General Structure Information
| PDB ID | 4g8a |
| HGNC Gene Label(s) | TLR4 |
| Structure Name | crystal structure of human tlr4 polymorphic variant d299g and t399i in complex with md-2 and lps |
| Resolution | 2.4Å |
| Reference | AUTH U.OHTO,N.YAMAKAWA,S.AKASHI-TAKAMURA,K.MIYAKE,T.SHIMIZUTITL STRUCTURAL ANALYSES OF HUMAN TOLL-LIKE RECEPTOR 4TITL 2 POLYMORPHISMS D299G AND T399IREF J.BIOL.CHEM. V. 287 40611 2012REFN ISSN 0021-9258PMID 23055527DOI 10.1074/JBC.M112.404608 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 601 |
| Number Of SNVs | 140 |
| Number Of Permutations | 70236 |
| Optimal Distance Threshold | 31.0 |
| K Statistic | 0.365 |
| p-value | 0.243 |
COSMIC
| Number Of Residues | 601 |
| Number Of SNVs | 21 |
| Number Of Permutations | 18827 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.043 |
| p-value | 0.496 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 140 |
| Number Of COSMIC SNVs | 16 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | 0.075 |
| p-value | 0.488 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 9:120466838 | COSM120821 | V>L | A:30 | (-11.81, 21.77, -74.63) |
| 9:120470844 | rs200405562 COSM1554086 |
V>I | A:33 | (-6.11, 14.70, -74.31) |
| 9:120470853 | I>V | A:36 | (-5.84, 12.46, -78.37) | |
| 9:120470864 | rs201589239 | Q>H | A:39 | (-15.47, 18.48, -75.19) |
| 9:120470866 | COSM76740 | C>Y | A:40 | (-16.52, 20.42, -79.59) |
| 9:120470871 | E>Q | A:42 | (-23.44, 23.38, -76.13) | |
| 9:120470884 | rs78848399 | Y>C | A:46 | (-24.48, 26.48, -88.49) |
| 9:120470892 | COSM140630 | P>S | A:49 | (-14.41, 20.94, -86.62) |
| 9:120470895 | COSM1643719 | D>N | A:50 | (-11.09, 22.98, -89.76) |
| 9:120470900 | rs148151027 | N>K | A:51 | (-9.43, 23.87, -85.94) |
| 9:120470940 | COSM334898 | P>S | A:65 | (-26.20, 23.24, -84.99) |
| 9:120470949 | H>D | A:68 | (-26.39, 17.83, -93.72) | |
| 9:120470966 | rs147453131 | S>R | A:73 | (-17.92, 15.15, -92.84) |
| 9:120470998 | D>A | A:84 | (-20.57, 12.29, -79.46) | |
| 9:120474678 | rs141943958 | Q>R | A:91 | (-32.91, 16.58, -90.33) |
| 9:120474679 | Q>H | A:91 | (-32.91, 16.58, -90.33) | |
| 9:120474681 | T>K | A:92 | (-29.71, 14.51, -93.34) | |
| 9:120474683 | rs56302444 | I>V | A:93 | (-26.71, 11.00, -92.58) |
| 9:120474696 | A>V | A:97 | (-20.39, 10.67, -93.93) | |
| 9:120474699 | Y>C | A:98 | (-19.88, 8.85, -90.74) | |
| 9:120474713 | H>Y | A:103 | (-9.21, 3.64, -87.41) | |
| 9:120474720 | S>C | A:105 | (-15.23, 2.12, -82.37) | |
| 9:120474750 | Q>R | A:115 | (-36.19, 12.86, -91.14) | |
| 9:120474767 | rs199985705 | A>S | A:121 | (-24.41, 6.31, -94.11) |
| 9:120474768 | A>V | A:121 | (-24.41, 6.31, -94.11) | |
| 9:120474800 | V>L | A:132 | (-25.62, 4.91, -80.03) | |
| 9:120474806 | rs370421152 | V>M | A:134 | (-30.84, 6.48, -78.62) |
| 9:120474807 | V>A | A:134 | (-30.84, 6.48, -78.62) | |
| 9:120474815 | N>Y | A:137 | (-37.22, 9.27, -85.91) | |
| 9:120474819 | rs188543451 | L>P | A:138 | (-35.48, 4.18, -85.76) |
| 9:120474832 | E>D | A:142 | (-36.04, -3.63, -92.07) | |
| 9:120474843 | rs201897073 | I>T | A:146 | (-26.39, -1.66, -89.90) |
| 9:120474845 | rs567339096 | G>R | A:147 | (-25.25, -4.85, -92.60) |
| 9:120474866 | E>K | A:154 | (-22.41, -2.32, -78.29) | |
| 9:120474885 | rs537921846 | N>S | A:160 | (-36.64, 4.87, -81.17) |
| 9:120474891 | rs200168998 | I>T | A:162 | (-38.99, 0.03, -83.26) |
| 9:120474929 | rs16906079 | T>A | A:175 | (-21.26, -12.33, -86.49) |
| 9:120474941 | rs201215262 | H>Y | A:179 | (-24.45, -6.10, -75.99) |
| 9:120474950 | rs373109368 | L>V | A:182 | (-34.98, -3.01, -78.79) |
| 9:120474966 | I>S | A:187 | (-42.29, -3.77, -79.51) | |
| 9:120474991 | L>F | A:195 | (-37.03, -14.83, -83.83) | |
| 9:120474992 | rs201943367 | R>W | A:196 | (-35.92, -15.86, -90.55) |
| 9:120474993 | rs200570847 COSM202374 |
R>Q | A:196 | (-35.92, -15.86, -90.55) |
| 9:120475002 | H>R | A:199 | (-34.21, -19.65, -85.18) | |
| 9:120475004 | COSM3653627 | Q>E | A:200 | (-30.79, -18.47, -89.85) |
| 9:120475013 | L>V | A:203 | (-22.76, -19.50, -82.48) | |
| 9:120475019 | rs200246890 | N>H | A:205 | (-23.30, -14.02, -77.11) |
| 9:120475055 | F>L | A:217 | (-48.75, -12.18, -78.22) | |
| 9:120475065 | COSM752876 | P>Q | A:220 | (-46.48, -19.35, -78.40) |
| 9:120475070 | rs572758278 | A>T | A:222 | (-40.86, -17.79, -80.56) |
| 9:120475094 | rs200759610 | K>E | A:230 | (-28.95, -10.35, -70.56) |
| 9:120475128 | N>S | A:241 | (-53.27, -11.71, -66.66) | |
| 9:120475133 | M>V | A:243 | (-46.41, -11.10, -66.81) | |
| 9:120475143 | rs5030714 | C>S | A:246 | (-45.88, -12.88, -72.52) |
| 9:120475146 | I>T | A:247 | (-43.72, -15.46, -69.41) | |
| 9:120475157 | rs573699173 | A>T | A:251 | (-41.28, -21.16, -74.06) |
| 9:120475175 | rs201835255 COSM607565 |
R>C | A:257 | (-28.63, -12.29, -65.91) |
| 9:120475185 | rs55799839 | L>P | A:260 | (-37.93, -9.82, -64.77) |
| 9:120475210 | N>K | A:268 | (-46.05, -0.44, -61.95) | |
| 9:120475217 | K>E | A:271 | (-52.27, -8.27, -59.41) | |
| 9:120475225 | D>E | A:273 | (-49.90, -13.96, -57.94) | |
| 9:120475227 | rs142144857 | K>R | A:274 | (-48.83, -18.05, -55.90) |
| 9:120475230 | S>C | A:275 | (-49.06, -17.01, -60.95) | |
| 9:120475232 | rs199885534 | A>S | A:276 | (-46.34, -14.65, -62.00) |
| 9:120475248 | rs138122523 | C>Y | A:281 | (-40.90, -23.67, -65.40) |
| 9:120475254 | rs201836189 | L>S | A:283 | (-37.64, -20.70, -69.58) |
| 9:120475256 | rs201497570 | T>A | A:284 | (-33.28, -22.73, -69.41) |
| 9:120475259 | I>V | A:285 | (-33.14, -19.51, -66.19) | |
| 9:120475266 | rs76014534 | E>G | A:287 | (-27.96, -15.65, -63.89) |
| 9:120475286 | rs139736045 | D>N | A:294 | (-44.74, -1.16, -56.52) |
| 9:120475298 | rs145284280 | D>N | A:298 | (-47.28, -11.20, -47.51) |
| 9:120475299 | D>A | A:298 | (-47.28, -11.20, -47.51) | |
| 9:120475300 | D>E | A:298 | (-47.28, -11.20, -47.51) | |
| 9:120475301 | COSM3653633 | D>Y | A:299 | (-44.84, -13.77, -49.64) |
| 9:120475302 | rs4986790 | D>G | A:299 | (-44.84, -13.77, -49.64) |
| 9:120475304 | I>V | A:300 | (-41.49, -15.91, -51.22) | |
| 9:120475307 | rs141534085 | I>V | A:301 | (-45.28, -19.35, -50.50) |
| 9:120475308 | rs201050092 | I>T | A:301 | (-45.28, -19.35, -50.50) |
| 9:120475316 | F>L | A:304 | (-39.63, -16.75, -56.46) | |
| 9:120475327 | COSM3779590 | L>F | A:307 | (-36.53, -19.72, -60.22) |
| 9:120475331 | N>Y | A:309 | (-32.44, -24.90, -60.79) | |
| 9:120475332 | N>S | A:309 | (-32.44, -24.90, -60.79) | |
| 9:120475349 | rs199637440 | L>M | A:315 | (-34.52, -10.08, -55.14) |
| 9:120475355 | S>R | A:317 | (-35.92, -3.05, -55.06) | |
| 9:120475365 | I>T | A:320 | (-40.63, -9.30, -48.82) | |
| 9:120475381 | D>E | A:325 | (-41.11, -18.26, -47.06) | |
| 9:120475389 | COSM326682 | Y>C | A:328 | (-38.54, -24.32, -50.32) |
| 9:120475391 | N>H | A:329 | (-33.98, -26.56, -50.16) | |
| 9:120475392 | rs5030715 | N>T | A:329 | (-33.98, -26.56, -50.16) |
| 9:120475397 | rs535260110 | G>R | A:331 | (-30.39, -24.36, -55.30) |
| 9:120475398 | rs376837568 | G>E | A:331 | (-30.39, -24.36, -55.30) |
| 9:120475407 | H>R | A:334 | (-25.53, -15.57, -56.11) | |
| 9:120475409 | L>I | A:335 | (-28.88, -15.03, -52.68) | |
| 9:120475412 | COSM390691 | E>K | A:336 | (-28.11, -10.36, -55.12) |
| 9:120475413 | rs544871818 | E>G | A:336 | (-28.11, -10.36, -55.12) |
| 9:120475417 | L>F | A:337 | (-31.14, -10.07, -51.18) | |
| 9:120475431 | rs5031050 | F>Y | A:342 | (-36.58, -7.92, -46.15) |
| 9:120475434 | rs200713994 | G>V | A:343 | (-39.61, -7.42, -41.61) |
| 9:120475451 | K>E | A:349 | (-32.81, -23.01, -43.66) | |
| 9:120475454 | rs200307408 | L>F | A:350 | (-30.03, -22.42, -48.81) |
| 9:120475458 | K>R | A:351 | (-28.64, -27.32, -47.94) | |
| 9:120475471 | R>S | A:355 | (-20.81, -15.88, -53.65) | |
| 9:120475476 | T>S | A:357 | (-25.16, -10.43, -51.51) | |
| 9:120475487 | rs61734367 | N>D | A:361 | (-31.27, -4.42, -47.49) |
| 9:120475488 | N>S | A:361 | (-31.27, -4.42, -47.49) | |
| 9:120475489 | N>K | A:361 | (-31.27, -4.42, -47.49) | |
| 9:120475492 | K>N | A:362 | (-34.47, -0.15, -46.78) | |
| 9:120475503 | A>G | A:366 | (-32.07, -8.43, -36.74) | |
| 9:120475512 | E>V | A:369 | (-29.38, -18.50, -36.26) | |
| 9:120475524 | rs370344294 | P>R | A:373 | (-23.84, -25.53, -45.54) |
| 9:120475534 | E>D | A:376 | (-17.22, -20.35, -49.83) | |
| 9:120475547 | rs201114738 COSM95363 |
S>G | A:381 | (-23.03, -4.88, -46.15) |
| 9:120475561 | rs11536884 | L>F | A:385 | (-27.77, -5.63, -39.78) |
| 9:120475571 | rs201746544 COSM3926060 |
G>C | A:389 | (-23.32, -12.69, -31.09) |
| 9:120475575 | C>S | A:390 | (-20.62, -12.18, -33.32) | |
| 9:120475602 | rs4986791 | T>I | A:399 | (-16.95, -25.10, -41.71) |
| 9:120475608 | L>Q | A:401 | (-16.89, -18.34, -44.21) | |
| 9:120475610 | rs539153708 | K>E | A:402 | (-13.02, -18.49, -47.56) |
| 9:120475626 | rs202089517 | S>T | A:407 | (-19.82, -3.34, -43.33) |
| 9:120475637 | rs145887797 | V>I | A:411 | (-24.72, -2.98, -32.79) |
| 9:120475650 | COSM607560 | S>T | A:415 | (-19.97, -13.59, -28.08) |
| 9:120475655 | N>D | A:417 | (-13.55, -16.44, -30.64) | |
| 9:120475667 | rs137906784 | L>V | A:421 | (-15.47, -19.21, -38.91) |
| 9:120475688 | rs376443096 | D>Y | A:428 | (-15.17, -5.62, -43.33) |
| 9:120475719 | rs142298021 | S>N | A:438 | (-11.64, -5.58, -24.88) |
| 9:120475749 | N>S | A:448 | (-6.22, -18.61, -41.96) | |
| 9:120475761 | L>R | A:452 | (-9.13, -6.97, -40.06) | |
| 9:120475772 | H>Y | A:456 | (-14.20, 4.43, -38.50) | |
| 9:120475798 | rs368504750 | N>K | A:464 | (-2.76, -6.04, -24.62) |
| 9:120475809 | N>S | A:468 | (-4.22, -12.66, -29.65) | |
| 9:120475848 | rs200621504 | N>S | A:481 | (-10.92, 3.30, -33.35) |
| 9:120475880 | rs200787883 | F>V | A:492 | (0.35, -4.77, -33.13) |
| 9:120475884 | rs144562288 | T>I | A:493 | (3.59, -9.35, -30.91) |
| 9:120475887 | E>A | A:494 | (0.43, -13.05, -32.50) | |
| 9:120475920 | rs199891172 | Q>R | A:505 | (-8.75, 8.88, -37.69) |
| 9:120475936 | rs5030719 | Q>H | A:510 | (1.98, 8.39, -25.84) |
| 9:120475949 | COSM233589 | A>T | A:515 | (4.65, -1.75, -30.82) |
| 9:120475952 | F>I | A:516 | (5.19, -0.76, -34.36) | |
| 9:120476000 | F>L | A:532 | (1.43, 11.27, -31.90) | |
| 9:120476016 | rs151068160 | T>M | A:537 | (12.48, 7.26, -34.94) |
| 9:120476025 | rs545104922 | Y>C | A:540 | (8.78, 3.76, -36.16) |
| 9:120476039 | S>T | A:545 | (9.76, -3.58, -44.94) | |
| 9:120476069 | rs202101018 | H>N | A:555 | (-0.83, 18.26, -33.20) |
| 9:120476081 | S>P | A:559 | (12.33, 15.29, -32.08) | |
| 9:120476091 | rs149793266 | Q>R | A:562 | (17.47, 13.41, -30.75) |
| 9:120476096 | rs200473735 | L>I | A:564 | (15.68, 11.97, -35.65) |
| 9:120476099 | rs201413217 | Q>K | A:565 | (19.59, 7.69, -35.63) |
| 9:120476121 | rs200676661 | A>V | A:572 | (10.47, 6.30, -49.10) |
| 9:120476135 | T>A | A:577 | (2.00, 16.98, -44.05) | |
| 9:120476166 | H>R | A:587 | (12.71, 23.08, -31.60) | |
| 9:120476167 | rs199700911 | H>Q | A:587 | (12.71, 23.08, -31.60) |
| 9:120476223 | COSM170668 | R>Q | A:606 | (0.56, 19.85, -47.47) |
| 9:120476262 | COSM3926065 | P>L | A:619 | (7.96, 27.00, -45.67) |
| 9:120476271 | rs146859162 | S>N | A:622 | (12.49, 27.90, -46.25) |
| 9:120476283 | rs201055270 COSM1173438 |
T>I | A:626 | (21.26, 31.06, -38.32) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 9:120470847 | COSM233588 | P>S | A:34 | (-3.24, 16.77, -75.63) |
| 9:120474738 | COSM3653625 | G>A | A:111 | (-31.18, 12.92, -80.60) |
| 9:120474743 | COSM95359 | P>T | A:113 | (-33.97, 14.63, -85.79) |
| 9:120474783 | COSM303395 | S>L | A:126 | (-14.41, -0.94, -90.86) |
| 9:120475046 | COSM3737332 | P>A | A:214 | (-45.88, -1.90, -75.18) |
| 9:120475079 | COSM1701623 | E>K | A:225 | (-34.41, -24.24, -80.74) |
| 9:120475251 | COSM72993 | N>S | A:282 | (-41.39, -23.70, -69.67) |
| 9:120475302 | COSM4988203 | D>G | A:299 | (-44.84, -13.77, -49.64) |
| 9:120475379 | COSM607563 | D>Y | A:325 | (-41.11, -18.26, -47.06) |
| 9:120475463 | COSM106873 | L>F | A:353 | (-25.78, -20.60, -50.97) |
| 9:120475602 | COSM4989617 | T>I | A:399 | (-16.95, -25.10, -41.71) |
| 9:120475662 | COSM335758 | L>W | A:419 | (-15.78, -21.13, -32.73) |
| 9:120475663 | COSM2150749 | L>F | A:419 | (-15.78, -21.13, -32.73) |
| 9:120475722 | COSM3903593 | E>V | A:439 | (-15.16, -8.23, -23.03) |
| 9:120475728 | COSM4402884 | S>L | A:441 | (-9.49, -12.91, -27.86) |
| 9:120475736 | COSM3395531 | L>I | A:444 | (-8.13, -16.57, -30.73) |
| 9:120475841 | COSM1459650 | A>T | A:479 | (-9.18, 3.75, -38.21) |
| 9:120475851 | COSM3926062 | S>F | A:482 | (-9.68, 4.25, -29.13) |
| 9:120475859 | COSM1701628 | E>K | A:485 | (-4.83, 6.12, -20.99) |
| 9:120475865 | COSM1267921 | F>V | A:487 | (-0.20, 3.35, -24.67) |
| 9:120475890 | COSM1104599 | L>P | A:495 | (0.29, -9.51, -36.11) |
| 9:120475898 | COSM3903596 | L>V | A:498 | (1.18, -6.86, -40.54) |
| 9:120475949 | COSM233589 | A>T | A:515 | (4.65, -1.75, -30.82) |
| 9:120476223 | COSM170668 | R>Q | A:606 | (0.56, 19.85, -47.47) |