General Structure Information
| PDB ID | 3b2d |
| HGNC Gene Label(s) | CD180 |
| Structure Name | crystal structure of human rp105/md-1 complex |
| Resolution | 2.8Å |
| Reference | AUTH U.OHTO,K.MIYAKE,T.SHIMIZUTITL CRYSTAL STRUCTURES OF MOUSE AND HUMAN RP105/MD-1 COMPLEXESTITL 2 REVEAL UNIQUE DIMER ORGANIZATION OF THE TOLL-LIKE RECEPTORTITL 3 FAMILY.REF J.MOL.BIOL. V. 413 815 2011REFN ISSN 0022-2836PMID 21959264DOI 10.1016/J.JMB.2011.09.020 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 601 |
| Number Of SNVs | 174 |
| Number Of Permutations | 32469 |
| Optimal Distance Threshold | 23.0 |
| K Statistic | 0.208 |
| p-value | 0.355 |
COSMIC
| Number Of Residues | 601 |
| Number Of SNVs | 10 |
| Number Of Permutations | 8772 |
| Optimal Distance Threshold | 4.0 |
| K Statistic | 0.022 |
| p-value | 0.147 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 174 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 4.0 |
| K Statistic | 0.047 |
| p-value | 0.823 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:66492387 | rs377501004 | C>Y | A:28 | (-2.07, -21.69, -17.37) |
| 5:66481842 | rs373888203 | E>Q | A:32 | (-0.04, -10.69, -10.79) |
| 5:66481829 | T>I | A:36 | (1.63, -12.50, -14.50) | |
| 5:66481826 | rs144258682 | Y>C | A:37 | (-1.12, -15.31, -16.61) |
| 5:66481823 | rs560455986 | N>S | A:38 | (3.88, -19.74, -16.21) |
| 5:66481821 | C>R | A:39 | (3.01, -21.20, -20.10) | |
| 5:66481790 | D>G | A:49 | (-8.46, -19.31, -26.38) | |
| 5:66481787 | rs369755502 | T>N | A:50 | (-7.67, -19.13, -21.45) |
| 5:66481781 | P>L | A:52 | (-6.02, -12.86, -20.37) | |
| 5:66481782 | rs375872136 | P>T | A:52 | (-6.02, -12.86, -20.37) |
| 5:66481777 | rs16875312 | N>K | A:53 | (-6.81, -9.60, -24.05) |
| 5:66481776 | T>P | A:54 | (-4.94, -7.84, -19.80) | |
| 5:66481743 | L>M | A:65 | (6.48, -21.67, -31.43) | |
| 5:66481736 | T>I | A:67 | (6.69, -20.53, -37.33) | |
| 5:66481721 | T>I | A:72 | (1.54, -15.92, -32.98) | |
| 5:66481715 | rs544292087 | S>N | A:74 | (-2.84, -11.35, -32.02) |
| 5:66481712 | rs369289821 | R>T | A:75 | (-5.53, -13.70, -28.00) |
| 5:66481710 | L>F | A:76 | (-1.64, -11.34, -26.08) | |
| 5:66481698 | T>A | A:80 | (5.69, -5.84, -21.50) | |
| 5:66480396 | I>K | A:92 | (11.05, -14.54, -36.71) | |
| 5:66480394 | H>N | A:93 | (7.85, -15.08, -40.62) | |
| 5:66480378 | Q>R | A:98 | (2.29, -5.36, -36.53) | |
| 5:66480374 | rs2230520 | S>R | A:99 | (0.41, -5.30, -32.92) |
| 5:66480360 | S>I | A:104 | (10.42, -4.21, -23.25) | |
| 5:66480357 | rs202004217 | T>I | A:105 | (11.62, -7.96, -22.67) |
| 5:66480333 | L>P | A:113 | (16.93, -18.58, -35.00) | |
| 5:66480331 | COSM1069536 | I>V | A:114 | (17.04, -20.48, -39.82) |
| 5:66480324 | rs150370779 | M>T | A:116 | (15.22, -12.58, -37.79) |
| 5:66480306 | N>S | A:122 | (9.27, -3.67, -36.81) | |
| 5:66480307 | N>H | A:122 | (9.27, -3.67, -36.81) | |
| 5:66480303 | G>E | A:123 | (6.47, -1.96, -33.23) | |
| 5:66480297 | rs201688318 | K>R | A:125 | (6.68, 2.42, -30.15) |
| 5:66480282 | L>P | A:130 | (17.15, -8.62, -27.43) | |
| 5:66480267 | rs372829866 | T>M | A:135 | (20.57, -18.46, -31.56) |
| 5:66480258 | rs138790017 | S>C | A:138 | (27.62, -16.39, -37.45) |
| 5:66480195 | N>I | A:159 | (26.39, -17.57, -30.42) | |
| 5:66480189 | rs199888058 | I>S | A:161 | (30.21, -14.43, -32.37) |
| 5:66480166 | D>Y | A:169 | (22.93, 0.89, -40.56) | |
| 5:66480153 | R>Q | A:173 | (22.02, 6.28, -30.15) | |
| 5:66480154 | rs142013803 | R>W | A:173 | (22.02, 6.28, -30.15) |
| 5:66480145 | rs200262932 | K>Q | A:176 | (23.89, 1.33, -21.31) |
| 5:66480136 | D>H | A:179 | (26.73, -10.38, -23.03) | |
| 5:66480133 | F>L | A:180 | (29.65, -10.53, -26.96) | |
| 5:66480106 | S>A | A:189 | (39.67, -4.26, -33.98) | |
| 5:66480090 | R>K | A:194 | (35.91, 2.47, -35.78) | |
| 5:66480088 | S>P | A:195 | (30.91, -0.18, -34.11) | |
| 5:66480075 | A>V | A:199 | (28.13, 4.03, -26.78) | |
| 5:66480051 | rs142324076 | N>S | A:207 | (33.14, -14.46, -19.57) |
| 5:66480039 | V>A | A:211 | (41.27, -12.34, -25.97) | |
| 5:66480033 | G>V | A:213 | (44.21, -9.90, -29.08) | |
| 5:66480022 | G>R | A:217 | (44.19, 1.48, -29.83) | |
| 5:66480006 | rs368311403 | T>M | A:222 | (37.57, 4.42, -24.44) |
| 5:66480004 | rs1697144 | I>V | A:223 | (34.56, 6.10, -21.33) |
| 5:66479997 | rs145421165 | Q>R | A:225 | (30.27, 1.08, -16.09) |
| 5:66479979 | rs376002971 COSM351251 |
G>E | A:231 | (39.40, -16.35, -18.88) |
| 5:66479968 | L>M | A:235 | (46.37, -10.55, -17.89) | |
| 5:66479957 | rs368540751 | I>M | A:238 | (43.91, -7.39, -21.69) |
| 5:66479958 | I>T | A:238 | (43.91, -7.39, -21.69) | |
| 5:66479950 | G>S | A:241 | (44.91, -2.76, -25.06) | |
| 5:66479935 | T>A | A:246 | (38.31, 4.91, -18.74) | |
| 5:66479925 | rs74683094 | S>Y | A:249 | (34.75, -2.43, -13.72) |
| 5:66479923 | L>F | A:250 | (38.67, -4.45, -15.04) | |
| 5:66479913 | COSM3920287 | G>E | A:253 | (39.36, -13.44, -13.70) |
| 5:66479914 | G>R | A:253 | (39.36, -13.44, -13.70) | |
| 5:66479898 | rs144473068 | I>N | A:258 | (40.96, -21.94, -16.64) |
| 5:66479896 | rs5744525 | D>N | A:259 | (45.12, -23.97, -17.11) |
| 5:66479890 | COSM194486 | E>K | A:261 | (49.19, -16.78, -16.81) |
| 5:66479871 | rs146834109 | M>T | A:267 | (51.89, -9.64, -16.53) |
| 5:66479863 | COSM3617596 | G>R | A:270 | (49.48, -1.17, -18.01) |
| 5:66479859 | rs143797212 | L>P | A:271 | (47.19, -0.73, -14.44) |
| 5:66479849 | M>I | A:274 | (44.76, 1.68, -17.47) | |
| 5:66479845 | V>I | A:276 | (40.98, 1.38, -13.32) | |
| 5:66479840 | rs536420835 COSM3617595 |
E>D | A:277 | (38.02, 3.44, -10.16) |
| 5:66479842 | E>K | A:277 | (38.02, 3.44, -10.16) | |
| 5:66479837 | S>R | A:278 | (37.38, -1.85, -9.87) | |
| 5:66479824 | E>Q | A:283 | (41.13, -18.50, -8.85) | |
| 5:66479817 | rs199660574 | R>H | A:285 | (49.10, -19.22, -8.14) |
| 5:66479813 | F>L | A:286 | (50.17, -12.93, -7.35) | |
| 5:66479793 | rs150637060 | T>I | A:293 | (53.40, -6.52, -7.71) |
| 5:66479773 | L>F | A:300 | (42.68, 0.96, -7.93) | |
| 5:66479769 | Q>P | A:301 | (39.31, 3.59, -5.28) | |
| 5:66479766 | rs377648375 | E>G | A:302 | (36.98, -1.26, -5.43) |
| 5:66479754 | T>I | A:306 | (39.26, -13.84, -4.23) | |
| 5:66479755 | T>P | A:306 | (39.26, -13.84, -4.23) | |
| 5:66479737 | rs373024946 COSM1438251 |
G>W | A:312 | (50.52, -12.43, 1.93) |
| 5:66479722 | rs181372281 | M>V | A:317 | (53.26, -2.00, -0.63) |
| 5:66479715 | G>D | A:319 | (49.98, 1.58, -4.48) | |
| 5:66479701 | K>E | A:324 | (38.61, 3.61, -0.10) | |
| 5:66479697 | K>T | A:325 | (36.16, -0.91, -1.19) | |
| 5:66479692 | V>F | A:327 | (38.45, -8.57, -1.23) | |
| 5:66479689 | rs148500952 | L>V | A:328 | (41.98, -10.33, 1.21) |
| 5:66479670 | D>G | A:334 | (48.19, -18.24, 9.40) | |
| 5:66479664 | L>S | A:336 | (44.95, -10.21, 10.54) | |
| 5:66479643 | rs142848963 | N>S | A:343 | (50.04, -1.11, 2.84) |
| 5:66479638 | rs138832030 | P>S | A:345 | (45.83, 4.29, 4.93) |
| 5:66479635 | rs373145754 | S>P | A:346 | (42.30, 5.27, 3.15) |
| 5:66479624 | rs368893764 | H>Q | A:349 | (34.67, -0.99, 2.85) |
| 5:66479617 | I>F | A:352 | (39.01, -11.35, 5.37) | |
| 5:66479605 | rs56752081 | V>M | A:356 | (41.65, -21.99, 3.36) |
| 5:66479592 | H>R | A:360 | (45.06, -17.11, 14.20) | |
| 5:66479581 | G>S | A:364 | (46.92, -4.78, 16.33) | |
| 5:66479572 | rs375032246 | E>Q | A:367 | (46.99, -0.39, 14.87) |
| 5:66479565 | L>P | A:369 | (42.69, 0.27, 9.28) | |
| 5:66479559 | N>S | A:371 | (39.31, 5.89, 7.99) | |
| 5:66479557 | L>V | A:372 | (37.80, 0.51, 8.59) | |
| 5:66479550 | rs372828314 | T>K | A:374 | (33.05, -2.51, 6.80) |
| 5:66479548 | L>V | A:375 | (35.58, -5.89, 9.49) | |
| 5:66479527 | I>L | A:382 | (38.02, -16.77, 14.24) | |
| 5:66479517 | S>F | A:385 | (39.38, -16.45, 24.85) | |
| 5:66479508 | C>Y | A:388 | (37.37, -7.80, 20.80) | |
| 5:66479505 | S>I | A:389 | (39.86, -4.88, 22.70) | |
| 5:66479499 | Q>R | A:391 | (41.53, -8.52, 18.92) | |
| 5:66479496 | L>P | A:392 | (38.90, -4.74, 17.08) | |
| 5:66479497 | L>I | A:392 | (38.90, -4.74, 17.08) | |
| 5:66479454 | rs137998891 | N>S | A:406 | (33.71, -18.05, 13.29) |
| 5:66479449 | P>S | A:408 | (34.13, -20.45, 19.86) | |
| 5:66479445 | rs534148374 | L>P | A:409 | (34.05, -15.75, 20.38) |
| 5:66479442 | G>A | A:410 | (34.98, -14.53, 24.40) | |
| 5:66479443 | G>R | A:410 | (34.98, -14.53, 24.40) | |
| 5:66479436 | Q>L | A:412 | (35.02, -9.85, 29.30) | |
| 5:66479433 | rs111374045 | S>N | A:413 | (32.25, -6.34, 29.81) |
| 5:66479428 | A>S | A:415 | (33.97, -6.35, 23.85) | |
| 5:66479412 | P>L | A:420 | (32.18, 3.17, 19.64) | |
| 5:66479398 | L>F | A:425 | (27.26, -7.08, 15.61) | |
| 5:66479389 | A>S | A:428 | (25.95, -15.86, 13.33) | |
| 5:66479383 | rs2230523 | T>A | A:430 | (29.63, -17.65, 16.53) |
| 5:66479379 | rs200803485 COSM3429592 |
R>H | A:431 | (28.85, -22.35, 20.15) |
| 5:66479380 | rs371897533 | R>C | A:431 | (28.85, -22.35, 20.15) |
| 5:66479374 | H>Y | A:433 | (31.96, -18.80, 25.51) | |
| 5:66479365 | A>T | A:436 | (27.17, -13.85, 34.63) | |
| 5:66479361 | P>L | A:437 | (26.49, -10.38, 35.52) | |
| 5:66479356 | S>C | A:439 | (27.28, -6.46, 29.58) | |
| 5:66479341 | L>F | A:444 | (27.34, -0.46, 21.56) | |
| 5:66479337 | H>R | A:445 | (25.46, 4.39, 23.12) | |
| 5:66479316 | L>P | A:452 | (22.83, -13.30, 18.46) | |
| 5:66479299 | D>H | A:458 | (22.85, -17.85, 29.48) | |
| 5:66479282 | rs201238605 | H>Q | A:463 | (22.36, -7.78, 33.35) |
| 5:66479275 | A>S | A:466 | (22.91, -3.85, 28.47) | |
| 5:66479256 | rs145898895 | R>Q | A:472 | (16.08, -1.44, 14.38) |
| 5:66479257 | rs368898682 | R>W | A:472 | (16.08, -1.44, 14.38) |
| 5:66479227 | Q>E | A:482 | (15.47, -22.28, 32.28) | |
| 5:66479224 | D>N | A:483 | (12.16, -24.67, 31.81) | |
| 5:66479220 | G>A | A:484 | (10.94, -23.08, 27.68) | |
| 5:66479217 | T>N | A:485 | (9.83, -20.35, 29.77) | |
| 5:66479211 | rs140748436 | T>M | A:487 | (9.81, -14.92, 32.64) |
| 5:66479207 | rs201778641 | K>N | A:488 | (7.32, -10.04, 34.14) |
| 5:66479206 | rs111590298 | T>A | A:489 | (11.74, -11.04, 34.57) |
| 5:66479201 | N>K | A:490 | (13.10, -11.00, 30.13) | |
| 5:66479197 | COSM1438249 | L>I | A:492 | (14.11, -8.99, 25.87) |
| 5:66479192 | Q>H | A:493 | (13.12, -6.24, 30.70) | |
| 5:66479190 | T>I | A:494 | (17.28, -3.84, 28.55) | |
| 5:66479178 | L>W | A:498 | (13.26, -3.97, 19.89) | |
| 5:66479179 | L>V | A:498 | (13.26, -3.97, 19.89) | |
| 5:66479176 | E>Q | A:499 | (11.48, -1.93, 15.62) | |
| 5:66479172 | V>A | A:500 | (12.78, -6.68, 14.78) | |
| 5:66479140 | I>V | A:511 | (5.44, -16.62, 26.10) | |
| 5:66479133 | Q>R | A:513 | (0.49, -12.43, 30.45) | |
| 5:66479115 | L>S | A:519 | (9.11, -4.64, 24.07) | |
| 5:66479088 | rs367881837 | S>N | A:528 | (8.65, -19.94, 14.16) |
| 5:66479083 | N>D | A:530 | (8.62, -23.00, 18.53) | |
| 5:66479068 | D>N | A:535 | (-1.91, -19.06, 26.51) | |
| 5:66479060 | I>M | A:537 | (-1.32, -15.02, 21.49) | |
| 5:66479046 | rs546205073 | H>L | A:542 | (1.47, -4.73, 24.13) |
| 5:66479037 | rs148764952 | G>V | A:545 | (0.75, -3.84, 13.36) |
| 5:66478993 | P>S | A:560 | (-12.42, -16.22, 22.32) | |
| 5:66478989 | R>H | A:561 | (-8.29, -14.76, 25.52) | |
| 5:66478990 | rs150000308 | R>C | A:561 | (-8.29, -14.76, 25.52) |
| 5:66478978 | I>L | A:565 | (-4.62, -9.90, 20.30) | |
| 5:66478964 | Q>H | A:569 | (-1.86, -7.34, 14.66) | |
| 5:66478956 | I>T | A:572 | (-1.09, -13.26, 11.17) | |
| 5:66478957 | I>V | A:572 | (-1.09, -13.26, 11.17) | |
| 5:66478938 | rs185244476 | P>L | A:578 | (-2.09, -28.30, 15.53) |
| 5:66478939 | rs370285296 COSM482986 |
P>S | A:578 | (-2.09, -28.30, 15.53) |
| 5:66478936 | rs372411044 | L>M | A:579 | (-5.51, -25.65, 14.25) |
| 5:66478920 | S>L | A:584 | (-14.58, -25.74, 20.63) | |
| 5:66478914 | I>T | A:586 | (-16.55, -21.57, 15.92) | |
| 5:66478902 | T>I | A:590 | (-15.47, -17.25, 11.87) | |
| 5:66478894 | K>E | A:593 | (-13.59, -17.89, 6.35) | |
| 5:66478884 | L>P | A:596 | (-8.29, -14.28, 3.96) | |
| 5:66478870 | G>C | A:601 | (-0.41, -18.96, 4.33) | |
| 5:66478866 | S>L | A:602 | (-3.82, -19.45, 3.69) | |
| 5:66478859 | rs201091750 | E>D | A:604 | (0.73, -23.26, 3.16) |
| 5:66478858 | T>A | A:605 | (-3.25, -23.52, 6.87) | |
| 5:66478854 | T>M | A:606 | (-3.98, -27.64, 8.33) | |
| 5:66478842 | P>L | A:610 | (-11.87, -33.88, 12.07) | |
| 5:66478843 | P>A | A:610 | (-11.87, -33.88, 12.07) | |
| 5:66478829 | R>S | A:614 | (-4.86, -34.28, 9.04) | |
| 5:66478816 | S>P | A:619 | (-10.69, -21.51, 3.48) | |
| 5:66478813 | D>N | A:620 | (-12.09, -24.72, 1.97) | |
| 5:66478803 | L>P | A:623 | (-18.54, -26.16, 11.02) | |
| 5:66478804 | L>V | A:623 | (-18.54, -26.16, 11.02) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:66481680 | COSM1671675 | R>G | A:86 | (15.51, -24.31, -25.90) |
| 5:66480374 | COSM149848 | S>R | A:99 | (0.41, -5.30, -32.92) |
| 5:66480342 | COSM3071793 | G>E | A:110 | (17.54, -21.58, -27.59) |
| 5:66480226 | COSM3617600 | E>K | A:149 | (16.98, 3.51, -32.60) |
| 5:66480154 | COSM3071789 | R>W | A:173 | (22.02, 6.28, -30.15) |
| 5:66479890 | COSM194486 | E>K | A:261 | (49.19, -16.78, -16.81) |
| 5:66479404 | COSM482987 | E>K | A:423 | (25.23, 1.28, 12.89) |
| 5:66479395 | COSM1069534 | D>N | A:426 | (26.72, -10.79, 12.16) |
| 5:66478990 | COSM738345 | R>C | A:561 | (-8.29, -14.76, 25.52) |
| 5:66478800 | COSM1438245 | S>F | A:624 | (-22.85, -26.35, 11.99) |