1GXD.B | MMP2 – ASTRID

1GXD.B | MMP2

General Structure Information

PDB ID	1gxd
HGNC Gene Label(s)	MMP2
Structure Name	prommp-2/timp-2 complex
Resolution	3.1Å
Reference	AUTH E.MORGUNOVA,A.TUUTTILA,U.BERGMANN,K.TRYGGVASONTITL STRUCTURAL INSIGHT INTO THE COMPLEX FORMATION OF LATENTTITL 2 MATRIX METALLOPROTEINASE 2 WITH TISSUE INHIBITOR OFTITL 3 METALLOPROTEINASE 2REF PROC.NATL.ACAD.SCI.USA V. 99 7414 2002REFN ISSN 0027-8424PMID 12032297DOI 10.1073/PNAS.102185399

Variant Set Distributions

ExAC Variants

Number Of Residues	623
Number Of SNVs	160
Number Of Permutations	46704
Optimal Distance Threshold	14.0
K Statistic	0.057
p-value	0.03

ClinVar

Number Of Residues	623
Number Of SNVs	3
Number Of Permutations	324
Optimal Distance Threshold	17.0
K Statistic	1.0
p-value	0.022

COSMIC

Number Of Residues	623
Number Of SNVs	17
Number Of Permutations	6884
Optimal Distance Threshold	14.0
K Statistic	0.096
p-value	0.524

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	160
Number Of ClinVar SNVs	3
Optimal Distance Threshold	17.0
K Statistic	0.903
p-value	0.018

Cosmic vs. ExAC

Number Of ExAC SNVs	160
Number Of COSMIC SNVs	16
Optimal Distance Threshold	14.0
K Statistic	0.034
p-value	0.401

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:55513498		K>R	B:7	(34.57, 113.78, 4.28)
16:55513542		V>L	B:22	(27.53, 119.30, 27.64)
16:55516843		G>D	B:30	(29.16, 119.98, 36.91)
16:55516870	rs146965045	F>S	B:39	(18.49, 123.21, 31.11)
16:55516872		V>L	B:40	(15.63, 125.72, 34.06)
16:55516885		T>I	B:44	(26.22, 126.38, 33.99)
16:55516891		K>M	B:46	(25.43, 132.41, 33.69)
16:55516909		F>S	B:52	(36.89, 132.11, 31.14)
16:55516924	COSM3370465	T>K	B:57	(24.35, 135.36, 27.83)
16:55516942		N>S	B:63	(32.39, 134.78, 22.27)
16:55516947		I>V	B:65	(31.70, 128.00, 21.34)
16:55516950		E>K	B:66	(36.12, 131.27, 20.50)
16:55516960		R>Q	B:69	(36.01, 124.68, 19.93)
16:55516974		G>S	B:74	(42.00, 119.14, 33.02)
16:55516986		V>L	B:78	(34.46, 124.14, 39.97)
16:55516990		A>V	B:79	(35.58, 124.66, 43.44)
16:55516993		N>S	B:80	(35.19, 121.53, 45.94)
16:55516999		N>S	B:82	(38.29, 115.17, 42.89)
16:55517003	rs368829695	F>L	B:83	(37.04, 109.90, 43.56)
16:55517019		K>E	B:89	(50.34, 121.83, 52.47)
16:55517028		K>E	B:92	(56.38, 117.11, 52.90)
16:55517938		Y>H	B:102	(60.18, 109.75, 29.17)
16:55517966		V>A	B:111	(61.66, 115.44, 29.13)
16:55517972		D>G	B:113	(65.61, 119.94, 31.71)
16:55517980	rs368499410	A>T	B:116	(63.28, 120.45, 36.30)
16:55517984		R>H	B:117	(63.09, 124.05, 32.87)
16:55518000		W>C	B:122	(55.65, 126.86, 41.42)
16:55518004	rs144334568	D>N	B:124	(62.76, 130.11, 42.37)
16:55518010		T>S	B:126	(59.13, 128.40, 47.79)
16:55518019	rs375159741	R>W	B:129	(63.99, 121.30, 49.33)
16:55518020	rs368486758 COSM1563071	R>Q	B:129	(63.99, 121.30, 49.33)
16:55518029	COSM167992	R>L	B:132	(64.80, 112.21, 38.52)
16:55518035		H>R	B:134	(65.61, 107.11, 39.22)
16:55518043	rs147947052	E>K	B:137	(55.53, 105.83, 45.14)
16:55518046	rs141565911	A>T	B:138	(56.80, 109.32, 44.55)
16:55518056		M>T	B:141	(54.31, 109.43, 40.01)
16:55518070		R>C	B:146	(46.18, 107.42, 23.81)
16:55519234		D>H	B:156	(40.78, 114.73, 24.28)
16:55519327		G>R	B:187	(56.76, 125.80, 21.71)
16:55519328		G>E	B:187	(56.76, 125.80, 21.71)
16:55519330		E>K	B:188	(59.24, 128.02, 19.41)
16:55519331		E>V	B:188	(59.24, 128.02, 19.41)
16:55519333		G>S	B:189	(57.80, 123.52, 17.58)
16:55519522	rs368282133	R>H	B:193	(69.17, 115.87, 21.01)
16:55519536		N>D	B:198	(78.45, 117.91, 11.92)
16:55519539	COSM32988	A>T	B:199	(76.21, 118.80, 15.20)
16:55519542		D>N	B:200	(75.75, 115.09, 17.89)
16:55519559	COSM1179632	K>N	B:205	(67.12, 125.70, 13.50)
16:55519575		N>H	B:211	(68.35, 124.04, -2.78)
16:55519578		G>S	B:212	(65.43, 127.36, -2.10)
16:55519579		G>D	B:212	(65.43, 127.36, -2.10)
16:55519581		K>E	B:213	(62.81, 124.17, -0.46)
16:55519584	rs577053508	E>K	B:214	(62.17, 127.47, 4.04)
16:55519600		T>S	B:219	(64.45, 115.75, 4.86)
16:55519606		T>N	B:221	(66.29, 116.00, 0.63)
16:55519611		R>C	B:223	(70.44, 110.85, 1.95)
16:55519626		L>F	B:228	(65.54, 111.42, 8.11)
16:55519635		S>P	B:231	(70.04, 122.11, 9.59)
16:55519636		S>F	B:231	(70.04, 122.11, 9.59)
16:55519685		H>Q	B:247	(62.44, 106.76, 12.78)
16:55522464		T>I	B:252	(68.90, 102.25, 17.26)
16:55522470		G>D	B:254	(72.35, 101.76, 22.10)
16:55522472	COSM377497	G>S	B:255	(72.76, 98.85, 23.09)
16:55522478		A>T	B:257	(72.31, 96.50, 17.97)
16:55522484		G>R	B:259	(72.24, 100.78, 15.38)
16:55522485		G>A	B:259	(72.24, 100.78, 15.38)
16:55522490	COSM3712048	P>T	B:261	(67.27, 99.06, 12.58)
16:55522508	rs545385578	R>C	B:267	(58.10, 86.07, 20.25)
16:55522509	rs200786490	R>H	B:267	(58.10, 86.07, 20.25)
16:55522512		F>Y	B:268	(59.94, 89.81, 24.99)
16:55522527	COSM94718	Y>C	B:273	(56.00, 93.82, 21.22)
16:55522550	COSM191659	R>C	B:281	(63.01, 99.06, 30.88)
16:55522551		R>L	B:281	(63.01, 99.06, 30.88)
16:55522554	rs144434779	T>M	B:282	(61.35, 100.84, 35.43)
16:55522556		D>H	B:283	(63.58, 103.29, 32.58)
16:55522565		R>C	B:286	(60.55, 104.28, 23.23)
16:55522566		R>H	B:286	(60.55, 104.28, 23.23)
16:55522574	rs543222717	G>S	B:289	(64.14, 94.84, 18.77)
16:55522580		T>P	B:291	(65.73, 90.42, 15.59)
16:55522586		D>N	B:293	(63.12, 86.09, 18.54)
16:55522595	rs202049962	R>C	B:296	(65.82, 83.46, 18.35)
16:55522596		R>H	B:296	(65.82, 83.46, 18.35)
16:55522598	rs371671100	D>N	B:297	(68.61, 86.64, 18.78)
16:55522599		D>V	B:297	(68.61, 86.64, 18.78)
16:55522600		D>E	B:297	(68.61, 86.64, 18.78)
16:55523571	COSM317636	T>A	B:310	(53.15, 114.13, 9.43)
16:55523572		T>I	B:310	(53.15, 114.13, 9.43)
16:55523580	rs537651079	G>W	B:313	(46.48, 110.60, 11.42)
16:55523592		G>S	B:317	(54.49, 110.45, 9.50)
16:55523596		A>D	B:318	(54.40, 110.50, 6.51)
16:55523617		T>I	B:325	(44.55, 115.60, -5.48)
16:55523626	COSM337017	G>A	B:328	(39.68, 117.76, -7.37)
16:55523643		C>G	B:334	(49.07, 122.39, 3.91)
16:55523652	rs377130479	A>T	B:337	(40.33, 121.24, 3.12)
16:55523655		G>S	B:338	(37.30, 119.67, 4.86)
16:55523659		R>H	B:339	(39.57, 119.39, 9.12)
16:55523667		G>R	B:342	(41.68, 124.82, 10.77)
16:55523674		M>T	B:344	(46.69, 123.16, 8.27)
16:55523677	rs150524555	W>S	B:345	(44.42, 118.12, 4.87)
16:55523700	rs555030156 COSM2835289	D>N	B:353	(40.20, 111.35, -3.78)
16:55523709		R>C	B:356	(40.48, 108.62, 0.55)
16:55523710	rs371828436	R>L	B:356	(40.48, 108.62, 0.55)
16:55523727	rs144793025	P>S	B:362	(53.44, 119.99, 12.13)
16:55525720	rs200772153	S>R	B:367	(55.49, 123.89, 26.28)
16:55525730	COSM71662	V>M	B:371	(52.01, 122.26, 30.47)
16:55525749	rs121908741	G>D	B:377	(50.75, 123.44, 40.89)
16:55525759	rs59727333	M>I	B:380	(52.33, 121.80, 44.81)
16:55525766		E>Q	B:383	(42.66, 125.58, 42.46)
16:55525781	COSM245730	P>T	B:388	(44.44, 136.35, 32.30)
16:55525790		L>M	B:391	(50.92, 129.56, 34.99)
16:55525817		K>E	B:400	(58.82, 134.78, 23.98)
16:55525819	rs201083413	K>N	B:400	(58.82, 134.78, 23.98)
16:55525827		R>H	B:403	(58.53, 136.55, 34.73)
16:55525859		E>K	B:414	(48.19, 131.42, 50.91)
16:55527073	rs17859943	A>V	B:418	(58.40, 133.11, 49.99)
16:55527081		D>N	B:421	(64.19, 127.68, 55.49)
16:55527105		T>A	B:429	(58.18, 147.54, 38.51)
16:55527115		L>P	B:432	(58.17, 138.92, 44.00)
16:55527120		P>S	B:434	(54.24, 139.98, 37.79)
16:55527126		T>P	B:436	(47.45, 141.98, 35.73)
16:55527147		D>N	B:443	(44.37, 155.58, 36.60)
16:55527151		I>T	B:444	(45.75, 152.73, 32.49)
16:55527153		V>I	B:445	(49.14, 155.10, 30.19)
16:55527154		V>A	B:445	(49.14, 155.10, 30.19)
16:55527165	rs142355142	I>L	B:449	(44.60, 152.71, 20.86)
16:55527168		A>T	B:450	(43.55, 150.44, 17.19)
16:55527177	rs151265434	R>C	B:453	(36.80, 143.31, 11.67)
16:55527178		R>H	B:453	(36.80, 143.31, 11.67)
16:55527181		G>D	B:454	(36.09, 146.50, 14.05)
16:55527189		F>I	B:457	(42.42, 145.51, 19.74)
16:55527204		R>W	B:462	(52.15, 140.39, 30.47)
16:55527205	rs200852686	R>Q	B:462	(52.15, 140.39, 30.47)
16:55530843		I>T	B:464	(45.03, 142.99, 24.59)
16:55530851		T>S	B:467	(35.86, 147.02, 21.90)
16:55530858	COSM33138	T>M	B:469	(30.45, 149.12, 21.02)
16:55530863	rs371281054 COSM703431	R>C	B:471	(26.68, 149.82, 23.12)
16:55530875		M>V	B:475	(35.51, 141.50, 25.95)
16:55530881		P>S	B:477	(42.03, 141.17, 30.30)
16:55530882		P>L	B:477	(42.03, 141.17, 30.30)
16:55530888		L>P	B:479	(47.79, 137.53, 27.03)
16:55530908		E>K	B:486	(55.67, 136.92, 16.87)
16:55530915		P>L	B:488	(57.37, 142.54, 21.54)
16:55530920		K>E	B:490	(56.60, 148.40, 25.75)
16:55530922		K>N	B:490	(56.60, 148.40, 25.75)
16:55530932		V>L	B:494	(48.89, 149.79, 15.80)
16:55530935		Y>H	B:495	(50.86, 151.12, 11.28)
16:55530938		E>K	B:496	(44.14, 150.39, 9.23)
16:55532204		N>S	B:509	(64.73, 150.14, 17.17)
16:55532218	rs369441378	Y>H	B:514	(51.95, 140.93, 12.59)
16:55532219	rs138709475	Y>C	B:514	(51.95, 140.93, 12.59)
16:55532225	rs143247099	A>V	B:516	(46.30, 136.88, 8.96)
16:55532236		E>K	B:520	(55.37, 138.60, 6.68)
16:55532240	rs373684923	R>Q	B:521	(60.73, 135.07, 4.76)
16:55532249		P>L	B:524	(62.21, 141.11, 12.73)
16:55532261		T>I	B:528	(67.16, 151.87, 11.47)
16:55532275	COSM4061267	P>A	B:533	(66.07, 159.02, 10.54)
16:55532276	rs370764157	P>L	B:533	(66.07, 159.02, 10.54)
16:55532281		D>N	B:535	(67.99, 159.21, 16.01)
16:55532291	rs147336184	R>Q	B:538	(61.31, 155.82, 21.58)
16:55532300	rs540892268	A>V	B:541	(52.39, 157.10, 16.89)
16:55532302	COSM1378382	A>T	B:542	(50.10, 155.76, 14.31)
16:55532303		A>V	B:542	(50.10, 155.76, 14.31)
16:55532310		N>K	B:544	(45.17, 155.43, 7.74)
16:55532315		S>N	B:546	(40.01, 159.27, 4.72)
16:55532327		K>M	B:550	(49.40, 158.93, 3.69)
16:55532342		A>V	B:555	(57.99, 161.82, 17.86)
16:55532344		G>R	B:556	(56.68, 164.96, 19.26)
16:55532347		D>N	B:557	(59.21, 167.50, 18.73)
16:55532349		D>E	B:557	(59.21, 167.50, 18.73)
16:55532352		K>N	B:558	(60.17, 166.54, 14.48)
16:55536706	COSM558303	K>N	B:566	(55.37, 155.69, -3.44)
16:55536709		K>N	B:567	(57.65, 150.89, 0.36)
16:55536710		K>E	B:568	(59.00, 157.01, -1.39)
16:55536713		M>V	B:569	(59.28, 158.36, 4.28)
16:55536714		M>T	B:569	(59.28, 158.36, 4.28)
16:55536719	rs183330767	P>T	B:571	(61.21, 164.57, 0.94)
16:55536720		P>L	B:571	(61.21, 164.57, 0.94)
16:55536722		G>C	B:572	(62.19, 166.11, 4.60)
16:55536723	rs142010233	G>V	B:572	(62.19, 166.11, 4.60)
16:55536782	rs16955280	V>L	B:592	(42.41, 155.30, 16.10)
16:55536797	rs146725576	G>S	B:597	(31.60, 160.88, 11.63)
16:55536798		G>D	B:597	(31.60, 160.88, 11.63)
16:55539278		Y>C	B:607	(42.09, 163.73, 29.26)
16:55539287		K>T	B:610	(36.02, 164.51, 18.31)
16:55539289		L>V	B:611	(40.28, 165.52, 14.31)
16:55539292		E>K	B:612	(36.45, 167.58, 11.37)
16:55539310		S>G	B:618	(36.10, 169.23, 15.06)
16:55539311		S>T	B:618	(36.10, 169.23, 15.06)
16:55539313	rs557085579 COSM1378386	V>M	B:619	(37.12, 169.78, 18.72)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:55516969	rs121912953	R>H	B:72	(41.18, 123.88, 29.72)
16:55519219	rs786205497	D>N	B:151	(43.02, 108.38, 35.86)
16:55525742	rs121912955	E>K	B:375	(50.73, 120.87, 36.86)

1GXD.B | MMP2.

1GXD.B | MMP2

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:55516959	COSM212670	R>W	B:69	(36.01, 124.68, 19.93)
16:55516975	COSM3510283	G>D	B:74	(42.00, 119.14, 33.02)
16:55517929	COSM1679097	I>L	B:99	(60.10, 110.57, 34.93)
16:55517983	COSM3510285	R>C	B:117	(63.09, 124.05, 32.87)
16:55518029	COSM167992	R>Q	B:132	(64.80, 112.21, 38.52)
16:55518071	COSM1749647	R>H	B:146	(46.18, 107.42, 23.81)
16:55519246	COSM1378376	G>R	B:160	(42.39, 120.24, 24.34)
16:55522490	COSM3712048	P>T	B:261	(67.27, 99.06, 12.58)
16:55522491	COSM217105	P>L	B:261	(67.27, 99.06, 12.58)
16:55522550	COSM191659	R>C	B:281	(63.01, 99.06, 30.88)
16:55523613	COSM337016	F>V	B:324	(47.53, 117.48, -2.11)
16:55523626	COSM337017	G>A	B:328	(39.68, 117.76, -7.37)
16:55523672	COSM3818100	K>N	B:343	(43.23, 121.30, 12.61)
16:55523700	COSM2835289	D>N	B:353	(40.20, 111.35, -3.78)
16:55525826	COSM162533	R>S	B:403	(58.53, 136.55, 34.73)
16:55530930	COSM558305	A>V	B:493	(52.25, 150.95, 17.45)
16:55539301	COSM1378384	S>G	B:615	(38.08, 170.59, 8.06)
16:55539335	COSM971563	S>F	B:626	(34.50, 157.46, 30.08)