General Structure Information
| PDB ID | 3dbr |
| HGNC Gene Label(s) | NAE1 |
| Structure Name | structural dissection of a gating mechanism preventing misactivation of ubiquitin by nedd8s e1 (appbp1- uba3arg190gln-nedd8ala72arg) |
| Resolution | 3.05Å |
| Reference | AUTH J.SOUPHRON,M.B.WADDELL,A.PAYDAR,Z.TOKGOZ-GROMLEY,AUTH 2 M.F.ROUSSEL,B.A.SCHULMANTITL STRUCTURAL DISSECTION OF A GATING MECHANISMTITL 2 PREVENTING MISACTIVATION OF UBIQUITIN BY NEDD8STITL 3 E1.REF BIOCHEMISTRY V. 47 8961 2008REFN ISSN 0006-2960PMID 18652489DOI 10.1021/BI800604C |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 517 |
| Number Of SNVs | 103 |
| Number Of Permutations | 29724 |
| Optimal Distance Threshold | 28.0 |
| K Statistic | 0.378 |
| p-value | 0.675 |
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 |
|---|---|---|---|---|
| 16:66864786 | rs368287571 | K>M | A:6 | (62.64, 109.31, 39.24) |
| 16:66864770 | Q>H | A:11 | (61.15, 105.86, 29.80) | |
| 16:66864754 | L>V | A:17 | (53.04, 112.49, 27.53) | |
| 16:66860673 | D>N | A:22 | (53.68, 116.68, 31.19) | |
| 16:66860669 | H>R | A:23 | (49.37, 119.36, 31.44) | |
| 16:66860658 | A>S | A:27 | (46.04, 115.21, 36.66) | |
| 16:66860601 | L>V | A:46 | (39.60, 100.33, 35.76) | |
| 16:66860477 | rs137985751 | S>L | A:56 | (43.88, 106.10, 42.80) |
| 16:66860471 | T>R | A:58 | (38.19, 102.34, 45.06) | |
| 16:66860465 | I>T | A:60 | (32.19, 99.94, 45.46) | |
| 16:66860451 | V>L | A:65 | (33.32, 85.40, 41.31) | |
| 16:66860447 | S>N | A:66 | (30.45, 83.82, 38.84) | |
| 16:66860444 | G>A | A:67 | (31.25, 81.67, 36.36) | |
| 16:66860445 | G>R | A:67 | (31.25, 81.67, 36.36) | |
| 16:66860435 | A>G | A:70 | (35.42, 84.16, 34.98) | |
| 16:66858772 | rs370582777 | S>G | A:79 | (41.39, 80.71, 41.10) |
| 16:66858763 | G>S | A:82 | (33.55, 83.01, 45.12) | |
| 16:66857499 | R>Q | A:85 | (32.17, 91.17, 41.32) | |
| 16:66857490 | A>V | A:88 | (39.53, 89.81, 42.52) | |
| 16:66857485 | rs200163314 | M>V | A:90 | (42.30, 95.16, 43.42) |
| 16:66857482 | E>Q | A:91 | (44.12, 90.85, 43.33) | |
| 16:66857474 | L>F | A:93 | (43.45, 95.54, 37.67) | |
| 16:66857451 | rs363212 | S>F | A:101 | (46.74, 102.82, 44.35) |
| 16:66857437 | rs371785034 | E>K | A:106 | (34.18, 93.55, 50.72) |
| 16:66857197 | L>F | A:112 | (27.75, 102.82, 50.69) | |
| 16:66857187 | rs140382369 | N>S | A:115 | (25.69, 102.83, 55.81) |
| 16:66857182 | P>A | A:117 | (26.03, 109.21, 52.22) | |
| 16:66857161 | T>A | A:124 | (37.60, 112.69, 40.74) | |
| 16:66857157 | V>A | A:125 | (35.16, 110.48, 38.77) | |
| 16:66855460 | T>I | A:135 | (21.07, 102.04, 42.53) | |
| 16:66855451 | R>H | A:138 | (19.52, 105.83, 45.97) | |
| 16:66855452 | R>C | A:138 | (19.52, 105.83, 45.97) | |
| 16:66855446 | COSM1743856 | A>S | A:140 | (22.55, 110.28, 40.71) |
| 16:66855423 | rs569000614 | Q>H | A:147 | (28.78, 119.23, 42.91) |
| 16:66855406 | rs370458994 | C>Y | A:153 | (28.05, 102.21, 32.26) |
| 16:66855382 | rs367874664 | Y>F | A:161 | (23.41, 103.49, 28.58) |
| 16:66855378 | M>I | A:162 | (27.88, 105.83, 27.80) | |
| 16:66855374 | rs555401377 | I>L | A:164 | (27.84, 111.96, 31.33) |
| 16:66855367 | I>T | A:166 | (28.74, 116.60, 34.72) | |
| 16:66855368 | I>V | A:166 | (28.74, 116.60, 34.72) | |
| 16:66855359 | H>Y | A:169 | (33.31, 119.90, 31.95) | |
| 16:66855356 | P>S | A:170 | (34.30, 123.84, 32.16) | |
| 16:66852501 | rs370972971 | R>Q | A:184 | (43.82, 139.18, 13.36) |
| 16:66852492 | rs377680125 COSM1193498 |
K>R | A:187 | (40.19, 142.66, 11.34) |
| 16:66852471 | E>V | A:194 | (54.36, 148.78, 11.32) | |
| 16:66852469 | H>D | A:195 | (56.38, 142.88, 9.06) | |
| 16:66851359 | I>T | A:218 | (48.32, 137.78, 0.43) | |
| 16:66851348 | L>V | A:222 | (45.23, 142.97, 0.24) | |
| 16:66850909 | T>M | A:236 | (33.16, 137.96, -4.36) | |
| 16:66850907 | rs201659718 | Y>D | A:237 | (33.09, 132.71, -3.92) |
| 16:66850894 | E>G | A:241 | (39.72, 133.78, -9.03) | |
| 16:66850501 | A>T | A:275 | (43.19, 134.40, 4.29) | |
| 16:66850486 | Q>E | A:280 | (34.23, 136.05, 13.13) | |
| 16:66847736 | I>T | A:285 | (32.66, 132.13, 22.48) | |
| 16:66847721 | rs367845618 | N>T | A:290 | (25.90, 136.27, 26.46) |
| 16:66847719 | D>N | A:291 | (26.13, 132.42, 30.42) | |
| 16:66847712 | R>H | A:293 | (28.18, 130.74, 36.15) | |
| 16:66847708 | C>W | A:294 | (29.76, 135.65, 32.56) | |
| 16:66847707 | COSM386742 | I>V | A:295 | (26.64, 138.49, 32.97) |
| 16:66847703 | N>S | A:296 | (26.06, 137.68, 36.97) | |
| 16:66847700 | I>S | A:297 | (30.55, 137.75, 38.98) | |
| 16:66847597 | rs375771532 | P>T | A:302 | (34.07, 129.73, 38.99) |
| 16:66847575 | rs35391524 | R>H | A:309 | (33.06, 139.23, 32.72) |
| 16:66847576 | R>C | A:309 | (33.06, 139.23, 32.72) | |
| 16:66847546 | G>R | A:319 | (39.83, 144.12, 21.07) | |
| 16:66847527 | V>A | A:325 | (46.08, 137.48, 18.79) | |
| 16:66847528 | rs569318459 | V>I | A:325 | (46.08, 137.48, 18.79) |
| 16:66847524 | R>Q | A:326 | (45.28, 131.89, 17.94) | |
| 16:66847518 | T>I | A:328 | (50.11, 130.70, 16.36) | |
| 16:66847501 | COSM4061692 | A>S | A:334 | (60.36, 130.79, 3.92) |
| 16:66847482 | I>T | A:340 | (61.60, 133.70, 12.94) | |
| 16:66844671 | R>C | A:347 | (56.06, 135.01, 19.97) | |
| 16:66844656 | K>E | A:352 | (51.18, 142.90, 24.02) | |
| 16:66844652 | D>G | A:353 | (46.30, 140.69, 23.83) | |
| 16:66844644 | rs186580935 | A>T | A:356 | (45.24, 142.65, 28.93) |
| 16:66844641 | V>L | A:357 | (43.28, 139.34, 29.63) | |
| 16:66844638 | rs550534934 | G>C | A:358 | (45.09, 140.04, 33.18) |
| 16:66844313 | P>S | A:372 | (45.18, 138.65, 42.82) | |
| 16:66844307 | S>P | A:374 | (43.63, 132.59, 41.88) | |
| 16:66844283 | L>I | A:382 | (46.17, 127.94, 27.96) | |
| 16:66842963 | F>C | A:389 | (39.69, 126.86, 20.33) | |
| 16:66842952 | COSM1167635 | V>L | A:393 | (29.59, 120.76, 28.83) |
| 16:66842942 | COSM972221 | R>Q | A:396 | (18.86, 117.04, 31.09) |
| 16:66842912 | T>I | A:406 | (11.51, 116.43, 32.70) | |
| 16:66842908 | I>M | A:407 | (10.96, 113.34, 28.97) | |
| 16:66842901 | D>Y | A:410 | (10.77, 116.16, 20.86) | |
| 16:66842892 | I>V | A:413 | (9.36, 111.51, 18.86) | |
| 16:66842509 | S>R | A:415 | (15.01, 110.07, 16.55) | |
| 16:66842504 | D>G | A:417 | (11.52, 109.52, 12.28) | |
| 16:66842463 | A>T | A:431 | (11.62, 98.13, 29.43) | |
| 16:66842436 | G>R | A:440 | (12.93, 90.14, 39.46) | |
| 16:66842432 | rs565276191 | R>K | A:441 | (13.06, 87.66, 35.77) |
| 16:66839912 | rs187763841 | V>I | A:450 | (12.81, 83.40, 25.80) |
| 16:66839899 | I>T | A:454 | (8.91, 87.56, 23.98) | |
| 16:66839900 | rs374385077 | I>V | A:454 | (8.91, 87.56, 23.98) |
| 16:66839857 | rs141920415 | Y>C | A:468 | (7.22, 108.63, 30.31) |
| 16:66839854 | G>V | A:469 | (3.58, 109.79, 25.80) | |
| 16:66839816 | F>L | A:482 | (16.84, 93.49, 23.98) | |
| 16:66839728 | rs369298591 | C>S | A:483 | (15.01, 88.05, 24.96) |
| 16:66839724 | R>Q | A:484 | (19.70, 86.22, 20.81) | |
| 16:66839707 | P>T | A:490 | (28.98, 90.62, 25.69) | |
| 16:66839687 | COSM3510823 | F>L | A:496 | (33.20, 100.01, 22.13) |
| 16:66837003 | V>G | A:505 | (37.01, 109.43, 32.84) | |
| 16:66836988 | rs141151787 | T>S | A:510 | (42.35, 116.24, 32.02) |
| 16:66836968 | N>H | A:517 | (25.62, 116.22, 26.17) | |
| 16:66836950 | S>G | A:523 | (24.94, 98.73, 17.78) | |
| 16:66836926 | T>A | A:531 | (24.90, 111.12, 20.90) | |
| 16:66836921 | F>L | A:532 | (20.76, 110.41, 21.52) | |
| 16:66836922 | F>S | A:532 | (20.76, 110.41, 21.52) | |
| 16:66836920 | Q>E | A:533 | (20.83, 116.53, 24.62) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 16:66860666 | COSM1679162 | G>E | A:24 | (47.75, 115.81, 32.41) |
| 16:66842915 | COSM78140 | D>A | A:405 | (6.72, 116.43, 32.91) |
| 16:66842898 | COSM1749686 | E>K | A:411 | (15.85, 113.74, 20.77) |