General Structure Information
| PDB ID | 4fgu |
| HGNC Gene Label(s) | LGMN |
| Structure Name | crystal structure of prolegumain |
| Resolution | 3.9Å |
| Reference | AUTH E.DALL,H.BRANDSTETTERTITL MECHANISTIC AND STRUCTURAL STUDIES ON LEGUMAIN EXPLAIN ITSTITL 2 ZYMOGENICITY, DISTINCT ACTIVATION PATHWAYS, AND REGULATION.REF PROC.NATL.ACAD.SCI.USA V. 110 10940 2013REFN ISSN 0027-8424PMID 23776206DOI 10.1073/PNAS.1300686110 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 404 |
| Number Of SNVs | 107 |
| Number Of Permutations | 48941 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.008 |
| p-value | 0.322 |
COSMIC
| Number Of Residues | 404 |
| Number Of SNVs | 3 |
| Number Of Permutations | 77 |
| Optimal Distance Threshold | 27.0 |
| K Statistic | 0.667 |
| p-value | 0.796 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 107 |
| Number Of COSMIC SNVs | 3 |
| Optimal Distance Threshold | 30.0 |
| K Statistic | 0.436 |
| p-value | 0.962 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:93199032 | V>M | B:34 | (48.96, -23.98, 5.30) | |
| 14:93199020 | N>D | B:38 | (37.87, -18.93, 2.24) | |
| 14:93185176 | H>R | B:51 | (44.69, -36.90, 3.81) | |
| 14:93185157 | COSM3886545 | H>Q | B:57 | (49.43, -38.44, 15.02) |
| 14:93185156 | COSM470355 | R>C | B:58 | (49.15, -43.22, 10.33) |
| 14:93185152 | N>S | B:59 | (53.75, -41.89, 11.10) | |
| 14:93185153 | rs375074674 | N>D | B:59 | (53.75, -41.89, 11.10) |
| 14:93185129 | rs118128989 | V>I | B:67 | (51.54, -25.90, 13.22) |
| 14:93185120 | rs146179634 | M>L | B:70 | (42.43, -24.63, 9.27) |
| 14:93185114 | rs143384572 | D>N | B:72 | (37.66, -24.52, 10.87) |
| 14:93185105 | A>S | B:75 | (33.24, -28.64, 9.42) | |
| 14:93185096 | E>Q | B:78 | (24.88, -23.58, 7.35) | |
| 14:93183804 | rs147987484 | N>S | B:80 | (28.68, -29.99, 5.91) |
| 14:93183798 | rs554526546 | T>I | B:82 | (28.89, -34.47, 7.36) |
| 14:93183790 | I>V | B:85 | (32.45, -35.65, 9.10) | |
| 14:93183771 | rs143487234 | N>S | B:91 | (32.49, -42.81, -0.28) |
| 14:93183766 | T>A | B:93 | (38.32, -42.02, 5.80) | |
| 14:93183760 | V>I | B:95 | (40.40, -36.56, 7.59) | |
| 14:93183747 | V>A | B:99 | (42.94, -31.43, 13.75) | |
| 14:93183748 | V>I | B:99 | (42.94, -31.43, 13.75) | |
| 14:93183744 | rs369016620 | P>L | B:100 | (45.86, -29.44, 15.93) |
| 14:93183733 | T>A | B:104 | (41.73, -20.33, 13.48) | |
| 14:93182565 | D>G | B:107 | (44.50, -15.81, 13.06) | |
| 14:93182559 | T>N | B:109 | (48.04, -14.38, 8.23) | |
| 14:93182560 | T>A | B:109 | (48.04, -14.38, 8.23) | |
| 14:93182548 | F>V | B:113 | (53.47, -18.92, 7.54) | |
| 14:93182539 | V>L | B:116 | (55.96, -20.24, 12.60) | |
| 14:93182527 | D>N | B:120 | (58.77, -14.48, 15.73) | |
| 14:93182512 | K>E | B:125 | (52.80, -13.33, 23.21) | |
| 14:93182505 | I>T | B:127 | (47.78, -15.03, 18.37) | |
| 14:93182506 | I>V | B:127 | (47.78, -15.03, 18.37) | |
| 14:93182497 | rs369708299 | G>S | B:130 | (51.49, -19.64, 19.33) |
| 14:93180782 | H>L | B:140 | (65.08, -33.41, 9.62) | |
| 14:93180780 | V>M | B:141 | (61.85, -28.98, 8.47) | |
| 14:93180771 | Y>N | B:144 | (50.98, -29.15, 2.31) | |
| 14:93180752 | rs559615556 | S>Y | B:150 | (50.12, -16.46, -8.67) |
| 14:93180740 | rs141510288 | L>P | B:154 | (51.39, -18.19, -2.02) |
| 14:93180728 | N>S | B:158 | (42.05, -11.72, 3.91) | |
| 14:93180223 | V>G | B:163 | (58.92, -14.61, -3.21) | |
| 14:93180194 | M>L | B:173 | (65.13, -20.72, 8.86) | |
| 14:93180172 | R>Q | B:180 | (70.74, -31.47, 8.65) | |
| 14:93179216 | M>L | B:182 | (63.66, -27.74, 4.66) | |
| 14:93179212 | V>A | B:183 | (60.82, -30.78, 2.38) | |
| 14:93179202 | I>M | B:186 | (53.91, -26.17, -2.78) | |
| 14:93179188 | rs370554711 | S>F | B:191 | (53.54, -23.03, -7.59) |
| 14:93179172 | N>K | B:196 | (61.88, -20.54, -9.67) | |
| 14:93179173 | N>S | B:196 | (61.88, -20.54, -9.67) | |
| 14:93179164 | P>L | B:199 | (69.13, -22.14, -3.70) | |
| 14:93179152 | N>S | B:203 | (70.43, -28.01, 2.84) | |
| 14:93178289 | T>A | B:208 | (55.70, -27.52, -7.36) | |
| 14:93178279 | rs143914416 | N>T | B:211 | (54.66, -24.89, -14.64) |
| 14:93178267 | S>L | B:215 | (46.73, -23.96, -13.31) | |
| 14:93178259 | A>T | B:218 | (40.64, -30.51, -9.11) | |
| 14:93178240 | K>T | B:224 | (26.18, -36.26, 0.16) | |
| 14:93178231 | rs199988257 | T>M | B:227 | (31.85, -29.58, -3.36) |
| 14:93178203 | N>K | B:236 | (48.74, -38.73, -6.67) | |
| 14:93178189 | S>L | B:241 | (52.06, -41.89, 1.66) | |
| 14:93178066 | rs370383475 | K>E | B:253 | (59.82, -44.25, -5.31) |
| 14:93178059 | Y>C | B:255 | (59.07, -35.66, -8.89) | |
| 14:93178057 | H>Y | B:256 | (59.25, -39.79, -11.82) | |
| 14:93178044 | COSM3815553 | S>L | B:260 | (53.12, -40.06, -13.80) |
| 14:93178042 | H>Y | B:261 | (49.92, -40.94, -11.05) | |
| 14:93178032 | rs367813667 | T>I | B:264 | (46.68, -31.86, -15.37) |
| 14:93178030 | S>G | B:265 | (50.09, -30.56, -14.48) | |
| 14:93178024 | rs376054031 COSM958887 |
V>I | B:267 | (55.11, -32.19, -11.21) |
| 14:93178020 | M>R | B:268 | (58.36, -29.22, -11.52) | |
| 14:93178008 | N>I | B:272 | (69.91, -30.40, -2.78) | |
| 14:93178005 | K>R | B:273 | (67.39, -31.99, -7.26) | |
| 14:93176192 | Q>P | B:282 | (64.40, -38.50, 7.56) | |
| 14:93176188 | COSM1707736 | F>L | B:283 | (61.57, -35.06, 5.91) |
| 14:93176175 | R>C | B:288 | (55.87, -45.94, 14.47) | |
| 14:93176168 | rs151054975 | A>G | B:290 | (55.44, -50.77, 9.44) |
| 14:93176160 | P>S | B:293 | (48.33, -48.94, 6.21) | |
| 14:93176157 | rs144367876 | V>I | B:294 | (46.00, -47.36, 3.81) |
| 14:93176153 | rs200318849 COSM3499021 |
P>L | B:295 | (43.58, -49.77, 1.84) |
| 14:93176154 | P>A | B:295 | (43.58, -49.77, 1.84) | |
| 14:93176144 | rs1803450 | P>L | B:298 | (38.87, -48.50, -6.82) |
| 14:93176141 | V>D | B:299 | (37.65, -43.92, -7.77) | |
| 14:93176134 | H>Q | B:301 | (33.87, -40.13, -8.66) | |
| 14:93176136 | rs375443194 COSM375203 |
H>Y | B:301 | (33.87, -40.13, -8.66) |
| 14:93176130 | COSM958886 | D>N | B:303 | (35.76, -35.25, -11.71) |
| 14:93176118 | S>G | B:307 | (41.20, -24.29, -9.48) | |
| 14:93176108 | rs147211899 | V>A | B:310 | (35.85, -24.98, -9.24) |
| 14:93176103 | L>V | B:312 | (31.79, -21.53, -12.81) | |
| 14:93176094 | M>V | B:315 | (27.51, -22.90, -10.31) | |
| 14:93176079 | COSM4053072 | M>V | B:320 | (22.33, -30.31, -16.02) |
| 14:93176047 | Q>H | B:330 | (18.32, -18.91, -6.48) | |
| 14:93176049 | Q>K | B:330 | (18.32, -18.91, -6.48) | |
| 14:93176042 | rs148659834 | T>M | B:332 | (21.53, -18.40, -13.56) |
| 14:93176036 | E>A | B:334 | (25.49, -17.33, -8.34) | |
| 14:93176027 | R>Q | B:337 | (27.61, -13.04, -9.36) | |
| 14:93176028 | rs570992743 | R>W | B:337 | (27.61, -13.04, -9.36) |
| 14:93176019 | rs137891145 | D>N | B:340 | (29.55, -10.46, -15.90) |
| 14:93172994 | rs201178397 | R>M | B:342 | (35.88, -15.09, -15.93) |
| 14:93172970 | COSM3722363 | R>H | B:350 | (42.88, -5.94, -24.37) |
| 14:93172971 | rs150729870 | R>C | B:350 | (42.88, -5.94, -24.37) |
| 14:93172962 | V>I | B:353 | (48.19, -2.79, -22.24) | |
| 14:93172952 | L>P | B:356 | (51.07, 1.51, -21.39) | |
| 14:93172950 | A>S | B:357 | (51.56, 0.46, -25.42) | |
| 14:93172946 | rs202013232 | A>V | B:358 | (52.31, 0.61, -28.87) |
| 14:93172943 | S>Y | B:359 | (48.98, -0.11, -30.17) | |
| 14:93172932 | COSM1582282 | V>M | B:363 | (48.73, -5.24, -26.81) |
| 14:93172923 | L>F | B:366 | (52.12, -7.34, -23.12) | |
| 14:93172914 | rs370307281 | E>K | B:369 | (54.62, -12.16, -24.24) |
| 14:93172898 | rs200336740 | T>M | B:374 | (63.38, -10.93, -12.34) |
| 14:93172835 | rs138973517 | S>C | B:395 | (36.06, -11.10, -3.29) |
| 14:93171049 | E>K | B:399 | (38.74, -16.56, -7.38) | |
| 14:93171039 | L>S | B:402 | (44.97, -14.91, -9.51) | |
| 14:93171036 | R>K | B:403 | (43.73, -17.59, -15.47) | |
| 14:93171033 | rs145149674 | H>R | B:404 | (44.15, -11.69, -15.81) |
| 14:93171025 | rs149227402 | V>M | B:407 | (49.81, -9.21, -17.57) |
| 14:93171019 | rs145185556 | V>I | B:409 | (55.27, -9.82, -14.96) |
| 14:93171001 | P>S | B:415 | (60.83, -1.90, -20.30) | |
| 14:93170994 | rs61734480 | P>L | B:417 | (57.16, 2.90, -15.91) |
| 14:93170698 | rs376864711 | L>S | B:423 | (48.92, 6.51, -13.78) |
| 14:93170693 | rs189997608 | M>V | B:425 | (45.79, 0.44, -12.85) |
| 14:93170684 | V>L | B:428 | (40.89, 2.06, -16.07) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:93185098 | COSM1749021 | S>F | B:77 | (29.16, -25.50, 7.24) |
| 14:93182544 | COSM3706440 | L>R | B:114 | (56.50, -15.74, 7.88) |
| 14:93178208 | COSM958888 | V>I | B:235 | (45.37, -36.70, -3.75) |