General Structure Information
| PDB ID | 2vxo |
| HGNC Gene Label(s) | GMPS |
| Structure Name | human gmp synthetase in complex with xmp |
| Resolution | 2.5Å |
| Reference | AUTH M.WELIN,L.LEHTIO,A.JOHANSSON,S.FLODIN,T.NYMAN,AUTH 2 L.TRESAUGUES,M.HAMMARSTROM,S.GRASLUND,P.NORDLUNDTITL SUBSTRATE SPECIFICITY AND OLIGOMERIZATION OF HUMANTITL 2 GMP SYNTHETASEREF J.MOL.BIOL. V. 425 4323 2013REFN ISSN 0022-2836PMID 23816837DOI 10.1016/J.JMB.2013.06.032 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 658 |
| Number Of SNVs | 129 |
| Number Of Permutations | 71235 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.014 |
| p-value | 0.069 |
COSMIC
| Number Of Residues | 658 |
| Number Of SNVs | 7 |
| Number Of Permutations | 2713 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.048 |
| p-value | 0.67 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 129 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.064 |
| p-value | 0.499 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:155611349 | Y>N | B:24 | (-1.72, -5.70, 16.87) | |
| 3:155611350 | Y>C | B:24 | (-1.72, -5.70, 16.87) | |
| 3:155611359 | A>V | B:27 | (-1.59, -11.52, 17.85) | |
| 3:155611391 | G>R | B:38 | (9.10, -13.90, 7.74) | |
| 3:155611406 | R>G | B:43 | (2.01, -17.37, 5.54) | |
| 3:155611407 | R>Q | B:43 | (2.01, -17.37, 5.54) | |
| 3:155611427 | COSM1040308 | V>M | B:50 | (-3.23, -16.44, 13.51) |
| 3:155611445 | P>A | B:56 | (11.87, -4.88, 13.69) | |
| 3:155611487 | rs557093697 COSM1040311 |
R>C | B:70 | (-1.79, -14.38, 22.89) |
| 3:155615720 | I>V | B:72 | (7.42, -13.71, 20.18) | |
| 3:155615723 | I>V | B:73 | (7.78, -16.22, 15.92) | |
| 3:155615726 | I>V | B:74 | (12.56, -15.23, 16.77) | |
| 3:155615741 | N>D | B:79 | (24.71, -16.15, 10.42) | |
| 3:155615747 | V>L | B:81 | (24.70, -15.15, 17.82) | |
| 3:155615751 | Y>C | B:82 | (28.24, -16.11, 19.95) | |
| 3:155615766 | P>L | B:87 | (22.14, -8.33, 14.90) | |
| 3:155615769 | W>L | B:88 | (20.20, -4.42, 20.04) | |
| 3:155615783 | rs199978101 | I>V | B:93 | (12.33, -10.33, 23.63) |
| 3:155615785 | rs201129196 | I>M | B:93 | (12.33, -10.33, 23.63) |
| 3:155615799 | K>R | B:98 | (4.51, -12.69, 25.95) | |
| 3:155615817 | C>F | B:104 | (17.49, -21.30, 13.80) | |
| 3:155615820 | Y>C | B:105 | (20.06, -15.76, 14.59) | |
| 3:155621654 | M>I | B:109 | (18.82, -15.41, 19.64) | |
| 3:155621685 | rs188563169 COSM1420202 |
K>E | B:120 | (34.00, -24.39, 18.16) |
| 3:155621687 | rs376876444 | K>N | B:120 | (34.00, -24.39, 18.16) |
| 3:155621689 | rs201024446 | K>R | B:121 | (33.05, -26.53, 15.58) |
| 3:155621691 | rs138147895 | S>C | B:122 | (30.94, -25.29, 12.83) |
| 3:155621718 | I>V | B:131 | (15.08, -35.68, 13.56) | |
| 3:155621721 | rs77673033 | S>G | B:132 | (14.80, -37.21, 17.38) |
| 3:155621744 | L>F | B:139 | (6.58, -27.55, 19.96) | |
| 3:155623950 | rs371139266 COSM1327768 |
G>S | B:142 | (1.44, -35.48, 17.70) |
| 3:155623971 | rs375164448 | V>I | B:149 | (13.59, -31.79, 9.51) |
| 3:155623990 | rs370614063 | D>V | B:155 | (26.66, -22.21, 15.34) |
| 3:155624007 | A>T | B:161 | (20.58, -23.25, 28.76) | |
| 3:155624031 | R>C | B:169 | (19.24, -35.02, 20.62) | |
| 3:155624032 | rs374038217 | R>H | B:169 | (19.24, -35.02, 20.62) |
| 3:155624043 | I>L | B:173 | (23.40, -31.99, 16.40) | |
| 3:155624044 | I>T | B:173 | (23.40, -31.99, 16.40) | |
| 3:155624046 | V>I | B:174 | (21.08, -29.78, 19.87) | |
| 3:155624049 | A>T | B:175 | (17.54, -29.61, 17.34) | |
| 3:155628483 | I>V | B:177 | (15.78, -25.83, 23.09) | |
| 3:155628513 | A>S | B:187 | (14.31, -24.94, 16.56) | |
| 3:155628524 | H>Q | B:190 | (13.45, -23.48, 9.04) | |
| 3:155628531 | V>I | B:193 | (9.30, -25.20, 5.25) | |
| 3:155628549 | rs549646564 | G>R | B:199 | (5.27, -28.01, 10.64) |
| 3:155628582 | I>V | B:210 | (1.84, -22.97, 23.71) | |
| 3:155628585 | rs186169824 | A>T | B:211 | (-0.39, -19.10, 22.94) |
| 3:155628609 | rs371983046 COSM3373067 |
V>M | B:219 | (-11.30, -14.42, 4.80) |
| 3:155628625 | L>H | B:224 | (-16.69, -8.52, 8.87) | |
| 3:155628630 | C>R | B:226 | (-12.75, -4.33, 5.47) | |
| 3:155628637 | rs138589926 | R>Q | B:228 | (-14.58, -1.18, 11.00) |
| 3:155628650 | E>D | B:232 | (-14.62, 5.27, 9.65) | |
| 3:155628652 | rs190756684 | R>T | B:233 | (-11.70, 7.43, 4.46) |
| 3:155628654 | V>I | B:234 | (-16.74, 6.56, 3.07) | |
| 3:155628660 | T>S | B:236 | (-22.43, 9.52, 3.58) | |
| 3:155628661 | rs571738939 | T>M | B:236 | (-22.43, 9.52, 3.58) |
| 3:155628909 | L>I | B:243 | (-16.60, -2.82, -13.46) | |
| 3:155628919 | G>E | B:246 | (-12.64, -8.46, -13.44) | |
| 3:155628930 | T>A | B:250 | (-16.21, -7.91, -9.58) | |
| 3:155628964 | COSM4114768 | N>S | B:261 | (-26.12, 2.23, 1.23) |
| 3:155628974 | Q>H | B:264 | (-23.00, 5.06, -0.82) | |
| 3:155628981 | A>P | B:267 | (-20.85, 1.00, -11.03) | |
| 3:155629015 | R>Q | B:278 | (-20.85, -11.98, -23.46) | |
| 3:155629045 | rs369699211 | K>R | B:288 | (-29.12, -6.84, -11.93) |
| 3:155629049 | K>N | B:289 | (-28.72, -10.78, -8.98) | |
| 3:155629050 | L>F | B:290 | (-25.98, -10.17, -6.07) | |
| 3:155629054 | G>E | B:291 | (-28.20, -5.85, -6.28) | |
| 3:155632217 | A>G | B:299 | (-17.44, 3.06, -26.07) | |
| 3:155632223 | H>R | B:301 | (-18.08, 2.76, -32.29) | |
| 3:155632225 | S>A | B:302 | (-14.97, 5.97, -28.88) | |
| 3:155632231 | Y>H | B:304 | (-13.47, 0.40, -32.24) | |
| 3:155632235 | rs373717937 | N>S | B:305 | (-12.58, 5.92, -34.10) |
| 3:155632247 | T>N | B:309 | (-0.35, 12.57, -28.25) | |
| 3:155632298 | T>M | B:326 | (-7.08, 5.75, -35.92) | |
| 3:155632306 | M>V | B:329 | (-5.72, 3.01, -39.30) | |
| 3:155632312 | T>A | B:331 | (0.34, -1.34, -36.66) | |
| 3:155632313 | T>R | B:331 | (0.34, -1.34, -36.66) | |
| 3:155632323 | COSM1316684 | E>D | B:334 | (3.94, 1.81, -27.68) |
| 3:155632349 | rs200285083 | T>N | B:343 | (-9.73, 6.83, -24.40) |
| 3:155633815 | N>S | B:349 | (-13.13, 12.78, -16.37) | |
| 3:155633837 | N>K | B:356 | (-22.93, 16.56, -11.49) | |
| 3:155633880 | rs368021083 | P>T | B:371 | (-1.50, -0.49, -4.64) |
| 3:155633890 | I>T | B:374 | (3.75, 7.34, -8.38) | |
| 3:155633893 | E>G | B:375 | (2.53, 3.89, -12.38) | |
| 3:155633905 | L>P | B:379 | (4.40, -0.32, -16.91) | |
| 3:155633907 | V>I | B:380 | (1.33, 2.72, -19.09) | |
| 3:155633922 | A>T | B:385 | (-1.12, -0.37, -14.97) | |
| 3:155633925 | E>K | B:386 | (-2.50, 1.92, -11.06) | |
| 3:155633945 | H>Q | B:392 | (-3.57, 10.97, -18.24) | |
| 3:155633961 | I>V | B:398 | (-9.44, 11.45, -12.28) | |
| 3:155633969 | rs542017631 | K>N | B:400 | (-9.41, 17.33, -8.33) |
| 3:155633976 | E>K | B:403 | (-3.94, 15.14, -6.00) | |
| 3:155637097 | E>Q | B:430 | (-16.62, -20.69, -8.66) | |
| 3:155640018 | rs529546850 | Y>C | B:454 | (9.02, -7.70, -40.07) |
| 3:155640030 | D>A | B:458 | (17.46, -11.04, -41.50) | |
| 3:155640031 | D>E | B:458 | (17.46, -11.04, -41.50) | |
| 3:155640042 | T>N | B:462 | (16.98, -16.78, -40.99) | |
| 3:155640077 | rs375802837 | A>S | B:474 | (19.87, -34.68, -44.43) |
| 3:155643057 | A>T | B:488 | (29.55, -24.13, -34.21) | |
| 3:155643066 | COSM249533 | T>A | B:491 | (25.45, -28.33, -28.07) |
| 3:155643075 | D>Y | B:494 | (21.37, -29.68, -28.82) | |
| 3:155643084 | rs543486361 | K>Q | B:497 | (17.62, -33.75, -28.86) |
| 3:155643098 | I>M | B:501 | (13.87, -34.68, -33.92) | |
| 3:155643135 | I>V | B:514 | (4.56, -11.60, -38.54) | |
| 3:155643139 | rs577316787 | K>R | B:515 | (6.29, -7.21, -35.87) |
| 3:155643142 | rs374436916 | T>N | B:516 | (6.15, -10.77, -31.92) |
| 3:155649563 | R>C | B:524 | (8.90, -5.82, -24.44) | |
| 3:155649564 | R>H | B:524 | (8.90, -5.82, -24.44) | |
| 3:155649576 | rs61750370 | Y>S | B:528 | (11.39, -12.08, -37.98) |
| 3:155649578 | V>M | B:529 | (7.16, -15.70, -36.00) | |
| 3:155649596 | K>E | B:535 | (3.71, -35.01, -44.08) | |
| 3:155649605 | P>T | B:538 | (2.27, -33.77, -33.77) | |
| 3:155649606 | rs61750371 | P>R | B:538 | (2.27, -33.77, -33.77) |
| 3:155649618 | rs539338092 | S>L | B:542 | (10.30, -32.50, -30.36) |
| 3:155649643 | rs190602670 | I>M | B:550 | (15.10, -21.91, -33.27) |
| 3:155649644 | P>S | B:551 | (15.32, -19.08, -30.15) | |
| 3:155649648 | R>H | B:552 | (19.16, -21.82, -27.68) | |
| 3:155649650 | M>V | B:553 | (20.49, -20.88, -33.32) | |
| 3:155649653 | C>G | B:554 | (18.09, -17.21, -34.03) | |
| 3:155649654 | C>Y | B:554 | (18.09, -17.21, -34.03) | |
| 3:155649660 | COSM1662005 | N>S | B:556 | (16.23, -12.97, -35.49) |
| 3:155649661 | N>K | B:556 | (16.23, -12.97, -35.49) | |
| 3:155649662 | rs368366043 | V>I | B:557 | (13.46, -15.58, -33.48) |
| 3:155652706 | V>F | B:560 | (8.39, -21.14, -32.21) | |
| 3:155652717 | I>M | B:563 | (1.59, -24.54, -38.55) | |
| 3:155652724 | rs375949741 | P>S | B:566 | (-1.05, -29.83, -44.24) |
| 3:155652740 | P>H | B:571 | (6.21, -20.13, -47.24) | |
| 3:155652806 | F>S | B:593 | (-17.02, -18.61, -27.42) | |
| 3:155652815 | H>R | B:596 | (-11.24, -19.82, -23.87) | |
| 3:155652818 | N>S | B:597 | (-16.12, -22.79, -24.63) | |
| 3:155652820 | rs369687989 | I>V | B:598 | (-13.14, -26.60, -26.06) |
| 3:155652827 | R>K | B:600 | (-14.30, -23.16, -18.46) | |
| 3:155654135 | rs376980044 | G>R | B:606 | (-6.98, -24.60, -14.26) |
| 3:155654145 | S>T | B:609 | (-2.56, -19.38, -16.30) | |
| 3:155654190 | P>L | B:624 | (2.54, -20.03, -55.91) | |
| 3:155654192 | L>F | B:625 | (2.58, -20.87, -59.92) | |
| 3:155654193 | L>P | B:625 | (2.58, -20.87, -59.92) | |
| 3:155654248 | rs369558652 | S>R | B:643 | (3.77, -18.40, -10.81) |
| 3:155654283 | rs372602278 | N>S | B:655 | (1.94, -32.82, -20.15) |
| 3:155654298 | E>G | B:660 | (-9.03, -35.04, -27.39) | |
| 3:155655384 | rs534566538 | V>A | B:662 | (-5.68, -28.83, -28.76) |
| 3:155655416 | COSM3589282 | P>A | B:673 | (-15.73, -17.76, -41.56) |
| 3:155655455 | P>T | B:686 | (12.23, -16.34, -21.56) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:155621691 | COSM4981092 | S>C | B:122 | (30.94, -25.29, 12.83) |
| 3:155628496 | COSM218754 | S>F | B:181 | (8.07, -22.68, 32.83) |
| 3:155628517 | COSM3737260 | Q>L | B:188 | (18.56, -25.61, 14.62) |
| 3:155628985 | COSM1420205 | V>A | B:268 | (-18.98, 2.56, -14.27) |
| 3:155652728 | COSM3589280 | P>L | B:567 | (2.72, -29.93, -45.29) |
| 3:155652730 | COSM3660294 | V>I | B:568 | (3.77, -25.28, -45.16) |
| 3:155652794 | COSM1040324 | R>H | B:589 | (-15.70, -11.18, -30.69) |
| 3:155655429 | COSM1040325 | R>Q | B:677 | (-2.99, -23.55, -41.80) |