0.022453
0.000000
0.000000
0.000000
0.013359
0.000000
0.000000
0.000000
0.010950
0.000000
0.000000
0.000000
Hodge, C.D.
Edwards, R.A.
Glover, J.N.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
44.538
74.855
91.325
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C11 H9 N O5 S
267.258
2-[(4-methylphenyl)sulfonyl]-5-nitrofuran
NSC697923
non-polymer
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
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
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
US
Acs Chem.Biol.
1554-8929
10
1718
1728
10.1021/acschembio.5b00222
25909880
Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.
2015
105
1
Mirrors
CCD
2012-08-21
RAYONIX MX300HE
SINGLE WAVELENGTH
M
x-ray
1
1.03321
1.0
08B1-1
CLSI
1.03321
SYNCHROTRON
CLSI BEAMLINE 08B1-1
17165.590
Ubiquitin-conjugating enzyme E2 variant 2
1
man
polymer
17942.631
Ubiquitin-conjugating enzyme E2 N
6.3.2.19
1
man
polymer
92.094
GLYCEROL
1
syn
non-polymer
267.258
2-[(4-methylphenyl)sulfonyl]-5-nitrofuran
1
syn
non-polymer
18.015
water
212
nat
water
DDVit 1, Enterocyte differentiation-associated factor 1, EDAF-1, Enterocyte differentiation-promoting factor 1, EDPF-1, MMS2 homolog, Vitamin D3-inducible protein
Bendless-like ubiquitin-conjugating enzyme, Ubc13, UbcH13, Ubiquitin carrier protein N, Ubiquitin-protein ligase N
no
no
GPLGSPEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPK
YPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
GPLGSPEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPK
YPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
A
polypeptide(L)
no
no
GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFM
TKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI
GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFM
TKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI
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
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
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
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
human
sample
MMS2, UBE2V2, UEV2
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
plasmid
pGEX6p1
human
sample
BLU, UBE2N
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
plasmid
pGEX6p1
1
2.17
43.27
VAPOR DIFFUSION, SITTING DROP
7.4
100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
pdbx_unobs_or_zero_occ_atoms
software
repository
Initial release
Database references
Advisory
Refinement description
1
0
2015-05-06
1
1
2015-08-05
1
2
2017-11-22
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.language
_software.location
_software.name
_software.type
_software.version
RCSB
Y
RCSB
2014-01-28
REL
REL
GOL
GLYCEROL
N2F
2-[(4-methylphenyl)sulfonyl]-5-nitrofuran
HOH
water
THE COMPOUND N2F LOSES THE 4-METHYLBENZENE-SULFINIC ACID GROUP ON INERACTING WITH UBC13 AND THE REMAINING PART OF N2F FORMS A COVALENT BOND WITH THE SG ATOM OF CYS B87
GOL
1
3
GOL
GOL
201
A
N2F
999
4
N2F
N2F
201
B
HOH
1
5
HOH
HOH
301
A
HOH
3
5
HOH
HOH
302
A
HOH
5
5
HOH
HOH
303
A
HOH
6
5
HOH
HOH
304
A
HOH
7
5
HOH
HOH
305
A
HOH
8
5
HOH
HOH
306
A
HOH
9
5
HOH
HOH
307
A
HOH
10
5
HOH
HOH
308
A
HOH
11
5
HOH
HOH
309
A
HOH
12
5
HOH
HOH
310
A
HOH
13
5
HOH
HOH
311
A
HOH
15
5
HOH
HOH
312
A
HOH
16
5
HOH
HOH
313
A
HOH
18
5
HOH
HOH
314
A
HOH
19
5
HOH
HOH
315
A
HOH
20
5
HOH
HOH
316
A
HOH
21
5
HOH
HOH
317
A
HOH
23
5
HOH
HOH
318
A
HOH
26
5
HOH
HOH
319
A
HOH
27
5
HOH
HOH
320
A
HOH
29
5
HOH
HOH
321
A
HOH
32
5
HOH
HOH
322
A
HOH
33
5
HOH
HOH
323
A
HOH
34
5
HOH
HOH
324
A
HOH
35
5
HOH
HOH
325
A
HOH
36
5
HOH
HOH
326
A
HOH
40
5
HOH
HOH
327
A
HOH
42
5
HOH
HOH
328
A
HOH
44
5
HOH
HOH
329
A
HOH
47
5
HOH
HOH
330
A
HOH
53
5
HOH
HOH
331
A
HOH
55
5
HOH
HOH
332
A
HOH
57
5
HOH
HOH
333
A
HOH
59
5
HOH
HOH
334
A
HOH
60
5
HOH
HOH
335
A
HOH
61
5
HOH
HOH
336
A
HOH
63
5
HOH
HOH
337
A
HOH
64
5
HOH
HOH
338
A
HOH
65
5
HOH
HOH
339
A
HOH
67
5
HOH
HOH
340
A
HOH
69
5
HOH
HOH
341
A
HOH
70
5
HOH
HOH
342
A
HOH
71
5
HOH
HOH
343
A
HOH
76
5
HOH
HOH
344
A
HOH
77
5
HOH
HOH
345
A
HOH
78
5
HOH
HOH
346
A
HOH
79
5
HOH
HOH
347
A
HOH
81
5
HOH
HOH
348
A
HOH
83
5
HOH
HOH
349
A
HOH
85
5
HOH
HOH
350
A
HOH
87
5
HOH
HOH
351
A
HOH
88
5
HOH
HOH
352
A
HOH
89
5
HOH
HOH
353
A
HOH
90
5
HOH
HOH
354
A
HOH
93
5
HOH
HOH
355
A
HOH
94
5
HOH
HOH
356
A
HOH
95
5
HOH
HOH
357
A
HOH
96
5
HOH
HOH
358
A
HOH
98
5
HOH
HOH
359
A
HOH
99
5
HOH
HOH
360
A
HOH
100
5
HOH
HOH
361
A
HOH
101
5
HOH
HOH
362
A
HOH
103
5
HOH
HOH
363
A
HOH
105
5
HOH
HOH
364
A
HOH
106
5
HOH
HOH
365
A
HOH
112
5
HOH
HOH
366
A
HOH
113
5
HOH
HOH
367
A
HOH
114
5
HOH
HOH
368
A
HOH
115
5
HOH
HOH
369
A
HOH
118
5
HOH
HOH
370
A
HOH
119
5
HOH
HOH
371
A
HOH
121
5
HOH
HOH
372
A
HOH
122
5
HOH
HOH
373
A
HOH
130
5
HOH
HOH
374
A
HOH
133
5
HOH
HOH
375
A
HOH
134
5
HOH
HOH
376
A
HOH
135
5
HOH
HOH
377
A
HOH
137
5
HOH
HOH
378
A
HOH
138
5
HOH
HOH
379
A
HOH
140
5
HOH
HOH
380
A
HOH
142
5
HOH
HOH
381
A
HOH
143
5
HOH
HOH
382
A
HOH
144
5
HOH
HOH
383
A
HOH
151
5
HOH
HOH
384
A
HOH
153
5
HOH
HOH
385
A
HOH
155
5
HOH
HOH
386
A
HOH
156
5
HOH
HOH
387
A
HOH
162
5
HOH
HOH
388
A
HOH
164
5
HOH
HOH
389
A
HOH
165
5
HOH
HOH
390
A
HOH
171
5
HOH
HOH
391
A
HOH
172
5
HOH
HOH
392
A
HOH
174
5
HOH
HOH
393
A
HOH
175
5
HOH
HOH
394
A
HOH
181
5
HOH
HOH
395
A
HOH
183
5
HOH
HOH
396
A
HOH
186
5
HOH
HOH
397
A
HOH
191
5
HOH
HOH
398
A
HOH
192
5
HOH
HOH
399
A
HOH
193
5
HOH
HOH
400
A
HOH
194
5
HOH
HOH
401
A
HOH
201
5
HOH
HOH
402
A
HOH
202
5
HOH
HOH
403
A
HOH
204
5
HOH
HOH
404
A
HOH
205
5
HOH
HOH
405
A
HOH
206
5
HOH
HOH
406
A
HOH
209
5
HOH
HOH
407
A
HOH
211
5
HOH
HOH
408
A
HOH
213
5
HOH
HOH
409
A
HOH
214
5
HOH
HOH
410
A
HOH
215
5
HOH
HOH
411
A
HOH
216
5
HOH
HOH
412
A
HOH
2
5
HOH
HOH
301
B
HOH
4
5
HOH
HOH
302
B
HOH
14
5
HOH
HOH
303
B
HOH
17
5
HOH
HOH
304
B
HOH
22
5
HOH
HOH
305
B
HOH
24
5
HOH
HOH
306
B
HOH
25
5
HOH
HOH
307
B
HOH
28
5
HOH
HOH
308
B
HOH
30
5
HOH
HOH
309
B
HOH
37
5
HOH
HOH
310
B
HOH
38
5
HOH
HOH
311
B
HOH
39
5
HOH
HOH
312
B
HOH
43
5
HOH
HOH
313
B
HOH
45
5
HOH
HOH
314
B
HOH
46
5
HOH
HOH
315
B
HOH
48
5
HOH
HOH
316
B
HOH
49
5
HOH
HOH
317
B
HOH
50
5
HOH
HOH
318
B
HOH
51
5
HOH
HOH
319
B
HOH
52
5
HOH
HOH
320
B
HOH
54
5
HOH
HOH
321
B
HOH
56
5
HOH
HOH
322
B
HOH
58
5
HOH
HOH
323
B
HOH
62
5
HOH
HOH
324
B
HOH
66
5
HOH
HOH
325
B
HOH
68
5
HOH
HOH
326
B
HOH
73
5
HOH
HOH
327
B
HOH
74
5
HOH
HOH
328
B
HOH
75
5
HOH
HOH
329
B
HOH
80
5
HOH
HOH
330
B
HOH
82
5
HOH
HOH
331
B
HOH
84
5
HOH
HOH
332
B
HOH
86
5
HOH
HOH
333
B
HOH
91
5
HOH
HOH
334
B
HOH
92
5
HOH
HOH
335
B
HOH
97
5
HOH
HOH
336
B
HOH
102
5
HOH
HOH
337
B
HOH
104
5
HOH
HOH
338
B
HOH
107
5
HOH
HOH
339
B
HOH
108
5
HOH
HOH
340
B
HOH
109
5
HOH
HOH
341
B
HOH
110
5
HOH
HOH
342
B
HOH
111
5
HOH
HOH
343
B
HOH
116
5
HOH
HOH
344
B
HOH
117
5
HOH
HOH
345
B
HOH
120
5
HOH
HOH
346
B
HOH
123
5
HOH
HOH
347
B
HOH
124
5
HOH
HOH
348
B
HOH
125
5
HOH
HOH
349
B
HOH
126
5
HOH
HOH
350
B
HOH
127
5
HOH
HOH
351
B
HOH
128
5
HOH
HOH
352
B
HOH
129
5
HOH
HOH
353
B
HOH
131
5
HOH
HOH
354
B
HOH
132
5
HOH
HOH
355
B
HOH
136
5
HOH
HOH
356
B
HOH
139
5
HOH
HOH
357
B
HOH
141
5
HOH
HOH
358
B
HOH
145
5
HOH
HOH
359
B
HOH
146
5
HOH
HOH
360
B
HOH
147
5
HOH
HOH
361
B
HOH
148
5
HOH
HOH
362
B
HOH
149
5
HOH
HOH
363
B
HOH
150
5
HOH
HOH
364
B
HOH
152
5
HOH
HOH
365
B
HOH
154
5
HOH
HOH
366
B
HOH
157
5
HOH
HOH
367
B
HOH
158
5
HOH
HOH
368
B
HOH
159
5
HOH
HOH
369
B
HOH
160
5
HOH
HOH
370
B
HOH
161
5
HOH
HOH
371
B
HOH
163
5
HOH
HOH
372
B
HOH
166
5
HOH
HOH
373
B
HOH
167
5
HOH
HOH
374
B
HOH
168
5
HOH
HOH
375
B
HOH
169
5
HOH
HOH
376
B
HOH
170
5
HOH
HOH
377
B
HOH
173
5
HOH
HOH
378
B
HOH
176
5
HOH
HOH
379
B
HOH
177
5
HOH
HOH
380
B
HOH
178
5
HOH
HOH
381
B
HOH
179
5
HOH
HOH
382
B
HOH
180
5
HOH
HOH
383
B
HOH
182
5
HOH
HOH
384
B
HOH
184
5
HOH
HOH
385
B
HOH
185
5
HOH
HOH
386
B
HOH
187
5
HOH
HOH
387
B
HOH
188
5
HOH
HOH
388
B
HOH
189
5
HOH
HOH
389
B
HOH
190
5
HOH
HOH
390
B
HOH
195
5
HOH
HOH
391
B
HOH
196
5
HOH
HOH
392
B
HOH
197
5
HOH
HOH
393
B
HOH
198
5
HOH
HOH
394
B
HOH
200
5
HOH
HOH
395
B
HOH
203
5
HOH
HOH
396
B
HOH
207
5
HOH
HOH
397
B
HOH
208
5
HOH
HOH
398
B
HOH
210
5
HOH
HOH
399
B
HOH
212
5
HOH
HOH
400
B
n
1
-7
A
n
2
-6
A
n
3
-5
A
n
4
-4
A
n
5
-3
A
n
6
-2
A
n
7
-1
A
n
8
0
A
n
9
1
A
n
10
2
A
n
11
3
A
n
12
4
A
n
13
5
A
GLY
6
n
14
GLY
6
A
VAL
7
n
15
VAL
7
A
LYS
8
n
16
LYS
8
A
VAL
9
n
17
VAL
9
A
PRO
10
n
18
PRO
10
A
ARG
11
n
19
ARG
11
A
ASN
12
n
20
ASN
12
A
PHE
13
n
21
PHE
13
A
ARG
14
n
22
ARG
14
A
LEU
15
n
23
LEU
15
A
LEU
16
n
24
LEU
16
A
GLU
17
n
25
GLU
17
A
GLU
18
n
26
GLU
18
A
LEU
19
n
27
LEU
19
A
GLU
20
n
28
GLU
20
A
GLU
21
n
29
GLU
21
A
GLY
22
n
30
GLY
22
A
GLN
23
n
31
GLN
23
A
LYS
24
n
32
LYS
24
A
GLY
25
n
33
GLY
25
A
VAL
26
n
34
VAL
26
A
GLY
27
n
35
GLY
27
A
ASP
28
n
36
ASP
28
A
GLY
29
n
37
GLY
29
A
THR
30
n
38
THR
30
A
VAL
31
n
39
VAL
31
A
SER
32
n
40
SER
32
A
TRP
33
n
41
TRP
33
A
GLY
34
n
42
GLY
34
A
LEU
35
n
43
LEU
35
A
GLU
36
n
44
GLU
36
A
ASP
37
n
45
ASP
37
A
ASP
38
n
46
ASP
38
A
GLU
39
n
47
GLU
39
A
ASP
40
n
48
ASP
40
A
MET
41
n
49
MET
41
A
THR
42
n
50
THR
42
A
LEU
43
n
51
LEU
43
A
THR
44
n
52
THR
44
A
ARG
45
n
53
ARG
45
A
TRP
46
n
54
TRP
46
A
THR
47
n
55
THR
47
A
GLY
48
n
56
GLY
48
A
MET
49
n
57
MET
49
A
ILE
50
n
58
ILE
50
A
ILE
51
n
59
ILE
51
A
GLY
52
n
60
GLY
52
A
PRO
53
n
61
PRO
53
A
PRO
54
n
62
PRO
54
A
ARG
55
n
63
ARG
55
A
THR
56
n
64
THR
56
A
ASN
57
n
65
ASN
57
A
TYR
58
n
66
TYR
58
A
GLU
59
n
67
GLU
59
A
ASN
60
n
68
ASN
60
A
ARG
61
n
69
ARG
61
A
ILE
62
n
70
ILE
62
A
TYR
63
n
71
TYR
63
A
SER
64
n
72
SER
64
A
LEU
65
n
73
LEU
65
A
LYS
66
n
74
LYS
66
A
VAL
67
n
75
VAL
67
A
GLU
68
n
76
GLU
68
A
CYS
69
n
77
CYS
69
A
GLY
70
n
78
GLY
70
A
PRO
71
n
79
PRO
71
A
LYS
72
n
80
LYS
72
A
TYR
73
n
81
TYR
73
A
PRO
74
n
82
PRO
74
A
GLU
75
n
83
GLU
75
A
ALA
76
n
84
ALA
76
A
PRO
77
n
85
PRO
77
A
PRO
78
n
86
PRO
78
A
SER
79
n
87
SER
79
A
VAL
80
n
88
VAL
80
A
ARG
81
n
89
ARG
81
A
PHE
82
n
90
PHE
82
A
VAL
83
n
91
VAL
83
A
THR
84
n
92
THR
84
A
LYS
85
n
93
LYS
85
A
ILE
86
n
94
ILE
86
A
ASN
87
n
95
ASN
87
A
MET
88
n
96
MET
88
A
ASN
89
n
97
ASN
89
A
GLY
90
n
98
GLY
90
A
ILE
91
n
99
ILE
91
A
ASN
92
n
100
ASN
92
A
ASN
93
n
101
ASN
93
A
SER
94
n
102
SER
94
A
SER
95
n
103
SER
95
A
GLY
96
n
104
GLY
96
A
MET
97
n
105
MET
97
A
VAL
98
n
106
VAL
98
A
ASP
99
n
107
ASP
99
A
ALA
100
n
108
ALA
100
A
ARG
101
n
109
ARG
101
A
SER
102
n
110
SER
102
A
ILE
103
n
111
ILE
103
A
PRO
104
n
112
PRO
104
A
VAL
105
n
113
VAL
105
A
LEU
106
n
114
LEU
106
A
ALA
107
n
115
ALA
107
A
LYS
108
n
116
LYS
108
A
TRP
109
n
117
TRP
109
A
GLN
110
n
118
GLN
110
A
ASN
111
n
119
ASN
111
A
SER
112
n
120
SER
112
A
TYR
113
n
121
TYR
113
A
SER
114
n
122
SER
114
A
ILE
115
n
123
ILE
115
A
LYS
116
n
124
LYS
116
A
VAL
117
n
125
VAL
117
A
VAL
118
n
126
VAL
118
A
LEU
119
n
127
LEU
119
A
GLN
120
n
128
GLN
120
A
GLU
121
n
129
GLU
121
A
LEU
122
n
130
LEU
122
A
ARG
123
n
131
ARG
123
A
ARG
124
n
132
ARG
124
A
LEU
125
n
133
LEU
125
A
MET
126
n
134
MET
126
A
MET
127
n
135
MET
127
A
SER
128
n
136
SER
128
A
LYS
129
n
137
LYS
129
A
GLU
130
n
138
GLU
130
A
ASN
131
n
139
ASN
131
A
MET
132
n
140
MET
132
A
LYS
133
n
141
LYS
133
A
LEU
134
n
142
LEU
134
A
PRO
135
n
143
PRO
135
A
GLN
136
n
144
GLN
136
A
PRO
137
n
145
PRO
137
A
PRO
138
n
146
PRO
138
A
GLU
139
n
147
GLU
139
A
GLY
140
n
148
GLY
140
A
GLN
141
n
149
GLN
141
A
THR
142
n
150
THR
142
A
TYR
143
n
151
TYR
143
A
ASN
144
n
152
ASN
144
A
ASN
145
n
153
ASN
145
A
n
1
-7
B
n
2
-6
B
n
3
-5
B
n
4
-4
B
n
5
-3
B
n
6
-2
B
n
7
-1
B
n
8
0
B
n
9
1
B
ALA
2
n
10
ALA
2
B
GLY
3
n
11
GLY
3
B
LEU
4
n
12
LEU
4
B
PRO
5
n
13
PRO
5
B
ARG
6
n
14
ARG
6
B
ARG
7
n
15
ARG
7
B
ILE
8
n
16
ILE
8
B
ILE
9
n
17
ILE
9
B
LYS
10
n
18
LYS
10
B
GLU
11
n
19
GLU
11
B
THR
12
n
20
THR
12
B
GLN
13
n
21
GLN
13
B
ARG
14
n
22
ARG
14
B
LEU
15
n
23
LEU
15
B
LEU
16
n
24
LEU
16
B
ALA
17
n
25
ALA
17
B
GLU
18
n
26
GLU
18
B
PRO
19
n
27
PRO
19
B
VAL
20
n
28
VAL
20
B
PRO
21
n
29
PRO
21
B
GLY
22
n
30
GLY
22
B
ILE
23
n
31
ILE
23
B
LYS
24
n
32
LYS
24
B
ALA
25
n
33
ALA
25
B
GLU
26
n
34
GLU
26
B
PRO
27
n
35
PRO
27
B
ASP
28
n
36
ASP
28
B
GLU
29
n
37
GLU
29
B
SER
30
n
38
SER
30
B
ASN
31
n
39
ASN
31
B
ALA
32
n
40
ALA
32
B
ARG
33
n
41
ARG
33
B
TYR
34
n
42
TYR
34
B
PHE
35
n
43
PHE
35
B
HIS
36
n
44
HIS
36
B
VAL
37
n
45
VAL
37
B
VAL
38
n
46
VAL
38
B
ILE
39
n
47
ILE
39
B
ALA
40
n
48
ALA
40
B
GLY
41
n
49
GLY
41
B
PRO
42
n
50
PRO
42
B
GLN
43
n
51
GLN
43
B
ASP
44
n
52
ASP
44
B
SER
45
n
53
SER
45
B
PRO
46
n
54
PRO
46
B
PHE
47
n
55
PHE
47
B
GLU
48
n
56
GLU
48
B
GLY
49
n
57
GLY
49
B
GLY
50
n
58
GLY
50
B
THR
51
n
59
THR
51
B
PHE
52
n
60
PHE
52
B
LYS
53
n
61
LYS
53
B
LEU
54
n
62
LEU
54
B
GLU
55
n
63
GLU
55
B
LEU
56
n
64
LEU
56
B
PHE
57
n
65
PHE
57
B
LEU
58
n
66
LEU
58
B
PRO
59
n
67
PRO
59
B
GLU
60
n
68
GLU
60
B
GLU
61
n
69
GLU
61
B
TYR
62
n
70
TYR
62
B
PRO
63
n
71
PRO
63
B
MET
64
n
72
MET
64
B
ALA
65
n
73
ALA
65
B
ALA
66
n
74
ALA
66
B
PRO
67
n
75
PRO
67
B
LYS
68
n
76
LYS
68
B
VAL
69
n
77
VAL
69
B
ARG
70
n
78
ARG
70
B
PHE
71
n
79
PHE
71
B
MET
72
n
80
MET
72
B
THR
73
n
81
THR
73
B
LYS
74
n
82
LYS
74
B
ILE
75
n
83
ILE
75
B
TYR
76
n
84
TYR
76
B
HIS
77
n
85
HIS
77
B
PRO
78
n
86
PRO
78
B
ASN
79
n
87
ASN
79
B
VAL
80
n
88
VAL
80
B
ASP
81
n
89
ASP
81
B
LYS
82
n
90
LYS
82
B
LEU
83
n
91
LEU
83
B
GLY
84
n
92
GLY
84
B
ARG
85
n
93
ARG
85
B
ILE
86
n
94
ILE
86
B
CYS
87
n
95
CYS
87
B
LEU
88
n
96
LEU
88
B
ASP
89
n
97
ASP
89
B
ILE
90
n
98
ILE
90
B
LEU
91
n
99
LEU
91
B
LYS
92
n
100
LYS
92
B
ASP
93
n
101
ASP
93
B
LYS
94
n
102
LYS
94
B
TRP
95
n
103
TRP
95
B
SER
96
n
104
SER
96
B
PRO
97
n
105
PRO
97
B
ALA
98
n
106
ALA
98
B
LEU
99
n
107
LEU
99
B
GLN
100
n
108
GLN
100
B
ILE
101
n
109
ILE
101
B
ARG
102
n
110
ARG
102
B
THR
103
n
111
THR
103
B
VAL
104
n
112
VAL
104
B
LEU
105
n
113
LEU
105
B
LEU
106
n
114
LEU
106
B
SER
107
n
115
SER
107
B
ILE
108
n
116
ILE
108
B
GLN
109
n
117
GLN
109
B
ALA
110
n
118
ALA
110
B
LEU
111
n
119
LEU
111
B
LEU
112
n
120
LEU
112
B
SER
113
n
121
SER
113
B
ALA
114
n
122
ALA
114
B
PRO
115
n
123
PRO
115
B
ASN
116
n
124
ASN
116
B
PRO
117
n
125
PRO
117
B
ASP
118
n
126
ASP
118
B
ASP
119
n
127
ASP
119
B
PRO
120
n
128
PRO
120
B
LEU
121
n
129
LEU
121
B
ALA
122
n
130
ALA
122
B
ASN
123
n
131
ASN
123
B
ASP
124
n
132
ASP
124
B
VAL
125
n
133
VAL
125
B
ALA
126
n
134
ALA
126
B
GLU
127
n
135
GLU
127
B
GLN
128
n
136
GLN
128
B
TRP
129
n
137
TRP
129
B
LYS
130
n
138
LYS
130
B
THR
131
n
139
THR
131
B
ASN
132
n
140
ASN
132
B
GLU
133
n
141
GLU
133
B
ALA
134
n
142
ALA
134
B
GLN
135
n
143
GLN
135
B
ALA
136
n
144
ALA
136
B
ILE
137
n
145
ILE
137
B
GLU
138
n
146
GLU
138
B
THR
139
n
147
THR
139
B
ALA
140
n
148
ALA
140
B
ARG
141
n
149
ARG
141
B
ALA
142
n
150
ALA
142
B
TRP
143
n
151
TRP
143
B
THR
144
n
152
THR
144
B
ARG
145
n
153
ARG
145
B
LEU
146
n
154
LEU
146
B
TYR
147
n
155
TYR
147
B
ALA
148
n
156
ALA
148
B
MET
149
n
157
MET
149
B
ASN
150
n
158
ASN
150
B
n
159
151
B
n
160
152
B
author_and_software_defined_assembly
PISA
2
dimeric
1720
-10
15180
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
N
GLY
34
A
N
GLY
42
A
O
THR
47
A
O
THR
55
A
N
ILE
50
A
N
ILE
58
A
O
TYR
63
A
O
TYR
71
A
N
GLU
68
A
N
GLU
76
A
O
SER
79
A
O
SER
87
B
N
GLU
26
B
N
GLU
34
B
O
HIS
36
B
O
HIS
44
B
N
PHE
35
B
N
PHE
43
B
O
LEU
56
B
O
LEU
64
B
N
GLU
55
B
N
GLU
63
B
O
ARG
70
B
O
ARG
78
1
A
GLY
-7
A
GLY
1
1
Y
1
A
PRO
-6
A
PRO
2
1
Y
1
A
LEU
-5
A
LEU
3
1
Y
1
A
GLY
-4
A
GLY
4
1
Y
1
A
SER
-3
A
SER
5
1
Y
1
A
PRO
-2
A
PRO
6
1
Y
1
A
GLU
-1
A
GLU
7
1
Y
1
A
PHE
0
A
PHE
8
1
Y
1
A
MET
1
A
MET
9
1
Y
1
A
ALA
2
A
ALA
10
1
Y
1
A
VAL
3
A
VAL
11
1
Y
1
A
SER
4
A
SER
12
1
Y
1
A
THR
5
A
THR
13
1
Y
1
B
GLY
-7
B
GLY
1
1
Y
1
B
PRO
-6
B
PRO
2
1
Y
1
B
LEU
-5
B
LEU
3
1
Y
1
B
GLY
-4
B
GLY
4
1
Y
1
B
SER
-3
B
SER
5
1
Y
1
B
PRO
-2
B
PRO
6
1
Y
1
B
GLU
-1
B
GLU
7
1
Y
1
B
PHE
0
B
PHE
8
1
Y
1
B
MET
1
B
MET
9
1
Y
1
B
ASN
151
B
ASN
159
1
Y
1
B
ILE
152
B
ILE
160
1
Y
1
B
LYS
92
-132.51
-108.53
79.900
25.0600
9.150
0.1923
0.1590
0.1607
1.3500
24.271
3585
67463
5.3100
99.4400
0.8944
0.1400
1
1.350
MOLECULAR REPLACEMENT
17.3000
0.9000
1.1100
ML
FLAT BULK SOLVENT MODEL
1.3500
24.271
212
2521
14
0
2295
0.013
2475
1.440
3377
0.095
359
0.008
450
13.111
973
0.2864
0.2441
1.3675
144
2320
2464
26
97.0000
0.2645
0.2164
1.3862
134
2441
2575
26
99.0000
0.2514
0.1945
1.4060
135
2402
2537
26
99.0000
0.2116
0.1734
1.4270
128
2406
2534
26
99.0000
0.2297
0.1655
1.4493
149
2418
2567
26
99.0000
0.1945
0.1524
1.4731
120
2445
2565
26
99.0000
0.1943
0.1496
1.4984
151
2398
2549
26
99.0000
0.1843
0.1452
1.5257
114
2436
2550
26
99.0000
0.1788
0.1361
1.5550
144
2413
2557
26
99.0000
0.2060
0.1318
1.5868
126
2445
2571
26
99.0000
0.1749
0.1261
1.6213
139
2425
2564
26
99.0000
0.1718
0.1218
1.6590
143
2441
2584
26
99.0000
0.1758
0.1233
1.7004
151
2442
2593
26
100.0000
0.1485
0.1241
1.7464
150
2412
2562
26
100.0000
0.1973
0.1260
1.7978
133
2463
2596
26
100.0000
0.1881
0.1313
1.8558
151
2472
2623
26
100.0000
0.1765
0.1307
1.9221
124
2451
2575
26
100.0000
0.1900
0.1403
1.9990
137
2463
2600
26
100.0000
0.1687
0.1372
2.0899
133
2475
2608
26
100.0000
0.2004
0.1515
2.2001
125
2491
2616
26
100.0000
0.1828
0.1530
2.3378
158
2475
2633
26
100.0000
0.2093
0.1643
2.5181
142
2478
2620
26
100.0000
0.2174
0.1803
2.7712
154
2500
2654
26
100.0000
0.2225
0.1827
3.1715
137
2525
2662
26
100.0000
0.2119
0.1671
3.9928
130
2560
2690
26
100.0000
0.1513
0.1682
24.271
133
2681
2814
26
100.0000
16.790
1.350
50.000
4ONM
67525
0.039
1.000
1
16.500
4.700
99.500
0.679
1.350
1.370
3291
1.012
1
4.000
98.600
0.595
1.370
1.400
3288
0.938
1
4.000
98.700
0.467
1.400
1.430
3331
0.925
1
4.000
98.800
0.391
1.430
1.450
3299
0.935
1
4.000
99.000
0.311
1.450
1.490
3348
1.000
1
4.000
99.200
0.276
1.490
1.520
3306
0.985
1
4.000
99.000
0.218
1.520
1.560
3348
1.007
1
4.000
99.400
0.175
1.560
1.600
3329
0.972
1
4.100
99.300
0.143
1.600
1.650
3333
1.092
1
4.100
99.600
0.127
1.650
1.700
3378
1.064
1
4.100
99.600
0.108
1.700
1.760
3350
1.034
1
4.100
99.700
0.086
1.760
1.830
3340
1.086
1
4.100
99.800
0.065
1.830
1.920
3392
1.022
1
4.100
99.900
0.056
1.920
2.020
3398
1.034
1
4.100
99.900
0.056
2.020
2.140
3405
1.047
1
4.100
99.900
0.060
2.140
2.310
3396
0.960
1
4.100
99.800
0.048
2.310
2.540
3419
0.983
1
4.700
99.900
0.047
2.540
2.910
3448
1.079
1
8.100
100.000
0.033
2.910
3.660
3482
0.926
1
8.000
100.000
0.024
3.660
50.000
3644
0.946
1
7.000
99.200
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.8.3_1479
data extraction
PDB
deposit@deposit.rcsb.org
Dec. 10, 2013
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.14
Ubiquitin-conjugating enzyme E2 variant 2, Ubiquitin-conjugating enzyme E2 N (E.C.6.3.2.19)
Crystal structure of human Mms2/Ubc13 - NSC697923
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
A
PRO
10
A
PRO
18
HELX_P
A
GLY
25
A
GLY
33
1
1
16
A
ASP
99
A
ASP
107
HELX_P
A
SER
102
A
SER
110
5
2
4
A
ILE
103
A
ILE
111
HELX_P
A
LYS
108
A
LYS
116
1
3
6
A
SER
114
A
SER
122
HELX_P
A
MET
127
A
MET
135
1
4
14
B
PRO
5
B
PRO
13
HELX_P
B
GLU
18
B
GLU
26
1
5
14
B
LEU
88
B
LEU
96
HELX_P
B
LYS
92
B
LYS
100
5
6
5
B
GLN
100
B
GLN
108
HELX_P
B
ALA
114
B
ALA
122
1
7
15
B
VAL
125
B
VAL
133
HELX_P
B
ASN
132
B
ASN
140
1
8
8
B
ASN
132
B
ASN
140
HELX_P
B
ALA
148
B
ALA
156
1
9
17
covale
1.746
B
CYS
87
B
SG
CYS
95
1_555
B
N2F
201
D
C5
N2F
1_555
LIGASE
E2 ubiquitin conjugating enzyme, E1, E3, ubiquitin, covalent adduct, LIGASE
A
TYR
73
A
TYR
81
1
A
PRO
74
A
PRO
82
1.02
B
TYR
62
B
TYR
70
1
B
PRO
63
B
PRO
71
6.67
UB2V2_HUMAN
UNP
1
1
Q15819
MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSV
RFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
UBE2N_HUMAN
UNP
2
1
P61088
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNV
DKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI
1
145
4ONM
1
145
Q15819
A
1
9
153
1
152
4ONM
1
152
P61088
B
2
9
160
1
EXPRESSION TAG
GLY
-7
4ONM
A
Q15819
UNP
1
1
EXPRESSION TAG
PRO
-6
4ONM
A
Q15819
UNP
2
1
EXPRESSION TAG
LEU
-5
4ONM
A
Q15819
UNP
3
1
EXPRESSION TAG
GLY
-4
4ONM
A
Q15819
UNP
4
1
EXPRESSION TAG
SER
-3
4ONM
A
Q15819
UNP
5
1
EXPRESSION TAG
PRO
-2
4ONM
A
Q15819
UNP
6
1
EXPRESSION TAG
GLU
-1
4ONM
A
Q15819
UNP
7
1
EXPRESSION TAG
PHE
0
4ONM
A
Q15819
UNP
8
2
EXPRESSION TAG
GLY
-7
4ONM
B
P61088
UNP
1
2
EXPRESSION TAG
PRO
-6
4ONM
B
P61088
UNP
2
2
EXPRESSION TAG
LEU
-5
4ONM
B
P61088
UNP
3
2
EXPRESSION TAG
GLY
-4
4ONM
B
P61088
UNP
4
2
EXPRESSION TAG
SER
-3
4ONM
B
P61088
UNP
5
2
EXPRESSION TAG
PRO
-2
4ONM
B
P61088
UNP
6
2
EXPRESSION TAG
GLU
-1
4ONM
B
P61088
UNP
7
2
EXPRESSION TAG
PHE
0
4ONM
B
P61088
UNP
8
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
31
A
VAL
39
A
LEU
35
A
LEU
43
A
ARG
45
A
ARG
53
A
ILE
51
A
ILE
59
A
ILE
62
A
ILE
70
A
GLU
68
A
GLU
76
A
SER
79
A
SER
87
A
PHE
82
A
PHE
90
B
ILE
23
B
ILE
31
B
PRO
27
B
PRO
35
B
TYR
34
B
TYR
42
B
ALA
40
B
ALA
48
B
THR
51
B
THR
59
B
PHE
57
B
PHE
65
B
LYS
68
B
LYS
76
B
PHE
71
B
PHE
79
BINDING SITE FOR RESIDUE GOL A 201
Software
8
BINDING SITE FOR RESIDUE N2F B 201
Software
11
A
ASN
60
A
ASN
68
8
4_455
A
ILE
62
A
ILE
70
8
4_455
A
GLY
90
A
GLY
98
8
1_555
A
ILE
91
A
ILE
99
8
1_555
A
ASN
92
A
ASN
100
8
1_555
A
ASN
93
A
ASN
101
8
1_555
A
HOH
379
E
HOH
8
4_455
A
HOH
399
E
HOH
8
1_555
B
PRO
78
B
PRO
86
11
1_555
B
ASN
79
B
ASN
87
11
1_555
B
VAL
80
B
VAL
88
11
1_555
B
ASP
81
B
ASP
89
11
1_555
B
ARG
85
B
ARG
93
11
1_555
B
ILE
86
B
ILE
94
11
1_555
B
CYS
87
B
CYS
95
11
1_555
B
LEU
121
B
LEU
129
11
1_555
B
ALA
122
B
ALA
130
11
1_555
B
ASN
123
B
ASN
131
11
1_555
B
HOH
305
F
HOH
11
1_555
19
P 21 21 21