4DYO.A | DNPEP

General Structure Information

PDB ID	4dyo
HGNC Gene Label(s)	DNPEP
Structure Name	crystal structure of human aspartyl aminopeptidase (dnpep) in complex with aspartic acid hydroxamate
Resolution	2.2Å
Reference	AUTH A.CHAIKUAD,E.S.PILKA,A.D.RISO,F.V.DELFT,K.L.KAVANAGH,AUTH 2 C.VENIEN-BRYAN,U.OPPERMANN,W.W.YUETITL STRUCTURE OF HUMAN ASPARTYL AMINOPEPTIDASE COMPLEXED WITHTITL 2 SUBSTRATE ANALOGUE: INSIGHT INTO CATALYTIC MECHANISM,TITL 3 SUBSTRATE SPECIFICITY AND M18 PEPTIDASE FAMILY.REF BMC STRUCT.BIOL. V. 12 14 2012REFN ESSN 1472-6807PMID 22720794DOI 10.1186/1472-6807-12-14

Variant Set Distributions

ExAC Variants

Number Of Residues	452
Number Of SNVs	133
Number Of Permutations	69427
Optimal Distance Threshold	7.0
K Statistic	0.016
p-value	0.605

COSMIC

Number Of Residues	452
Number Of SNVs	9
Number Of Permutations	6543
Optimal Distance Threshold	13.0
K Statistic	0.056
p-value	1.0

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	133
Number Of COSMIC SNVs	8
Optimal Distance Threshold	8.0
K Statistic	-0.022
p-value	0.787

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:220251863		R>L	A:10	(114.06, 34.06, 68.39)
2:220251852		V>L	A:14	(113.15, 38.91, 65.79)
2:220251849	rs556988881	Q>K	A:15	(114.78, 43.10, 66.52)
2:220251839	rs375414611	A>G	A:18	(112.24, 43.56, 61.25)
2:220251819	rs372371866	V>M	A:25	(108.71, 49.39, 53.40)
2:220251810		S>C	A:28	(108.59, 50.50, 48.51)
2:220251685	rs11539909	N>H	A:40	(117.55, 45.03, 43.09)
2:220251671		Q>H	A:44	(122.54, 40.76, 44.78)
2:220251651		K>R	A:51	(112.48, 39.52, 28.12)
2:220251633		N>S	A:57	(116.02, 27.64, 27.38)
2:220251631		I>F	A:58	(113.62, 27.31, 31.22)
2:220251625	rs534944028	P>T	A:60	(117.31, 22.52, 35.11)
2:220251495		F>L	A:65	(113.56, 38.25, 37.24)
2:220251496		F>S	A:65	(113.56, 38.25, 37.24)
2:220251493		M>T	A:66	(108.70, 38.20, 34.81)
2:220251491		T>A	A:67	(108.40, 42.16, 35.10)
2:220251481		S>F	A:70	(106.89, 47.66, 36.24)
2:220251470		I>V	A:74	(106.70, 36.21, 38.29)
2:220251466	COSM442347	A>V	A:75	(109.91, 34.43, 40.78)
2:220251451	COSM1530838	G>D	A:80	(116.77, 19.51, 39.27)
2:220251431		G>S	A:87	(105.09, 21.13, 40.10)
2:220251422		L>F	A:90	(103.18, 28.86, 44.18)
2:220251416	COSM1186123	G>R	A:92	(101.51, 35.01, 47.12)
2:220251406		T>M	A:95	(102.67, 45.20, 44.96)
2:220251399		S>R	A:97	(98.78, 49.77, 48.90)
2:220251397	rs373627281	P>L	A:98	(95.86, 51.55, 50.09)
2:220251398		P>S	A:98	(95.86, 51.55, 50.09)
2:220251394	rs569772365	C>F	A:99	(96.81, 55.34, 47.84)
2:220251395		C>R	A:99	(96.81, 55.34, 47.84)
2:220251389	COSM3768955	R>W	A:101	(97.67, 57.02, 42.06)
2:220251133		V>L	A:102	(98.66, 62.32, 40.73)
2:220251127	rs554588805	R>C	A:104	(96.71, 61.04, 34.45)
2:220251123	rs572312244	R>Q	A:105	(94.38, 67.99, 33.40)
2:220251120	rs376714406	S>Y	A:106	(96.83, 68.32, 38.85)
2:220251117	rs372081874	R>H	A:107	(97.40, 74.02, 37.22)
2:220251118	COSM4091672	R>C	A:107	(97.40, 74.02, 37.22)
2:220251115		R>C	A:108	(92.74, 71.47, 41.90)
2:220251106		V>L	A:111	(93.53, 81.11, 48.37)
2:220251091	rs558527256	V>I	A:116	(98.15, 68.27, 43.46)
2:220251085		V>M	A:118	(94.39, 63.56, 44.25)
2:220251072		G>D	A:122	(91.38, 52.08, 47.52)
2:220251066		G>V	A:124	(91.23, 53.97, 52.64)
2:220251050	rs201927429	W>C	A:129	(97.00, 59.45, 53.23)
2:220251042		R>H	A:132	(100.32, 62.03, 58.12)
2:220251043		R>C	A:132	(100.32, 62.03, 58.12)
2:220251033		T>I	A:135	(106.11, 62.47, 48.80)
2:220251021		R>H	A:139	(105.34, 54.45, 35.67)
2:220251018		V>A	A:140	(108.15, 58.91, 34.26)
2:220251019	rs372079508	V>I	A:140	(108.15, 58.91, 34.26)
2:220250817		P>S	A:145	(115.55, 64.07, 23.50)
2:220250804		R>Q	A:149	(112.87, 56.41, 22.22)
2:220250797	rs367736817	E>D	A:151	(113.09, 56.03, 27.93)
2:220250781		V>M	A:157	(110.70, 63.28, 46.06)
2:220250775		R>W	A:159	(111.85, 67.31, 49.60)
2:220250769	rs6742404	I>V	A:161	(106.72, 67.96, 48.51)
2:220250762	rs530171374	R>H	A:163	(100.57, 68.76, 54.82)
2:220250757		P>A	A:165	(95.44, 70.43, 55.30)
2:220250732		R>Q	A:173	(83.23, 74.52, 67.12)
2:220250730		N>D	A:174	(80.81, 69.09, 65.52)
2:220250703		T>P	A:183	(87.05, 62.12, 48.35)
2:220250695		M>I	A:185	(86.48, 68.98, 46.95)
2:220250690		L>R	A:187	(91.71, 64.47, 50.01)
2:220250409		A>T	A:194	(102.29, 82.06, 44.38)
2:220250400		E>K	A:197	(106.25, 80.28, 41.58)
2:220250387		K>T	A:201	(111.04, 80.23, 39.45)
2:220250246	rs199600488	R>Q	A:215	(99.93, 67.80, 32.24)
2:220250241		H>N	A:217	(100.83, 73.89, 39.28)
2:220250237	rs149936277	S>L	A:218	(105.46, 74.52, 37.07)
2:220250227		M>I	A:221	(106.62, 69.28, 35.88)
2:220250226		S>P	A:222	(110.39, 71.58, 37.96)
2:220250207		L>Q	A:228	(114.17, 62.63, 35.75)
2:220250186	rs549968429	I>T	A:235	(107.37, 64.45, 30.71)
2:220250162		A>V	A:243	(103.94, 58.96, 50.25)
2:220250156		T>I	A:245	(108.13, 61.20, 54.52)
2:220250147	rs907679	V>A	A:248	(109.73, 52.73, 59.03)
2:220250148		V>L	A:248	(109.73, 52.73, 59.03)
2:220249160	rs374335152	L>F	A:250	(110.99, 49.19, 65.47)
2:220249153	rs181316361	A>S	A:253	(108.79, 49.70, 75.16)
2:220249149		Y>F	A:254	(109.65, 45.92, 75.95)
2:220249147	rs200396385	D>N	A:255	(111.53, 48.20, 70.11)
2:220249144		E>K	A:256	(106.87, 44.66, 70.84)
2:220249125		R>Q	A:262	(103.78, 50.83, 52.33)
2:220249126		R>W	A:262	(103.78, 50.83, 52.33)
2:220249089		Q>R	A:274	(114.42, 36.67, 51.55)
2:220247932		L>S	A:276	(112.57, 31.95, 46.91)
2:220247918	rs188238123	A>T	A:281	(121.43, 29.68, 49.00)
2:220247912		P>S	A:283	(125.50, 24.65, 47.87)
2:220247905		S>F	A:285	(119.63, 24.01, 47.20)
2:220247887		H>R	A:291	(107.91, 20.92, 42.65)
2:220247885	COSM1530842	V>M	A:292	(108.98, 25.21, 40.03)
2:220247881	COSM1250504	R>H	A:293	(111.60, 26.27, 44.90)
2:220247882		R>C	A:293	(111.60, 26.27, 44.90)
2:220247878		M>T	A:294	(106.74, 30.59, 41.51)
2:220247879		M>V	A:294	(106.74, 30.59, 41.51)
2:220247876		V>F	A:295	(107.21, 34.36, 44.09)
2:220247866	rs201424405	Y>C	A:298	(99.97, 38.97, 41.38)
2:220247863		D>G	A:299	(99.34, 45.56, 40.78)
2:220247860	rs375215381	N>S	A:300	(95.79, 46.09, 40.80)
2:220246860		V>A	A:303	(91.25, 47.54, 42.91)
2:220246857		G>V	A:304	(90.18, 43.40, 42.04)
2:220246837		A>S	A:311	(95.35, 37.94, 39.74)
2:220246833	rs570417572	Q>L	A:312	(91.32, 38.41, 37.52)
2:220246824		L>P	A:315	(100.64, 36.67, 33.42)
2:220246807		R>W	A:321	(100.38, 26.54, 29.35)
2:220246804	COSM387216	R>W	A:322	(106.51, 30.85, 28.13)
2:220246788		C>F	A:327	(107.51, 17.87, 22.62)
2:220246786		Q>E	A:328	(108.61, 14.85, 25.14)
2:220246779	COSM122663	P>L	A:330	(101.34, 16.83, 25.37)
2:220246749		S>F	A:340	(100.36, 22.49, 42.47)
2:220246744		M>V	A:342	(99.41, 29.37, 46.12)
2:220246735		A>T	A:345	(100.12, 36.09, 51.44)
2:220246717		V>M	A:351	(92.29, 41.49, 68.48)
2:220246283	rs536978105	R>Q	A:364	(89.71, 37.02, 70.28)
2:220246274		F>S	A:367	(100.54, 41.58, 67.89)
2:220246271		H>R	A:368	(104.45, 38.64, 69.30)
2:220246157	rs35978112	G>V	A:370	(101.51, 33.82, 64.45)
2:220246152	COSM1405633	V>M	A:372	(96.70, 33.98, 60.75)
2:220246146	rs200549109	K>E	A:374	(93.04, 33.94, 56.45)
2:220246137		S>G	A:377	(83.34, 28.50, 53.77)
2:220246127	rs569695061	R>H	A:380	(85.47, 36.66, 50.61)
2:220246128	rs112463725	R>C	A:380	(85.47, 36.66, 50.61)
2:220246124		Y>C	A:381	(89.60, 34.23, 53.22)
2:220246119		S>P	A:383	(91.20, 27.99, 53.08)
2:220246112	rs201204134 COSM3407592	A>V	A:385	(91.15, 20.93, 55.34)
2:220246091	rs201486555 COSM3721544	R>Q	A:392	(98.06, 23.51, 60.82)
2:220246079		N>S	A:396	(105.36, 20.52, 63.42)
2:220246077		K>E	A:397	(108.21, 19.34, 60.12)
2:220246068		V>I	A:400	(106.00, 28.07, 63.14)
2:220239737		M>T	A:406	(86.51, 32.40, 61.23)
2:220239731	COSM573624	R>Q	A:408	(80.68, 38.54, 64.52)
2:220239732	rs375968327	R>W	A:408	(80.68, 38.54, 64.52)
2:220239719	rs200988234	P>R	A:412	(81.41, 41.83, 56.49)
2:220239707	rs200051333	T>I	A:416	(92.39, 37.48, 48.93)
2:220239686		S>F	A:423	(89.73, 30.15, 39.90)
2:220239671	rs369409896	R>Q	A:428	(95.34, 22.32, 46.57)
2:220239672		R>W	A:428	(95.34, 22.32, 46.57)
2:220239669		V>L	A:429	(95.03, 28.12, 47.68)
2:220239638		M>T	A:439	(94.40, 46.76, 57.46)
2:220239632	rs376806983	S>C	A:441	(96.56, 53.17, 57.42)
2:220239603	rs368993821	V>I	A:451	(108.99, 38.78, 59.93)
2:220239596	rs376715559	Q>R	A:453	(107.10, 33.55, 62.98)
2:220239593		T>N	A:454	(106.56, 34.25, 57.85)
2:220239585		L>V	A:457	(106.30, 28.84, 57.29)
2:220239577		K>N	A:459	(113.12, 28.05, 54.19)
2:220239579		K>E	A:459	(113.12, 28.05, 54.19)
2:220239063		G>D	A:460	(109.63, 25.20, 54.44)
2:220239057		F>S	A:462	(109.44, 27.29, 48.85)

4DYO.A | DNPEP.

4DYO.A | DNPEP

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:220251467	COSM1016731	A>T	A:75	(109.91, 34.43, 40.78)
2:220251446	COSM1669779	Y>H	A:82	(110.72, 20.73, 36.19)
2:220251123	COSM3044940	R>Q	A:105	(94.38, 67.99, 33.40)
2:220251079	COSM3044939	T>A	A:120	(90.96, 57.60, 45.49)
2:220250763	COSM3909645	R>C	A:163	(100.57, 68.76, 54.82)
2:220249150	COSM1752369	Y>N	A:254	(109.65, 45.92, 75.95)
2:220246734	COSM3714132	A>E	A:345	(100.12, 36.09, 51.44)
2:220246152	COSM1405633	V>M	A:372	(96.70, 33.98, 60.75)
2:220239708	COSM1752368	T>S	A:416	(92.39, 37.48, 48.93)