0.025886
0.000000
0.000000
0.000000
0.020054
0.000000
0.000000
0.000000
0.013017
0.00000
0.00000
0.00000
Bosch, D.E.
Siderovski, D.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
38.631
49.865
76.824
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
O
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
S
N
291
N
O
N
292
N
O
N
293
N
O
N
294
N
O
N
295
N
N
N
296
S
C
N
297
N
C
N
298
N
O
N
299
R
C
N
300
N
O
N
301
N
C
N
302
N
O
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
N
323
N
O
N
324
N
O
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
C
N
342
N
C
N
343
N
O
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
doub
N
278
N
doub
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
doub
N
313
N
sing
Y
314
N
doub
N
315
N
sing
Y
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
288
2290
2302
10.1074/jbc.M112.417337
23209297
Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica.
2013
10.2210/pdb4gsw/pdb
pdb_00004gsw
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
2012-04-08
MAR scanner 300 mm plate
double crystal
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
23-ID-B
APS
1.000
SYNCHROTRON
APS BEAMLINE 23-ID-B
8982.275
Ubiquitin
2
man
polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
44
nat
water
Ubiquitin, putative
no
no
SNAMQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQKESTLHLVLRLRGGY
SNAMQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQKESTLHLVLRLRGGY
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
EhUBI1, EHI_083270, EHI_083410, EHI_156660, EHI_178340
5759
Entamoeba histolytica
562
Escherichia coli
plasmid
pLIC His
1
2.06
40.27
VAPOR DIFFUSION, HANGING DROP
5.5
EhUbiquitin at 13 mg/mL in S200 buffer was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 3350, 200 mM LiSO4, and 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-12-12
1
1
2012-12-19
1
2
2013-02-13
1
3
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-08-28
REL
REL
SO4
SULFATE ION
HOH
water
1UBQ
PDB entry 1UBQ
PDB
experimental model
SO4
1
2
SO4
SO4
101
A
SO4
2
2
SO4
SO4
102
A
HOH
2
3
HOH
HOH
201
A
HOH
3
3
HOH
HOH
202
A
HOH
4
3
HOH
HOH
203
A
HOH
5
3
HOH
HOH
204
A
HOH
7
3
HOH
HOH
205
A
HOH
8
3
HOH
HOH
206
A
HOH
13
3
HOH
HOH
207
A
HOH
14
3
HOH
HOH
208
A
HOH
15
3
HOH
HOH
209
A
HOH
18
3
HOH
HOH
210
A
HOH
19
3
HOH
HOH
211
A
HOH
20
3
HOH
HOH
212
A
HOH
21
3
HOH
HOH
213
A
HOH
24
3
HOH
HOH
214
A
HOH
25
3
HOH
HOH
215
A
HOH
36
3
HOH
HOH
216
A
HOH
38
3
HOH
HOH
217
A
HOH
1
3
HOH
HOH
101
B
HOH
6
3
HOH
HOH
102
B
HOH
9
3
HOH
HOH
103
B
HOH
10
3
HOH
HOH
104
B
HOH
11
3
HOH
HOH
105
B
HOH
12
3
HOH
HOH
106
B
HOH
16
3
HOH
HOH
107
B
HOH
17
3
HOH
HOH
108
B
HOH
22
3
HOH
HOH
109
B
HOH
23
3
HOH
HOH
110
B
HOH
26
3
HOH
HOH
111
B
HOH
27
3
HOH
HOH
112
B
HOH
28
3
HOH
HOH
113
B
HOH
29
3
HOH
HOH
114
B
HOH
30
3
HOH
HOH
115
B
HOH
31
3
HOH
HOH
116
B
HOH
32
3
HOH
HOH
117
B
HOH
33
3
HOH
HOH
118
B
HOH
34
3
HOH
HOH
119
B
HOH
35
3
HOH
HOH
120
B
HOH
37
3
HOH
HOH
121
B
HOH
39
3
HOH
HOH
122
B
HOH
40
3
HOH
HOH
123
B
HOH
41
3
HOH
HOH
124
B
HOH
42
3
HOH
HOH
125
B
HOH
43
3
HOH
HOH
126
B
HOH
44
3
HOH
HOH
127
B
n
1
1
A
ASN
2
n
2
ASN
2
A
ALA
3
n
3
ALA
3
A
MET
4
n
4
MET
4
A
GLN
5
n
5
GLN
5
A
ILE
6
n
6
ILE
6
A
PHE
7
n
7
PHE
7
A
VAL
8
n
8
VAL
8
A
LYS
9
n
9
LYS
9
A
THR
10
n
10
THR
10
A
LEU
11
n
11
LEU
11
A
THR
12
n
12
THR
12
A
GLY
13
n
13
GLY
13
A
LYS
14
n
14
LYS
14
A
THR
15
n
15
THR
15
A
ILE
16
n
16
ILE
16
A
THR
17
n
17
THR
17
A
LEU
18
n
18
LEU
18
A
GLU
19
n
19
GLU
19
A
VAL
20
n
20
VAL
20
A
GLU
21
n
21
GLU
21
A
PRO
22
n
22
PRO
22
A
ASN
23
n
23
ASN
23
A
ASP
24
n
24
ASP
24
A
SER
25
n
25
SER
25
A
ILE
26
n
26
ILE
26
A
ASP
27
n
27
ASP
27
A
ALA
28
n
28
ALA
28
A
ILE
29
n
29
ILE
29
A
LYS
30
n
30
LYS
30
A
ALA
31
n
31
ALA
31
A
LYS
32
n
32
LYS
32
A
ILE
33
n
33
ILE
33
A
GLN
34
n
34
GLN
34
A
GLU
35
n
35
GLU
35
A
LYS
36
n
36
LYS
36
A
GLU
37
n
37
GLU
37
A
GLY
38
n
38
GLY
38
A
ILE
39
n
39
ILE
39
A
PRO
40
n
40
PRO
40
A
PRO
41
n
41
PRO
41
A
ASP
42
n
42
ASP
42
A
GLN
43
n
43
GLN
43
A
GLN
44
n
44
GLN
44
A
ARG
45
n
45
ARG
45
A
LEU
46
n
46
LEU
46
A
ILE
47
n
47
ILE
47
A
PHE
48
n
48
PHE
48
A
ALA
49
n
49
ALA
49
A
GLY
50
n
50
GLY
50
A
LYS
51
n
51
LYS
51
A
GLN
52
n
52
GLN
52
A
LEU
53
n
53
LEU
53
A
GLU
54
n
54
GLU
54
A
GLU
55
n
55
GLU
55
A
GLY
56
n
56
GLY
56
A
LYS
57
n
57
LYS
57
A
THR
58
n
58
THR
58
A
LEU
59
n
59
LEU
59
A
SER
60
n
60
SER
60
A
ASP
61
n
61
ASP
61
A
TYR
62
n
62
TYR
62
A
ASN
63
n
63
ASN
63
A
ILE
64
n
64
ILE
64
A
GLN
65
n
65
GLN
65
A
LYS
66
n
66
LYS
66
A
GLU
67
n
67
GLU
67
A
SER
68
n
68
SER
68
A
THR
69
n
69
THR
69
A
LEU
70
n
70
LEU
70
A
HIS
71
n
71
HIS
71
A
LEU
72
n
72
LEU
72
A
VAL
73
n
73
VAL
73
A
LEU
74
n
74
LEU
74
A
ARG
75
n
75
ARG
75
A
n
76
76
A
n
77
77
A
n
78
78
A
n
79
79
A
n
80
80
A
n
1
1
B
n
2
2
B
n
3
3
B
MET
4
n
4
MET
4
B
GLN
5
n
5
GLN
5
B
ILE
6
n
6
ILE
6
B
PHE
7
n
7
PHE
7
B
VAL
8
n
8
VAL
8
B
LYS
9
n
9
LYS
9
B
THR
10
n
10
THR
10
B
LEU
11
n
11
LEU
11
B
THR
12
n
12
THR
12
B
GLY
13
n
13
GLY
13
B
LYS
14
n
14
LYS
14
B
THR
15
n
15
THR
15
B
ILE
16
n
16
ILE
16
B
THR
17
n
17
THR
17
B
LEU
18
n
18
LEU
18
B
GLU
19
n
19
GLU
19
B
VAL
20
n
20
VAL
20
B
GLU
21
n
21
GLU
21
B
PRO
22
n
22
PRO
22
B
ASN
23
n
23
ASN
23
B
ASP
24
n
24
ASP
24
B
SER
25
n
25
SER
25
B
ILE
26
n
26
ILE
26
B
ASP
27
n
27
ASP
27
B
ALA
28
n
28
ALA
28
B
ILE
29
n
29
ILE
29
B
LYS
30
n
30
LYS
30
B
ALA
31
n
31
ALA
31
B
LYS
32
n
32
LYS
32
B
ILE
33
n
33
ILE
33
B
GLN
34
n
34
GLN
34
B
GLU
35
n
35
GLU
35
B
LYS
36
n
36
LYS
36
B
GLU
37
n
37
GLU
37
B
GLY
38
n
38
GLY
38
B
ILE
39
n
39
ILE
39
B
PRO
40
n
40
PRO
40
B
PRO
41
n
41
PRO
41
B
ASP
42
n
42
ASP
42
B
GLN
43
n
43
GLN
43
B
GLN
44
n
44
GLN
44
B
ARG
45
n
45
ARG
45
B
LEU
46
n
46
LEU
46
B
ILE
47
n
47
ILE
47
B
PHE
48
n
48
PHE
48
B
ALA
49
n
49
ALA
49
B
GLY
50
n
50
GLY
50
B
LYS
51
n
51
LYS
51
B
GLN
52
n
52
GLN
52
B
LEU
53
n
53
LEU
53
B
GLU
54
n
54
GLU
54
B
GLU
55
n
55
GLU
55
B
GLY
56
n
56
GLY
56
B
LYS
57
n
57
LYS
57
B
THR
58
n
58
THR
58
B
LEU
59
n
59
LEU
59
B
SER
60
n
60
SER
60
B
ASP
61
n
61
ASP
61
B
TYR
62
n
62
TYR
62
B
ASN
63
n
63
ASN
63
B
ILE
64
n
64
ILE
64
B
GLN
65
n
65
GLN
65
B
LYS
66
n
66
LYS
66
B
GLU
67
n
67
GLU
67
B
SER
68
n
68
SER
68
B
THR
69
n
69
THR
69
B
LEU
70
n
70
LEU
70
B
HIS
71
n
71
HIS
71
B
LEU
72
n
72
LEU
72
B
VAL
73
n
73
VAL
73
B
LEU
74
n
74
LEU
74
B
ARG
75
n
75
ARG
75
B
LEU
76
n
76
LEU
76
B
n
77
77
B
n
78
78
B
n
79
79
B
n
80
80
B
8.8825
4.2839
-6.4294
7.5101
-5.5208
7.7505
-0.1363
0.0645
-0.1283
-0.5750
0.0903
0.4981
0.2889
0.1123
0.0082
0.3596
-0.0260
-0.0121
0.3096
-0.0856
0.4316
refined
-2.9252
-17.0672
16.8572
X-RAY DIFFRACTION
8.7358
4.4651
-1.0012
3.6026
-2.1792
4.2165
0.1084
-0.0855
-0.0624
-0.4293
-0.1908
-0.3767
0.0558
-0.0522
0.0436
0.3324
0.0713
-0.0259
0.2434
-0.0233
0.4811
refined
-5.1492
-8.0573
14.2490
X-RAY DIFFRACTION
6.8637
-5.0076
0.9368
7.1349
0.0418
3.5057
0.1044
-0.2153
0.9020
0.4530
-0.0121
0.0763
-0.1947
0.1502
0.0079
0.4440
0.0032
-0.0267
0.2985
-0.0085
0.4650
refined
-5.5120
-7.0095
25.2201
X-RAY DIFFRACTION
6.0129
-0.3649
-3.3947
4.8498
-0.0770
2.1587
-0.0693
-0.3594
-0.0825
-0.0779
-0.1956
-0.0386
0.0691
0.2466
0.2527
0.2423
0.0302
-0.1238
0.2914
0.0047
0.3544
refined
1.2656
-9.2786
21.3620
X-RAY DIFFRACTION
9.3361
6.6156
-2.8801
5.9387
-2.0463
3.0799
0.3154
0.1665
-0.5305
0.7282
-0.0346
-1.3257
0.2901
0.3948
-0.4972
0.4475
-0.0134
-0.0807
0.4096
-0.0300
0.3950
refined
-11.3566
3.6142
1.4181
X-RAY DIFFRACTION
4.4323
2.3395
1.5656
2.1660
3.4670
9.0985
0.1158
-0.0723
0.1625
-0.1913
-0.1121
0.0043
-0.1042
0.0305
0.0683
0.2925
0.0341
0.0161
0.2180
0.0265
0.4959
refined
-10.1049
2.2378
12.3134
X-RAY DIFFRACTION
4.1818
1.6119
-1.3273
5.3056
1.8039
4.8203
-0.1059
0.0158
-0.1921
-0.2086
-0.0002
-0.0343
0.2476
-0.7675
0.0439
0.3401
0.0264
-0.0946
0.4227
0.0791
0.4536
refined
-22.1508
-0.0980
8.1131
X-RAY DIFFRACTION
3.6481
-0.3188
-0.1683
4.8238
3.9109
3.2613
0.2274
0.2805
-0.2308
-0.2513
0.0457
-0.7924
-0.2597
-0.7043
-0.0281
0.4043
0.0307
0.0149
0.3796
0.0829
0.5466
refined
-17.0472
6.3741
5.4694
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(CHAIN A AND RESID 2:18)
X-RAY DIFFRACTION
2
(CHAIN A AND RESID 19:37)
X-RAY DIFFRACTION
3
(CHAIN A AND RESID 38:55)
X-RAY DIFFRACTION
4
(CHAIN A AND RESID 56:75)
X-RAY DIFFRACTION
5
(CHAIN B AND RESID 4:23)
X-RAY DIFFRACTION
6
(CHAIN B AND RESID 24:44)
X-RAY DIFFRACTION
7
(CHAIN B AND RESID 45:64)
X-RAY DIFFRACTION
8
(CHAIN B AND RESID 65:76)
author_and_software_defined_assembly
PISA
1
monomeric
author_and_software_defined_assembly
PISA
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LEU
18
A
O
LEU
18
A
N
ILE
6
A
N
ILE
6
A
N
LYS
9
A
N
LYS
9
A
O
LEU
70
A
O
LEU
70
A
O
VAL
73
A
O
VAL
73
A
N
ARG
45
A
N
ARG
45
A
N
LEU
46
A
N
LEU
46
A
O
LEU
53
A
O
LEU
53
B
O
LEU
18
B
O
LEU
18
B
N
ILE
6
B
N
ILE
6
B
N
PHE
7
B
N
PHE
7
B
O
LEU
70
B
O
LEU
70
B
O
VAL
73
B
O
VAL
73
B
N
ARG
45
B
N
ARG
45
B
N
PHE
48
B
N
PHE
48
B
O
LYS
51
B
O
LYS
51
1
B
CA
LEU
76
B
CA
LEU
76
0
Y
1
A
SER
1
A
SER
1
1
Y
1
A
LEU
76
A
LEU
76
1
Y
1
A
ARG
77
A
ARG
77
1
Y
1
A
GLY
78
A
GLY
78
1
Y
1
A
GLY
79
A
GLY
79
1
Y
1
A
TYR
80
A
TYR
80
1
Y
1
B
SER
1
B
SER
1
1
Y
1
B
ASN
2
B
ASN
2
1
Y
1
B
ALA
3
B
ALA
3
1
Y
1
B
ARG
77
B
ARG
77
1
Y
1
B
GLY
78
B
GLY
78
1
Y
1
B
GLY
79
B
GLY
79
1
Y
1
B
TYR
80
B
TYR
80
1
Y
1
B
B
O
O
HOH
HOH
124
127
2.02
1
B
B
O
O
HOH
HOH
119
121
2.14
1
B
B
O
O
HOH
HOH
119
120
2.18
1
A
ALA
3
-48.41
152.55
1
B
THR
10
-78.18
-166.72
0.2561
0.1932
0.1994
2.15
34.513
840
8591
8379
10.03
97.53
0.29
RANDOM
1
1.34
MOLECULAR REPLACEMENT
29.07
1.00
1.20
PDB entry 1UBQ
ML
FLAT BULK SOLVENT MODEL
2.15
34.513
44
1219
10
0
1165
0.014
1192
1.493
1606
16.107
470
0.094
191
0.007
204
0.3505
0.2658
2.2772
129
1154
1154
92.00
0.3471
0.2456
2.4530
135
1213
97.00
0.3361
0.2415
2.6997
141
1260
99.00
0.2710
0.2206
3.0902
141
1276
99.00
0.2642
0.1768
3.8924
145
1293
99.00
0.1930
0.1598
34.5176
149
1343
98.00
32.8
2.15
40.0
4GSW
8593
8430
0
0
0.085
1
13.6
3.5
98.1
0.2790
2.15
2.17
3.1
210
1
3.3
96.8
data collection
HKL-2000
model building
PHENIX
AutoMR
refinement
PHENIX
(phenix.refine: 1.8_1069)
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
AutoMR
Crystal structure of ubiquitin from Entamoeba histolytica to 2.15 Angstrom
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
A
SER
25
A
SER
25
HELX_P
A
GLY
38
A
GLY
38
1
1
14
A
PRO
40
A
PRO
40
HELX_P
A
ASP
42
A
ASP
42
5
2
3
A
THR
58
A
THR
58
HELX_P
A
ASN
63
A
ASN
63
5
3
6
B
SER
25
B
SER
25
HELX_P
B
GLY
38
B
GLY
38
1
4
14
B
PRO
40
B
PRO
40
HELX_P
B
ASP
42
B
ASP
42
5
5
3
B
THR
58
B
THR
58
HELX_P
B
ASN
63
B
ASN
63
5
6
6
PROTEIN BINDING
ubiquitin, ubiquitin-like modifier, ubiquitin fold, post-translational modification, EhUbc5, EhUba1, ubiquitination, isopeptide bond, PROTEIN BINDING
C4M760_ENTHI
UNP
1
1
C4M760
MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQKESTLHLVLRLRGGY
1
77
4GSW
4
80
C4M760
A
1
4
80
1
77
4GSW
4
80
C4M760
B
1
4
80
1
expression tag
SER
1
4GSW
A
C4M760
UNP
1
1
expression tag
ASN
2
4GSW
A
C4M760
UNP
2
1
expression tag
ALA
3
4GSW
A
C4M760
UNP
3
2
expression tag
SER
1
4GSW
B
C4M760
UNP
1
2
expression tag
ASN
2
4GSW
B
C4M760
UNP
2
2
expression tag
ALA
3
4GSW
B
C4M760
UNP
3
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
15
A
THR
15
A
VAL
20
A
VAL
20
A
MET
4
A
MET
4
A
LYS
9
A
LYS
9
A
THR
69
A
THR
69
A
LEU
74
A
LEU
74
A
GLN
44
A
GLN
44
A
PHE
48
A
PHE
48
A
LYS
51
A
LYS
51
A
LEU
53
A
LEU
53
B
THR
15
B
THR
15
B
GLU
19
B
GLU
19
B
GLN
5
B
GLN
5
B
LYS
9
B
LYS
9
B
THR
69
B
THR
69
B
LEU
74
B
LEU
74
B
GLN
44
B
GLN
44
B
PHE
48
B
PHE
48
B
LYS
51
B
LYS
51
B
GLN
52
B
GLN
52
BINDING SITE FOR RESIDUE SO4 A 101
A
SO4
101
Software
3
BINDING SITE FOR RESIDUE SO4 A 102
A
SO4
102
Software
3
A
ASN
2
A
ASN
2
3
1_555
A
GLU
21
A
GLU
21
3
1_555
A
ASN
23
A
ASN
23
3
1_555
B
LYS
9
B
LYS
9
3
2_455
B
HOH
115
F
HOH
3
2_455
B
HOH
121
F
HOH
3
3_545
19
P 21 21 21