10:111652800 | COSM218262 | A>P | A:51 | (18.50, 45.24, 70.55) |
| 10:111651564 | COSM1721007 | E>K | A:68 | (30.49, 31.87, 59.49) |
| 10:111642207 | COSM328531 | S>R | A:299 | (-2.01, 35.20, 56.22) |
| 10:111628455 | COSM1602954 | R>W | A:554 | (-19.80, 64.73, 42.22) |