1SU3.A | MMP1 – ASTRID

1SU3.A | MMP1

General Structure Information

PDB ID	1su3
HGNC Gene Label(s)	MMP1
Structure Name	x-ray structure of human prommp-1: new insights into collagenase action
Resolution	2.2Å
Reference	AUTH D.JOZIC,G.BOURENKOV,N.H.LIM,R.VISSE,H.NAGASE,AUTH 2 W.BODE,K.MASKOSTITL X-RAY STRUCTURE OF HUMAN PROMMP-1: NEW INSIGHTSTITL 2 INTO PROCOLLAGENASE ACTIVATION AND COLLAGENTITL 3 BINDING.REF J.BIOL.CHEM. V. 280 9578 2005REFN ISSN 0021-9258PMID 15611040DOI 10.1074/JBC.M411084200

Variant Set Distributions

ExAC Variants

Number Of Residues	415
Number Of SNVs	136
Number Of Permutations	64018
Optimal Distance Threshold	8.0
K Statistic	0.026
p-value	0.6

COSMIC

Number Of Residues	415
Number Of SNVs	15
Number Of Permutations	3784
Optimal Distance Threshold	26.0
K Statistic	0.533
p-value	0.156

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	136
Number Of COSMIC SNVs	13
Optimal Distance Threshold	28.0
K Statistic	0.275
p-value	0.016

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:102668730		D>Y	A:32	(64.91, -26.54, 70.90)
11:102668219		K>E	A:40	(57.34, -33.74, 62.68)
11:102668159	rs200810479	V>L	A:60	(70.16, -27.81, 61.95)
11:102668135		Q>K	A:68	(63.73, -19.41, 57.78)
11:102668125		F>S	A:71	(56.79, -20.74, 56.77)
11:102668122	COSM352328	G>E	A:72	(59.15, -15.92, 54.66)
11:102668114		V>L	A:75	(67.07, -16.88, 55.17)
11:102668111	rs148103425	T>P	A:76	(69.58, -16.97, 59.20)
11:102668102	COSM1350403	P>A	A:79	(66.77, -19.26, 66.27)
11:102668095	rs376694849	A>V	A:81	(61.18, -14.79, 67.61)
11:102668089	rs143788145	T>N	A:83	(61.19, -18.71, 63.59)
11:102668082		K>N	A:85	(55.19, -16.69, 66.06)
11:102668077		M>T	A:87	(58.33, -23.49, 64.97)
11:102668072	rs371763181	Q>E	A:89	(51.85, -21.50, 64.10)
11:102668045		A>S	A:98	(60.36, -34.62, 50.57)
11:102668017		P>L	A:107	(50.32, -39.81, 43.39)
11:102668014	rs201865180	R>H	A:108	(45.90, -39.28, 39.30)
11:102668015	rs534208150	R>C	A:108	(45.90, -39.28, 39.30)
11:102667999	rs554687805	H>R	A:113	(34.44, -41.67, 39.51)
11:102668000		H>Y	A:113	(34.44, -41.67, 39.51)
11:102667890		I>M	A:118	(32.99, -41.10, 58.18)
11:102667880		T>S	A:122	(33.67, -35.85, 67.02)
11:102667876		P>L	A:123	(32.22, -35.93, 70.47)
11:102667871		L>M	A:125	(30.42, -31.52, 66.28)
11:102667868		P>S	A:126	(26.74, -32.75, 65.71)
11:102667862		A>P	A:128	(25.44, -33.88, 60.75)
11:102667851		D>E	A:131	(28.50, -35.98, 57.68)
11:102667849		H>L	A:132	(27.76, -30.11, 55.82)
11:102667843		I>T	A:134	(33.69, -34.15, 55.32)
11:102667813		V>A	A:144	(37.85, -27.42, 40.37)
11:102667761		I>M	A:161	(37.53, -40.12, 57.46)
11:102667763		I>L	A:161	(37.53, -40.12, 57.46)
11:102667760		S>T	A:162	(39.45, -40.92, 61.50)
11:102667754		V>F	A:164	(42.44, -40.41, 66.31)
11:102667750		R>K	A:165	(42.93, -39.82, 72.19)
11:102667514		R>Q	A:169	(48.64, -47.24, 64.14)
11:102667515	rs200717412	R>W	A:169	(48.64, -47.24, 64.14)
11:102667510		D>E	A:170	(49.85, -44.50, 61.70)
11:102667508		N>S	A:171	(54.30, -45.06, 62.55)
11:102667505		S>C	A:172	(51.85, -40.90, 62.94)
11:102667461		P>A	A:187	(47.45, -41.11, 46.77)
11:102667449	rs17879973	I>V	A:191	(46.66, -46.16, 54.78)
11:102667443		G>R	A:193	(43.82, -41.28, 51.69)
11:102667440		D>H	A:194	(43.39, -42.61, 54.89)
11:102667430		F>S	A:197	(40.71, -35.40, 61.47)
11:102667431	rs371484770	F>L	A:197	(40.71, -35.40, 61.47)
11:102667420	rs369054402	D>E	A:200	(42.88, -34.47, 71.85)
11:102667413	COSM3808188	W>R	A:203	(38.02, -30.59, 65.54)
11:102667409		T>I	A:204	(34.40, -26.05, 65.23)
11:102666327		H>Y	A:213	(35.04, -27.39, 55.99)
11:102666324	COSM540587 COSM922289	R>C	A:214	(40.72, -24.98, 56.70)
11:102666321		V>F	A:215	(41.23, -29.14, 58.67)
11:102666317	COSM3981246 COSM1638721	A>V	A:216	(39.22, -31.33, 55.81)
11:102666312		H>Y	A:218	(45.02, -29.33, 54.37)
11:102666308		E>V	A:219	(43.48, -33.26, 54.38)
11:102666303	rs200875962	G>S	A:221	(44.45, -32.90, 49.45)
11:102666280		H>Q	A:228	(52.05, -28.60, 52.67)
11:102666282		H>N	A:228	(52.05, -28.60, 52.67)
11:102666275		T>I	A:230	(54.45, -21.23, 50.13)
11:102666267		G>R	A:233	(45.96, -18.42, 51.13)
11:102666254		Y>C	A:237	(50.30, -22.06, 54.98)
11:102666249		S>R	A:239	(49.60, -23.40, 59.21)
11:102666234		G>S	A:244	(35.46, -17.16, 56.54)
11:102666227		V>D	A:246	(36.22, -22.40, 53.44)
11:102666215		Q>R	A:250	(43.69, -19.76, 41.73)
11:102666209	rs513964	D>G	A:252	(44.46, -24.51, 46.18)
11:102666207	COSM540588	I>V	A:253	(42.25, -24.13, 41.71)
11:102666200	COSM1676392	G>D	A:255	(47.11, -27.90, 41.71)
11:102666188		I>T	A:259	(46.89, -33.72, 39.59)
11:102666016		S>C	A:263	(35.71, -28.73, 35.13)
11:102666005		V>F	A:267	(31.91, -21.52, 35.25)
11:102665999		P>S	A:269	(35.95, -22.35, 38.63)
11:102665996		I>F	A:270	(37.75, -17.78, 40.28)
11:102665992	rs374600625	G>A	A:271	(40.13, -17.67, 43.08)
11:102665983	rs149392574	T>I	A:274	(47.69, -14.05, 47.43)
11:102665974	rs371416460 COSM1196481	A>V	A:277	(54.35, -6.73, 48.00)
11:102665968		D>V	A:279	(52.95, -6.62, 42.32)
11:102665947	COSM2108432 COSM685765	A>V	A:286	(42.57, 0.02, 52.91)
11:102665948		A>T	A:286	(42.57, 0.02, 52.91)
11:102665941	rs186925812	T>I	A:288	(45.04, 2.44, 59.13)
11:102665942	rs377717830	T>A	A:288	(45.04, 2.44, 59.13)
11:102665936	rs199702254	I>L	A:290	(47.10, 0.63, 64.16)
11:102665932	rs374237181	R>Q	A:291	(47.84, 0.49, 68.98)
11:102665933	rs200225512 COSM1676391	R>W	A:291	(47.84, 0.49, 68.98)
11:102665924		V>L	A:294	(50.91, 1.44, 58.53)
11:102663461		M>T	A:303	(50.03, -5.96, 53.78)
11:102663456	rs56028730	T>A	A:305	(56.44, -3.24, 57.85)
11:102663452		N>S	A:306	(57.97, -7.23, 60.34)
11:102663449	rs189548101	P>L	A:307	(61.54, -6.69, 61.18)
11:102663440		P>L	A:310	(61.95, -9.77, 54.01)
11:102663441		P>S	A:310	(61.95, -9.77, 54.01)
11:102663426		N>D	A:315	(48.23, -12.95, 57.68)
11:102663418		I>M	A:317	(42.04, -9.32, 58.25)
11:102663419		I>T	A:317	(42.04, -9.32, 58.25)
11:102663417		S>P	A:318	(41.17, -13.19, 60.74)
11:102663406		W>C	A:321	(40.80, -7.16, 63.46)
11:102663391		N>K	A:326	(35.56, -10.05, 52.56)
11:102663389		G>E	A:327	(36.11, -6.26, 51.84)
11:102663375		Y>D	A:332	(38.71, 6.22, 60.99)
11:102663372	COSM1350401	E>K	A:333	(43.52, 5.31, 64.57)
11:102663365	rs200931880 COSM312899	A>G	A:335	(43.61, 8.06, 68.79)
11:102663363	COSM3931210	D>N	A:336	(41.42, 10.34, 72.05)
11:102663356	rs375378659	D>V	A:338	(42.78, 3.12, 71.32)
11:102663354	rs542710164	E>Q	A:339	(38.34, 3.44, 68.18)
11:102663348		R>W	A:341	(36.18, 4.02, 63.71)
11:102663336		G>R	A:345	(29.14, 0.03, 52.91)
11:102662217		Y>C	A:348	(30.69, 1.84, 61.82)
11:102662197		N>D	A:355	(38.92, -5.28, 70.55)
11:102662194	rs368596887	V>M	A:356	(35.45, -6.04, 68.09)
11:102662185	rs376000351	G>R	A:359	(27.03, -3.14, 68.37)
11:102662178		P>L	A:361	(27.41, -3.84, 62.72)
11:102662176		K>E	A:362	(27.07, 0.84, 64.51)
11:102662173	COSM3442717	D>N	A:363	(24.13, 2.79, 60.17)
11:102662170		I>V	A:364	(27.03, 5.25, 57.64)
11:102662162		S>R	A:366	(23.06, 6.90, 62.29)
11:102662160	rs556086714	S>F	A:367	(26.74, 7.25, 63.10)
11:102662154	COSM1350400	G>V	A:369	(25.27, 11.81, 58.51)
11:102662155		G>C	A:369	(25.27, 11.81, 58.51)
11:102662148	COSM1676389	P>R	A:371	(23.54, 11.25, 52.83)
11:102662140	rs59142365	V>M	A:374	(26.32, 7.70, 50.69)
11:102662131		I>V	A:377	(33.41, 5.03, 52.37)
11:102662128		D>N	A:378	(36.06, 5.18, 48.59)
11:102662121	rs371023437	A>V	A:380	(39.58, 7.39, 55.62)
11:102662116	rs139040854	S>P	A:382	(41.53, 10.92, 61.67)
11:102662110		E>K	A:384	(46.42, 12.71, 66.36)
11:102662088		F>C	A:391	(34.62, 10.14, 55.98)
11:102662076		N>S	A:395	(33.91, 13.34, 43.19)
11:102662065	rs150423527	R>G	A:399	(35.73, 18.54, 57.85)
11:102661535		Y>C	A:400	(32.32, 13.34, 61.90)
11:102661520	rs17879165	R>Q	A:405	(29.11, 12.11, 67.91)
11:102661518	rs17884120	S>T	A:406	(28.89, 16.35, 63.46)
11:102661496		K>R	A:413	(33.95, 20.30, 50.03)
11:102661483		H>Q	A:417	(37.90, 22.11, 44.22)
11:102661469		I>T	A:422	(44.95, 13.12, 43.95)
11:102661452	rs370930997	A>T	A:428	(43.51, 4.86, 50.22)
11:102661449	rs141429213	V>L	A:429	(44.10, 7.67, 53.10)
11:102661443		M>L	A:431	(47.91, 11.37, 58.89)
11:102661437	rs369712925 COSM376590	D>N	A:433	(54.73, 12.86, 59.82)
11:102661248		F>L	A:435	(53.05, 14.90, 55.29)
11:102661241		F>L	A:438	(45.91, 10.79, 49.16)
11:102661222		Q>R	A:444	(52.19, 6.57, 47.35)
11:102661220		Y>N	A:445	(49.43, 10.70, 44.75)
11:102661216		K>R	A:446	(54.13, 12.97, 50.40)
11:102661211		D>Y	A:448	(51.60, 19.39, 52.27)
11:102661201	rs146623880	T>M	A:451	(51.34, 23.59, 50.46)
11:102661198		K>R	A:452	(46.79, 22.52, 48.56)
11:102661192		I>S	A:454	(52.13, 16.41, 44.95)
11:102661160		N>D	A:465	(61.83, -3.40, 52.18)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:102668102	COSM1350403	P>S	A:79	(66.77, -19.26, 66.27)
11:102667841	COSM540585	E>Q	A:135	(29.55, -32.65, 51.69)
11:102667484	COSM2108440	G>E	A:179	(49.64, -28.62, 67.01)
11:102665974	COSM1196481	A>V	A:277	(54.35, -6.73, 48.00)
11:102665949	COSM2156677	D>E	A:285	(40.94, -2.41, 49.59)
11:102665933	COSM1676391	R>W	A:291	(47.84, 0.49, 68.98)
11:102665916	COSM1676390	F>L	A:296	(49.18, -1.23, 53.99)
11:102663438	COSM3868286	E>K	A:311	(59.21, -8.65, 50.98)
11:102663435	COSM1157775	V>I	A:312	(55.69, -7.95, 54.03)
11:102663381	COSM162530	A>S	A:330	(37.73, 1.92, 54.74)
11:102663372	COSM1350401	E>K	A:333	(43.52, 5.31, 64.57)
11:102662154	COSM1350400	G>D	A:369	(25.27, 11.81, 58.51)
11:102662113	COSM1350399	E>K	A:383	(43.90, 15.56, 61.86)
11:102661500	COSM3442714	P>S	A:412	(29.48, 18.02, 50.20)
11:102661190	COSM922283	L>V	A:455	(56.16, 16.20, 48.30)

1SU3.A | MMP1.

1SU3.A | MMP1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants