General Structure Information
| PDB ID | 3hl2 |
| HGNC Gene Label(s) | SEPSECS |
| Structure Name | the crystal structure of the human sepsecs-trnasec complex |
| Resolution | 2.81Å |
| Reference | AUTH S.PALIOURA,R.L.SHERRER,T.A.STEITZ,D.SOLL,AUTH 2 M.SIMONOVICTITL THE HUMAN SEPSECS-TRNASEC COMPLEX REVEALS THETITL 2 MECHANISM OF SELENOCYSTEINE FORMATION.REF SCIENCE V. 325 321 2009REFN ISSN 0036-8075PMID 19608919DOI 10.1126/SCIENCE.1173755 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 443 |
| Number Of SNVs | 108 |
| Number Of Permutations | 60699 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.072 |
| p-value | 0.71 |
COSMIC
| Number Of Residues | 443 |
| Number Of SNVs | 7 |
| Number Of Permutations | 3748 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | 0.19 |
| p-value | 0.525 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 108 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 32.0 |
| K Statistic | -0.219 |
| p-value | 0.213 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:25161918 | rs564871717 | R>L | B:25 | (79.04, -54.11, -21.88) |
| 4:25161909 | H>R | B:28 | (77.36, -49.01, -20.60) | |
| 4:25161898 | rs369863497 | I>V | B:32 | (84.41, -46.54, -21.86) |
| 4:25160720 | P>T | B:42 | (82.43, -36.47, -19.84) | |
| 4:25160710 | G>V | B:45 | (77.46, -37.42, -16.78) | |
| 4:25160687 | L>V | B:53 | (81.45, -51.58, -15.61) | |
| 4:25160668 | rs193096404 | A>G | B:59 | (91.09, -53.55, -11.38) |
| 4:25160666 | COSM1149918 | I>V | B:60 | (90.37, -56.92, -13.62) |
| 4:25160650 | N>S | B:65 | (93.11, -58.25, -8.77) | |
| 4:25160627 | G>R | B:73 | (107.15, -60.43, -3.01) | |
| 4:25160615 | G>R | B:77 | (98.87, -56.24, -2.92) | |
| 4:25160597 | COSM3661039 | L>V | B:83 | (86.35, -53.19, 4.77) |
| 4:25160588 | rs373439857 | R>C | B:86 | (84.78, -53.81, -1.28) |
| 4:25160580 | H>Q | B:88 | (90.65, -48.17, -1.85) | |
| 4:25160576 | R>G | B:90 | (88.87, -54.95, -5.52) | |
| 4:25158588 | H>R | B:93 | (100.06, -52.25, -6.81) | |
| 4:25158589 | rs151255181 | H>Y | B:93 | (100.06, -52.25, -6.81) |
| 4:25158576 | rs370020609 COSM1054639 COSM1594510 |
R>Q | B:97 | (108.09, -48.57, -12.28) |
| 4:25158571 | COSM1429242 COSM1429241 |
G>C | B:99 | (111.30, -43.63, -11.01) |
| 4:25158567 | D>G | B:100 | (109.15, -42.35, -13.49) | |
| 4:25158547 | rs372235675 | K>E | B:107 | (103.42, -55.42, -10.77) |
| 4:25158541 | A>T | B:109 | (97.87, -51.61, -15.75) | |
| 4:25158531 | rs368335242 | S>N | B:112 | (98.70, -47.03, -14.86) |
| 4:25158529 | L>F | B:113 | (94.82, -46.59, -17.66) | |
| 4:25158520 | K>E | B:116 | (98.15, -41.76, -17.88) | |
| 4:25158515 | I>M | B:117 | (92.44, -41.34, -17.55) | |
| 4:25158508 | S>P | B:120 | (93.37, -36.04, -19.13) | |
| 4:25158495 | D>A | B:124 | (89.73, -30.94, -20.06) | |
| 4:25158493 | I>L | B:125 | (88.79, -29.15, -16.03) | |
| 4:25157814 | rs142338876 | V>A | B:131 | (94.51, -21.96, -18.40) |
| 4:25157815 | V>I | B:131 | (94.51, -21.96, -18.40) | |
| 4:25157800 | N>D | B:136 | (101.28, -31.04, -18.73) | |
| 4:25157781 | M>T | B:142 | (101.45, -34.27, -2.11) | |
| 4:25157722 | A>S | B:162 | (119.82, -20.63, -4.58) | |
| 4:25157715 | Y>F | B:164 | (117.69, -15.74, -0.56) | |
| 4:25157703 | rs142910181 | P>L | B:168 | (104.22, -12.02, -2.14) |
| 4:25157695 | D>H | B:171 | (98.84, -14.46, 6.51) | |
| 4:25157691 | rs376301014 | Q>R | B:172 | (98.38, -20.19, 4.73) |
| 4:25157678 | F>L | B:176 | (105.92, -19.28, 5.29) | |
| 4:25156769 | F>L | B:184 | (115.16, -22.80, -0.36) | |
| 4:25156758 | rs542097910 | V>A | B:188 | (108.44, -11.40, 3.39) |
| 4:25156759 | V>L | B:188 | (108.44, -11.40, 3.39) | |
| 4:25156737 | rs139718374 | G>D | B:195 | (92.28, 1.19, -0.46) |
| 4:25156728 | L>P | B:198 | (96.18, -5.76, 0.63) | |
| 4:25156726 | R>C | B:199 | (96.93, -4.92, -5.41) | |
| 4:25156711 | A>T | B:204 | (109.69, -4.28, -3.42) | |
| 4:25156707 | V>A | B:205 | (109.86, -7.37, -5.73) | |
| 4:25156702 | rs376967065 | A>T | B:207 | (114.47, -4.26, -4.72) |
| 4:25156688 | E>D | B:211 | (119.20, -6.45, -1.86) | |
| 4:25156677 | D>V | B:215 | (122.07, -15.71, -9.68) | |
| 4:25156656 | S>F | B:222 | (102.76, -16.11, -6.55) | |
| 4:25156651 | T>A | B:224 | (96.01, -16.43, -6.76) | |
| 4:25156644 | C>S | B:226 | (93.14, -15.05, -1.24) | |
| 4:25156639 | A>S | B:228 | (90.04, -10.67, 2.15) | |
| 4:25156630 | V>M | B:231 | (94.02, -9.23, -3.95) | |
| 4:25153671 | rs267607035 CM106589 |
A>T | B:239 | (105.99, -12.35, -15.31) |
| 4:25153664 | rs373816934 | I>T | B:241 | (110.04, -9.05, -12.90) |
| 4:25153665 | rs76429098 | I>V | B:241 | (110.04, -9.05, -12.90) |
| 4:25153638 | I>V | B:250 | (106.13, -20.91, -8.58) | |
| 4:25153626 | A>T | B:254 | (95.02, -23.23, -4.21) | |
| 4:25153613 | rs369165895 | Q>R | B:258 | (86.81, -21.86, -7.75) |
| 4:25153602 | C>S | B:262 | (92.26, -16.45, -11.14) | |
| 4:25153595 | rs377197666 | H>R | B:264 | (91.07, -15.89, -17.55) |
| 4:25153596 | H>Y | B:264 | (91.07, -15.89, -17.55) | |
| 4:25146752 | A>S | B:270 | (102.02, -16.80, -19.85) | |
| 4:25146748 | rs573577287 | R>Q | B:271 | (99.98, -12.94, -23.89) |
| 4:25146739 | R>K | B:274 | (109.49, -17.19, -16.44) | |
| 4:25146737 | I>V | B:275 | (104.20, -18.86, -15.38) | |
| 4:25146731 | A>T | B:277 | (104.29, -23.37, -12.25) | |
| 4:25146680 | I>L | B:294 | (97.00, -30.20, -9.87) | |
| 4:25146668 | F>L | B:298 | (102.45, -22.79, -19.29) | |
| 4:25146653 | I>V | B:303 | (105.89, -30.23, -15.73) | |
| 4:25146648 | Q>H | B:304 | (107.57, -34.63, -16.89) | |
| 4:25146645 | E>D | B:305 | (112.21, -31.73, -14.85) | |
| 4:25146641 | rs150309842 | S>G | B:307 | (107.24, -35.94, -12.11) |
| 4:25146626 | G>R | B:312 | (108.29, -43.33, -6.05) | |
| 4:25146485 | R>G | B:313 | (104.84, -47.47, -6.11) | |
| 4:25146475 | rs551551280 | A>V | B:316 | (95.51, -43.60, -5.86) |
| 4:25146452 | I>V | B:324 | (84.75, -40.99, -9.20) | |
| 4:25146434 | G>R | B:330 | (81.03, -33.30, -16.10) | |
| 4:25128933 | A>D | B:358 | (72.25, -2.73, 10.55) | |
| 4:25128927 | N>S | B:360 | (77.05, 1.09, 11.91) | |
| 4:25128928 | rs542031330 | N>D | B:360 | (77.05, 1.09, 11.91) |
| 4:25128912 | H>R | B:365 | (85.74, -1.89, -2.88) | |
| 4:25128909 | rs370101229 | T>I | B:366 | (87.59, -6.20, -2.50) |
| 4:25128901 | N>D | B:369 | (88.68, -11.21, -4.21) | |
| 4:25128894 | I>T | B:371 | (86.54, -16.14, -3.91) | |
| 4:25128888 | L>S | B:373 | (83.76, -11.16, 0.83) | |
| 4:25127404 | M>V | B:375 | (82.21, -7.30, 7.69) | |
| 4:25127383 | rs190476418 | E>K | B:382 | (88.74, -5.71, 21.98) |
| 4:25127380 | H>Y | B:383 | (90.20, -3.34, 24.41) | |
| 4:25127376 | R>H | B:384 | (87.06, -3.54, 26.23) | |
| 4:25127368 | A>T | B:387 | (84.26, -8.56, 20.92) | |
| 4:25127346 | rs527970470 | M>T | B:394 | (79.95, -16.50, 19.26) |
| 4:25127322 | G>E | B:402 | (84.70, -20.13, 7.33) | |
| 4:25125837 | L>F | B:408 | (93.75, -5.17, 15.26) | |
| 4:25125830 | S>C | B:410 | (97.91, -10.70, 15.66) | |
| 4:25125824 | Q>P | B:412 | (101.73, -16.26, 14.96) | |
| 4:25125809 | Y>C | B:417 | (108.89, -14.29, 9.97) | |
| 4:25125802 | COSM3603064 COSM3603063 |
F>L | B:419 | (104.11, -13.25, 10.55) |
| 4:25125801 | R>G | B:420 | (103.45, -7.94, 12.93) | |
| 4:25125794 | F>S | B:422 | (99.02, -13.84, 11.45) | |
| 4:25125790 | M>I | B:423 | (94.92, -13.52, 10.40) | |
| 4:25125783 | rs142133435 | T>A | B:426 | (99.42, -6.35, 6.86) |
| 4:25125767 | C>Y | B:431 | (90.07, -2.69, 10.46) | |
| 4:25125768 | rs572892329 | C>G | B:431 | (90.07, -2.69, 10.46) |
| 4:25125755 | N>S | B:435 | (86.73, -13.29, 6.14) | |
| 4:25125743 | A>D | B:439 | (83.00, -21.72, -2.51) | |
| 4:25125738 | G>R | B:441 | (79.09, -25.78, -3.37) | |
| 4:25125733 | M>I | B:442 | (78.10, -22.13, -1.15) | |
| 4:25125725 | Q>R | B:445 | (71.14, -23.68, 3.42) | |
| 4:25125715 | rs147623769 | D>E | B:448 | (70.41, -17.67, 4.12) |
| 4:25125717 | rs575049079 | D>N | B:448 | (70.41, -17.67, 4.12) |
| 4:25125708 | I>V | B:451 | (73.25, -13.59, 7.24) | |
| 4:25125703 | rs2302566 | K>N | B:452 | (69.67, -16.52, 11.12) |
| 4:25125705 | K>E | B:452 | (69.67, -16.52, 11.12) | |
| 4:25125677 | V>G | B:461 | (77.67, -8.70, 21.66) | |
| 4:25125678 | V>I | B:461 | (77.67, -8.70, 21.66) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:25160704 | COSM1133223 | D>G | B:47 | (75.10, -43.73, -14.65) |
| 4:25160597 | COSM3661039 | L>V | B:83 | (86.35, -53.19, 4.77) |
| 4:25160585 | COSM3714857 | R>C | B:87 | (88.26, -47.49, 1.13) |
| 4:25158580 | COSM1753692 | G>R | B:96 | (103.97, -45.98, -10.61) |
| 4:25153662 | COSM1670922 | C>G | B:242 | (110.68, -13.27, -13.98) |
| 4:25146754 | COSM1618728 | G>E | B:269 | (101.36, -14.28, -17.78) |
| 4:25127356 | COSM1618726 | L>F | B:391 | (82.39, -13.07, 17.19) |