Search

Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin
Authors
Connelly, E.M., Rintala-Dempsey, A.C., Gundogdu, M., Freeman, E.A., Koszela, J., Aguirre, J.D., Zhu, G., Kamarainen, O., Tadayon, R., Walden, H., Shaw, G.S.
Assembly
E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin
Entity
1. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 1 (polymer), 73 monomers, 8269.334 Da Detail

TVDPNRAAEA RWDEASNVTI KVSTKPCPKC RTPTERDGGC MHMVCTRAGC GFEWCWVCQT EWTRDCMGAH WFG


2. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 2 (polymer), 75 monomers, 8507.679 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG


3. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity ZN (non-polymer), 65.409 × 2 Da
4. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 4LJ (non-polymer), 138.006 Da
Total weight
17045.836 Da
Max. entity weight
8507.679 Da
Source organism
Drosophila melanogaster , Homo sapiens
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chemical Shifts 1
1H: 60, 13C: 125, 15N: 60 assignments Detail
IDEntity IDSeq IDComp IDAtom IDAtom typeValVal errAmbig. code
112VALCAC62.10420.00001
213ASPHH8.53160.00001
313ASPCAC51.91990.00001
413ASPNN126.53590.00001
514PROCAC63.91860.00001
614PROCBC31.20860.00001
715ASNHH8.50380.00001
815ASNCAC53.96810.00001
915ASNCBC37.63970.00001
1015ASNNN117.25510.00001
1116ARGHH7.87610.00001
1216ARGCAC56.49970.00001
1316ARGCBC29.59640.00001
1416ARGNN120.86630.00001
1517ALAHH8.16690.00001
1617ALACAC53.30150.00001
1717ALACBC18.04100.00001
1817ALANN124.64720.00001
1918ALAHH8.15940.00001
2018ALACAC53.18990.00001
2118ALACBC18.12980.00001
2218ALANN122.57320.00001
2319GLUHH8.15540.00001
2419GLUCAC56.93170.00001
2519GLUCBC29.27360.00001
2619GLUNN119.04860.00001
27110ALAHH8.19890.00001
28110ALACAC53.05860.00001
29110ALACBC19.30670.00001
30110ALANN124.93070.00001
31111ARGHH8.10130.00001
32111ARGCAC55.13940.00001
33111ARGCBC29.94120.00001
34111ARGNN119.86990.00001
35112TRPHH8.15630.00001
36112TRPCAC57.72140.00001
37112TRPCBC28.46730.00001
38112TRPNN122.09620.00001
39113ASPHH8.18550.00001
40113ASPCAC54.86260.00001
41113ASPCBC39.73160.00001
42113ASPNN121.70600.00001
43114GLUHH8.12900.00001
44114GLUCAC57.68760.00001
45114GLUCBC29.07570.00001
46114GLUNN121.80750.00001
47115ALAHH8.15690.00001
48115ALACAC53.18870.00001
49115ALACBC18.01770.00001
50115ALANN123.84250.00001
51116SERHH8.06050.00001
52116SERCAC58.70740.00001
53116SERCBC62.70470.00001
54116SERNN113.89870.00001
55117ASNHH8.25860.00001
56117ASNCAC53.53440.00001
57117ASNCBC37.75320.00001
58117ASNNN120.49360.00001
59118VALHH7.95510.00001
60118VALCAC62.56560.00001
61118VALCBC31.78440.00001
62118VALNN119.45450.00001
63119THRHH8.22340.00001
64119THRCAC62.25510.00001
65119THRCBC68.82900.00001
66119THRNN118.19890.00001
67120ILEHH8.13900.00001
68120ILECAC61.08350.00001
69120ILECBC37.64320.00001
70120ILENN123.99430.00001
71121LYSHH8.40180.00001
72121LYSCAC56.11930.00001
73121LYSCBC32.44790.00001
74121LYSNN126.18290.00001
75122VALHH8.28120.00001
76122VALCAC62.28740.00001
77122VALCBC33.23920.00001
78122VALNN121.75340.00001
79123SERCAC57.72110.00001
80123SERCBC63.32780.00001
81124THRHH7.93320.00001
82124THRCAC60.60390.00001
83124THRCBC71.22380.00001
84124THRNN114.32980.00001
85125LYSHH8.89200.00001
86125LYSCAC54.53220.00001
87125LYSCBC37.07510.00001
88125LYSNN122.01970.00001
89126PROCAC60.25900.00001
90126PROCBC30.08680.00001
91127CYSHH7.75290.00001
92127CYSCAC54.73020.00001
93127CYSCBC31.65870.00001
94127CYSNN125.04190.00001
95128PROCAC64.12660.00001
96128PROCBC31.45940.00001
97129LYSHH8.32050.00001
98129LYSCAC57.82760.00001
99129LYSCBC32.06630.00001
100129LYSNN118.60860.00001
101130CYSHH8.41050.00001
102130CYSCAC59.48770.00001
103130CYSCBC30.22660.00001
104130CYSNN119.07360.00001
105131ARGHH8.08810.00001
106131ARGCAC56.80710.00001
107131ARGCBC25.04450.00001
108131ARGNN116.90810.00001
109132THRHH8.63760.00001
110132THRCAC63.36060.00001
111132THRCBC69.02520.00001
112132THRNN122.23190.00001
113133PROCAC64.20760.00001
114133PROCBC30.84900.00001
115134THRHH9.03980.00001
116134THRCAC62.46830.00001
117134THRCBC70.24800.00001
118134THRNN122.61890.00001
119135GLUHH8.73360.00001
120135GLUCAC55.19790.00001
121135GLUCBC30.67210.00001
122135GLUNN126.22780.00001
123136ARGHH8.17400.00001
124136ARGCAC52.27780.00001
125136ARGCBC31.90530.00001
126136ARGNN124.12640.00001
127137ASPHH8.54620.00001
128137ASPCAC51.95600.00001
129137ASPCBC40.25300.00001
130137ASPNN126.74000.00001
131138GLYHH8.10860.00001
132138GLYCAC45.30200.00001
133138GLYNN111.49170.00001
134139GLYHH8.42810.00001
135139GLYCAC44.11810.00001
136139GLYNN109.89270.00001
137140CYSHH7.81780.00001
138140CYSCAC59.52590.00001
139140CYSCBC28.00910.00001
140140CYSNN120.48540.00001
141141METCAC54.17760.00001
142141METCBC33.10090.00001
143142HISHH7.56020.00001
144142HISCAC53.88380.00001
145142HISCBC26.93630.00001
146142HISNN119.84360.00001
147143METHH9.10970.00001
148143METCAC52.77820.00001
149143METCBC28.18460.00001
150143METNN128.55790.00001
151144VALHH8.04850.00001
152144VALCAC60.55070.00001
153144VALCBC32.03030.00001
154144VALNN121.81060.00001
155145CYSHH8.99740.00001
156145CYSCAC60.70350.00001
157145CYSCBC32.28700.00001
158145CYSNN130.30330.00001
159146THRHH8.51500.00001
160146THRCAC61.57390.00001
161146THRCBC68.33400.00001
162146THRNN118.95000.00001
163147ARGHH9.03020.00001
164147ARGCAC57.23270.00001
165147ARGCBC29.10600.00001
166147ARGNN128.63000.00001
167148ALAHH9.00240.00001
168148ALACAC54.28280.00001
169148ALACBC16.87580.00001
170148ALANN132.72640.00001
171149GLYHH8.83260.00001
172149GLYCAC45.68340.00001
173149GLYNN111.40100.00001
174150CYSHH8.08350.00001
175150CYSCAC60.73660.00001
176150CYSCBC30.28430.00001
177150CYSNN123.14980.00001
178151GLYHH7.60030.00001
179151GLYCAC46.41600.00001
180151GLYNN109.670.00001
181152PHEHH8.89030.00001
182152PHECAC60.47540.00001
183152PHECBC37.87940.00001
184152PHENN124.71240.00001
185153GLUHH7.76500.00001
186153GLUCAC57.03880.00001
187153GLUCBC30.16380.00001
188153GLUNN125.66310.00001
189154TRPHH9.08860.00001
190154TRPCAC54.14820.00001
191154TRPCBC31.92850.00001
192154TRPNN120.92700.00001
193155CYSHH8.84090.00001
194155CYSCAC58.06880.00001
195155CYSCBC31.77780.00001
196155CYSNN120.87110.00001
197156TRPHH9.81190.00001
198156TRPCAC60.29250.00001
199156TRPCBC30.20630.00001
200156TRPNN131.08780.00001
201157VALHH8.65320.00001
202157VALCAC65.72480.00001
203157VALCBC33.35700.00001
204157VALNN118.43020.00001
205159GLNHH6.88470.00001
206159GLNCAC58.47570.00001
207159GLNNN118.46330.00001
208160THRHH7.08910.00001
209160THRCAC59.25780.00001
210160THRCBC71.30180.00001
211160THRNN130.78240.00001
212161GLUHH8.90440.00001
213161GLUCAC56.98160.00001
214161GLUCBC29.94310.00001
215161GLUNN121.18510.00001
216162TRPHH8.39880.00001
217162TRPCAC58.56230.00001
218162TRPNN126.88370.00001
219163THRHH8.06140.00001
220163THRCAC65.25020.00001
221163THRNN117.31120.00001
222164ARGHH8.51780.00001
223164ARGCAC58.53800.00001
224164ARGCBC28.61420.00001
225164ARGNN118.91420.00001
226165ASPHH7.73700.00001
227165ASPCAC56.92290.00001
228165ASPCBC39.41520.00001
229165ASPNN119.59640.00001
230166CYSHH6.98930.00001
231166CYSCAC64.66620.00001
232166CYSCBC29.14230.00001
233166CYSNN120.69120.00001
234167METCAC58.04900.00001
235168GLYHH9.15260.00001
236168GLYCAC45.90460.00001
237168GLYNN112.27920.00001
238169ALAHH7.30590.00001
239169ALACAC53.53040.00001
240169ALACBC18.26440.00001
241169ALANN121.31700.00001
242170HISHH8.18250.00001
243170HISCAC58.22860.00001
244170HISCBC30.240.00001
245170HISNN115.38320.00001

Chemical Shifts 2
1H: 57, 13C: 105, 15N: 57 assignments Detail
IDEntity IDSeq IDComp IDAtom IDAtom typeValVal errAmbig. code
24621METCAC54.63270.00001
24721METCBC33.22330.00001
24822GLNHH8.95340.00001
24922GLNCAC54.93650.00001
25022GLNCBC30.56450.00001
25122GLNNN123.00110.00001
25223ILEHH8.32950.00001
25323ILECAC59.59980.00001
25423ILECBC42.12380.00001
25523ILENN115.21450.00001
25624PHEHH8.64330.00001
25724PHECAC55.15070.00001
25824PHECBC41.53540.00001
25924PHENN118.77590.00001
26025VALHH9.31130.00001
26125VALCAC60.63210.00001
26225VALNN121.30940.00001
26326LYSHH8.98600.00001
26426LYSCAC54.76530.00001
26526LYSCBC34.62720.00001
26626LYSNN128.05080.00001
26727THRHH8.75910.00001
26827THRCAC60.62860.00001
26927THRNN115.44850.00001
27028LEUCBC41.94760.00001
27129THRHH7.64930.00001
27229THRCAC61.48260.00001
27329THRCBC69.08530.00001
27429THRNN105.77160.00001
275210GLYHH7.82990.00001
276210GLYCAC45.43360.00001
277210GLYNN109.35620.00001
278211LYSHH7.28400.00001
279211LYSCAC56.34860.00001
280211LYSCBC33.58130.00001
281211LYSNN121.84520.00001
282212THRHH8.65200.00001
283212THRCAC62.39340.00001
284212THRNN120.63770.00001
285214THRHH8.75040.00001
286214THRCAC62.24270.00001
287214THRCBC72.06150.00001
288214THRNN121.90110.00001
289215LEUHH8.76420.00001
290215LEUCAC52.85010.00001
291215LEUCBC46.87150.00001
292215LEUNN125.10760.00001
293216GLUHH8.15260.00001
294216GLUCAC54.84710.00001
295216GLUCBC29.95090.00001
296216GLUNN122.63660.00001
297217VALHH8.94780.00001
298217VALCAC58.42920.00001
299217VALCBC36.47330.00001
300217VALNN117.64300.00001
301218GLUHH8.68860.00001
302218GLUCAC52.85750.00001
303218GLUCBC30.89150.00001
304218GLUNN119.43050.00001
305219PROCAC65.36380.00001
306220SERHH7.04710.00001
307220SERCAC57.32580.00001
308220SERCBC63.39270.00001
309220SERNN103.51960.00001
310221ASPHH8.06780.00001
311221ASPCAC55.86120.00001
312221ASPCBC40.93740.00001
313221ASPNN123.99720.00001
314222THRHH7.88360.00001
315222THRCAC59.58920.00001
316222THRCBC71.21750.00001
317222THRNN109.03410.00001
318223ILEHH8.53720.00001
319223ILECAC62.36870.00001
320223ILENN121.35710.00001
321224GLUCAC53.17630.00001
322225ASNHH7.94020.00001
323225ASNCAC56.01950.00001
324225ASNCBC38.40810.00001
325225ASNNN121.49010.00001
326226VALHH8.10950.00001
327226VALCAC67.67430.00001
328226VALNN122.25720.00001
329227LYSHH8.57520.00001
330227LYSCAC59.38450.00001
331227LYSNN119.03740.00001
332228ALAHH7.98180.00001
333228ALACAC55.38290.00001
334228ALACBC18.25380.00001
335228ALANN123.52010.00001
336229LYSHH7.87440.00001
337229LYSCAC59.81590.00001
338229LYSCBC33.41270.00001
339229LYSNN120.30690.00001
340230ILEHH8.29320.00001
341230ILECAC66.05900.00001
342230ILECBC36.76140.00001
343230ILENN121.39820.00001
344231GLNHH8.56780.00001
345231GLNCAC60.00080.00001
346231GLNNN123.57780.00001
347232ASPHH8.05340.00001
348232ASPCAC57.26590.00001
349232ASPCBC41.14810.00001
350232ASPNN119.88930.00001
351233LYSHH7.44880.00001
352233LYSCAC58.14490.00001
353233LYSCBC34.06640.00001
354233LYSNN115.60140.00001
355234GLUHH8.75020.00001
356234GLUCAC55.45310.00001
357234GLUCBC33.28500.00001
358234GLUNN114.40780.00001
359235GLYHH8.51190.00001
360235GLYCAC46.13480.00001
361235GLYNN108.90810.00001
362236ILEHH6.17430.00001
363236ILENN120.26040.00001
364238PROCAC66.24300.00001
365238PROCBC32.88580.00001
366239ASPHH8.54050.00001
367239ASPCAC55.81690.00001
368239ASPCBC39.96960.00001
369239ASPNN113.66540.00001
370240GLNHH7.80930.00001
371240GLNCAC55.54420.00001
372240GLNCBC29.73910.00001
373240GLNNN116.94850.00001
374241GLNHH7.45180.00001
375241GLNCAC56.57690.00001
376241GLNNN118.15590.00001
377244ILEHH9.13910.00001
378244ILENN122.54670.00001
379246ALAHH8.99910.00001
380246ALACAC52.62190.00001
381246ALACBC17.12170.00001
382246ALANN101.04080.00001
383247GLYHH8.10870.00001
384247GLYCAC45.48120.00001
385247GLYNN102.58770.00001
386248LYSHH7.99350.00001
387248LYSCAC54.70070.00001
388248LYSCBC34.62720.00001
389248LYSNN121.89500.00001
390249GLNHH8.66520.00001
391249GLNCAC55.83940.00001
392249GLNNN122.87980.00001
393250LEUCAC54.25430.00001
394250LEUCBC41.50200.00001
395251GLUHH8.40360.00001
396251GLUCAC56.01330.00001
397251GLUCBC31.88840.00001
398251GLUNN123.26030.00001
399252ASPHH8.17370.00001
400252ASPCAC56.42980.00001
401252ASPCBC40.81930.00001
402252ASPNN120.53500.00001
403253GLYCAC45.25430.00001
404254ARGHH7.47700.00001
405254ARGCAC54.26580.00001
406254ARGCBC32.84400.00001
407254ARGNN119.48640.00001
408255THRHH8.84830.00001
409255THRCAC59.64950.00001
410255THRCBC72.27860.00001
411255THRNN108.95770.00001
412256LEUHH8.16390.00001
413256LEUCAC58.84020.00001
414256LEUCBC40.42960.00001
415256LEUNN118.13240.00001
416257SERHH8.48910.00001
417257SERCAC60.96880.00001
418257SERCBC62.28410.00001
419257SERNN113.53600.00001
420258ASPHH7.94830.00001
421258ASPCAC57.46520.00001
422258ASPCBC40.46910.00001
423258ASPNN124.61950.00001
424259TYRHH7.26680.00001
425259TYRCAC58.25230.00001
426259TYRCBC40.14850.00001
427259TYRNN115.83640.00001
428260ASNHH8.16310.00001
429260ASNCAC54.18330.00001
430260ASNCBC37.44620.00001
431260ASNNN116.02780.00001
432261ILEHH7.25660.00001
433261ILECAC62.51710.00001
434261ILECBC37.02300.00001
435261ILENN118.99470.00001
436262GLNHH7.63460.00001
437262GLNCAC53.61630.00001
438262GLNCBC31.69650.00001
439262GLNNN125.05470.00001
440263LYSHH8.49800.00001
441263LYSCAC57.85280.00001
442263LYSCBC32.44790.00001
443263LYSNN120.67080.00001
444264GLUHH9.33900.00001
445264GLUCAC58.01720.00001
446264GLUCBC26.39570.00001
447264GLUNN114.67430.00001
448265SERHH7.68040.00001
449265SERCAC60.91750.00001
450265SERCBC64.84360.00001
451265SERNN115.08500.00001
452266THRHH8.73150.00001
453266THRCAC62.51040.00001
454266THRCBC70.14540.00001
455266THRNN117.59110.00001
456267LEUHH9.38950.00001
457267LEUCAC53.96000.00001
458267LEUCBC44.28670.00001
459267LEUNN127.83770.00001
460268HISHH9.19650.00001
461268HISCAC56.09870.00001
462268HISNN119.54510.00001
463269LEUHH8.33960.00001
464269LEUNN123.88670.00001

Release date
2024-06-23
Citation
Capturing the catalytic intermediates of parkin ubiquitination
Connelly, E.M., Rintala-Dempsey, A.C., Gundogdu, M., Freeman, E.A., Koszela, J., Aguirre, J.D., Zhu, G., Kamarainen, O., Tadayon, R., Walden, H., Shaw, G.S.
Proc. Natl. Acad. Sci. U. S. A. (2024), 121, e2403114121-e2403114121, PubMed 39078678 , DOI 10.1073/pnas.2403114121 ,
Related entities 1. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 1, : 1 : 2 : 51 entities Detail
Related entities 2. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 2, : 303 : 11 : 80 : 315 entities Detail
Interaction partners 2. E3 ubiquitin-protein ligase parkin (E.C.2.3.2.31), Ubiquitin, entity 2, : 27 interactors Detail
Experiments performed 13 experiments Detail
Chemical shift validation 7 contents Detail
Keywords Covalent complex E3 ligase Thioether Haddock, LIGASE