0.009363
0.000000
0.003092
0.000000
0.011349
0.000000
0.000000
0.000000
0.011672
0.00000
0.00000
0.00000
Hymowitz, S.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
108.28
90.00
106.806
88.117
90.226
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
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
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
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
134
668
678
10.1016/j.cell.2008.07.039
18724939
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
2008
10.2210/pdb3dvg/pdb
pdb_00003dvg
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
180
1
CCD
2008-01-16
ADSC QUANTUM 315
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.97607
1.0
BL7-1
SSRL
0.97607
SYNCHROTRON
SSRL BEAMLINE BL7-1
23731.301
Human IgG1 fab fragment light chain
1
man
polymer
24590.514
Human IgG1 fab fragment heavy chain
1
man
polymer
8974.193
Ubiquitin D77
D77
1
man
polymer
8887.120
Ubiquitin
K63R
1
man
polymer
18.015
water
25
nat
water
no
no
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSARSLYSGVPSRFSGSRSGTDFTLTISSLQ
PEDFATYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSARSLYSGVPSRFSGSRSGTDFTLTISSLQ
PEDFATYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
A
polypeptide(L)
no
no
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQAPGKGLEWVAYITPYYGSTSYADSVKGRFTISADTSKN
TAYLQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQAPGKGLEWVAYITPYYGSTSYADSVKGRFTISADTSKN
TAYLQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
B
polypeptide(L)
no
no
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD
X
polypeptide(L)
no
no
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
Y
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
Protein selected by phage display
fab fragment light chain
9606
Homo sapiens
562
Escherichia coli
plasmid
pET15b
Human
sample
Protein selected by phage display
fab fragment light chain
9606
Homo sapiens
562
Escherichia coli
plasmid
pET15b
Human
sample
RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
9606
Homo sapiens
562
Escherichia coli
plasmid
pET15b
Human
sample
RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
9606
Homo sapiens
562
Escherichia coli
plasmid
pET15b
1
3.03
59.46
VAPOR DIFFUSION, SITTING DROP
7.3
protein: 17.0 mg/mL in 20 mM Tris-HCl pH 7.3, 150 mM NaCl
well solution: 0.1M Tris-HCl pH 8.0, 1.6M LiS04 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
291
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Advisory
Refinement description
Version format compliance
Database references
Derived calculations
1
0
2008-09-30
1
1
2011-07-13
1
2
2021-10-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2008-07-18
REL
REL
HOH
water
HOH
1
5
HOH
HOH
217
A
HOH
2
5
HOH
HOH
218
A
HOH
3
5
HOH
HOH
219
A
HOH
4
5
HOH
HOH
220
A
HOH
5
5
HOH
HOH
221
A
HOH
6
5
HOH
HOH
222
A
HOH
7
5
HOH
HOH
223
A
HOH
8
5
HOH
HOH
224
A
HOH
9
5
HOH
HOH
225
A
HOH
10
5
HOH
HOH
226
A
HOH
11
5
HOH
HOH
227
A
HOH
12
5
HOH
HOH
228
A
HOH
13
5
HOH
HOH
229
A
HOH
14
5
HOH
HOH
230
A
HOH
17
5
HOH
HOH
231
A
HOH
18
5
HOH
HOH
232
A
HOH
19
5
HOH
HOH
233
A
HOH
26
5
HOH
HOH
234
A
HOH
20
5
HOH
HOH
228
B
HOH
21
5
HOH
HOH
229
B
HOH
22
5
HOH
HOH
230
B
HOH
23
5
HOH
HOH
231
B
HOH
24
5
HOH
HOH
232
B
HOH
25
5
HOH
HOH
233
B
HOH
28
5
HOH
HOH
234
B
n
1
0
A
n
2
1
A
n
3
2
A
n
4
3
A
n
5
4
A
THR
5
n
6
THR
5
A
GLN
6
n
7
GLN
6
A
SER
7
n
8
SER
7
A
PRO
8
n
9
PRO
8
A
SER
9
n
10
SER
9
A
SER
10
n
11
SER
10
A
LEU
11
n
12
LEU
11
A
SER
12
n
13
SER
12
A
ALA
13
n
14
ALA
13
A
SER
14
n
15
SER
14
A
VAL
15
n
16
VAL
15
A
GLY
16
n
17
GLY
16
A
ASP
17
n
18
ASP
17
A
ARG
18
n
19
ARG
18
A
VAL
19
n
20
VAL
19
A
THR
20
n
21
THR
20
A
ILE
21
n
22
ILE
21
A
THR
22
n
23
THR
22
A
CYS
23
n
24
CYS
23
A
ARG
24
n
25
ARG
24
A
ALA
25
n
26
ALA
25
A
SER
26
n
27
SER
26
A
GLN
27
n
28
GLN
27
A
SER
28
n
29
SER
28
A
VAL
29
n
30
VAL
29
A
SER
30
n
31
SER
30
A
SER
31
n
32
SER
31
A
ALA
32
n
33
ALA
32
A
VAL
33
n
34
VAL
33
A
ALA
34
n
35
ALA
34
A
TRP
35
n
36
TRP
35
A
TYR
36
n
37
TYR
36
A
GLN
37
n
38
GLN
37
A
GLN
38
n
39
GLN
38
A
LYS
39
n
40
LYS
39
A
PRO
40
n
41
PRO
40
A
GLY
41
n
42
GLY
41
A
LYS
42
n
43
LYS
42
A
ALA
43
n
44
ALA
43
A
PRO
44
n
45
PRO
44
A
LYS
45
n
46
LYS
45
A
LEU
46
n
47
LEU
46
A
LEU
47
n
48
LEU
47
A
ILE
48
n
49
ILE
48
A
TYR
49
n
50
TYR
49
A
SER
50
n
51
SER
50
A
ALA
51
n
52
ALA
51
A
ARG
52
n
53
ARG
52
A
SER
53
n
54
SER
53
A
LEU
54
n
55
LEU
54
A
TYR
55
n
56
TYR
55
A
SER
56
n
57
SER
56
A
GLY
57
n
58
GLY
57
A
VAL
58
n
59
VAL
58
A
PRO
59
n
60
PRO
59
A
SER
60
n
61
SER
60
A
ARG
61
n
62
ARG
61
A
PHE
62
n
63
PHE
62
A
SER
63
n
64
SER
63
A
GLY
64
n
65
GLY
64
A
SER
65
n
66
SER
65
A
ARG
66
n
67
ARG
66
A
SER
67
n
68
SER
67
A
GLY
68
n
69
GLY
68
A
THR
69
n
70
THR
69
A
ASP
70
n
71
ASP
70
A
PHE
71
n
72
PHE
71
A
THR
72
n
73
THR
72
A
LEU
73
n
74
LEU
73
A
THR
74
n
75
THR
74
A
ILE
75
n
76
ILE
75
A
SER
76
n
77
SER
76
A
SER
77
n
78
SER
77
A
LEU
78
n
79
LEU
78
A
GLN
79
n
80
GLN
79
A
PRO
80
n
81
PRO
80
A
GLU
81
n
82
GLU
81
A
ASP
82
n
83
ASP
82
A
PHE
83
n
84
PHE
83
A
ALA
84
n
85
ALA
84
A
THR
85
n
86
THR
85
A
TYR
86
n
87
TYR
86
A
TYR
87
n
88
TYR
87
A
CYS
88
n
89
CYS
88
A
GLN
89
n
90
GLN
89
A
GLN
90
n
91
GLN
90
A
TYR
91
n
92
TYR
91
A
SER
92
n
93
SER
92
A
SER
93
n
94
SER
93
A
TYR
94
n
95
TYR
94
A
SER
95
n
96
SER
95
A
SER
96
n
97
SER
96
A
LEU
97
n
98
LEU
97
A
PHE
98
n
99
PHE
98
A
THR
99
n
100
THR
99
A
PHE
100
n
101
PHE
100
A
GLY
101
n
102
GLY
101
A
GLN
102
n
103
GLN
102
A
GLY
103
n
104
GLY
103
A
THR
104
n
105
THR
104
A
LYS
105
n
106
LYS
105
A
VAL
106
n
107
VAL
106
A
GLU
107
n
108
GLU
107
A
ILE
108
n
109
ILE
108
A
LYS
109
n
110
LYS
109
A
ARG
110
n
111
ARG
110
A
THR
111
n
112
THR
111
A
VAL
112
n
113
VAL
112
A
ALA
113
n
114
ALA
113
A
ALA
114
n
115
ALA
114
A
PRO
115
n
116
PRO
115
A
SER
116
n
117
SER
116
A
VAL
117
n
118
VAL
117
A
PHE
118
n
119
PHE
118
A
ILE
119
n
120
ILE
119
A
PHE
120
n
121
PHE
120
A
PRO
121
n
122
PRO
121
A
PRO
122
n
123
PRO
122
A
SER
123
n
124
SER
123
A
ASP
124
n
125
ASP
124
A
GLU
125
n
126
GLU
125
A
GLN
126
n
127
GLN
126
A
LEU
127
n
128
LEU
127
A
LYS
128
n
129
LYS
128
A
SER
129
n
130
SER
129
A
GLY
130
n
131
GLY
130
A
THR
131
n
132
THR
131
A
ALA
132
n
133
ALA
132
A
SER
133
n
134
SER
133
A
VAL
134
n
135
VAL
134
A
VAL
135
n
136
VAL
135
A
CYS
136
n
137
CYS
136
A
LEU
137
n
138
LEU
137
A
LEU
138
n
139
LEU
138
A
ASN
139
n
140
ASN
139
A
ASN
140
n
141
ASN
140
A
PHE
141
n
142
PHE
141
A
TYR
142
n
143
TYR
142
A
PRO
143
n
144
PRO
143
A
ARG
144
n
145
ARG
144
A
GLU
145
n
146
GLU
145
A
ALA
146
n
147
ALA
146
A
LYS
147
n
148
LYS
147
A
VAL
148
n
149
VAL
148
A
GLN
149
n
150
GLN
149
A
TRP
150
n
151
TRP
150
A
LYS
151
n
152
LYS
151
A
VAL
152
n
153
VAL
152
A
ASP
153
n
154
ASP
153
A
ASN
154
n
155
ASN
154
A
ALA
155
n
156
ALA
155
A
LEU
156
n
157
LEU
156
A
GLN
157
n
158
GLN
157
A
SER
158
n
159
SER
158
A
GLY
159
n
160
GLY
159
A
ASN
160
n
161
ASN
160
A
SER
161
n
162
SER
161
A
GLN
162
n
163
GLN
162
A
GLU
163
n
164
GLU
163
A
SER
164
n
165
SER
164
A
VAL
165
n
166
VAL
165
A
THR
166
n
167
THR
166
A
GLU
167
n
168
GLU
167
A
GLN
168
n
169
GLN
168
A
ASP
169
n
170
ASP
169
A
SER
170
n
171
SER
170
A
LYS
171
n
172
LYS
171
A
ASP
172
n
173
ASP
172
A
SER
173
n
174
SER
173
A
THR
174
n
175
THR
174
A
TYR
175
n
176
TYR
175
A
SER
176
n
177
SER
176
A
LEU
177
n
178
LEU
177
A
SER
178
n
179
SER
178
A
SER
179
n
180
SER
179
A
THR
180
n
181
THR
180
A
LEU
181
n
182
LEU
181
A
THR
182
n
183
THR
182
A
LEU
183
n
184
LEU
183
A
SER
184
n
185
SER
184
A
LYS
185
n
186
LYS
185
A
ALA
186
n
187
ALA
186
A
ASP
187
n
188
ASP
187
A
TYR
188
n
189
TYR
188
A
GLU
189
n
190
GLU
189
A
LYS
190
n
191
LYS
190
A
HIS
191
n
192
HIS
191
A
LYS
192
n
193
LYS
192
A
VAL
193
n
194
VAL
193
A
TYR
194
n
195
TYR
194
A
ALA
195
n
196
ALA
195
A
CYS
196
n
197
CYS
196
A
GLU
197
n
198
GLU
197
A
VAL
198
n
199
VAL
198
A
THR
199
n
200
THR
199
A
HIS
200
n
201
HIS
200
A
GLN
201
n
202
GLN
201
A
GLY
202
n
203
GLY
202
A
LEU
203
n
204
LEU
203
A
SER
204
n
205
SER
204
A
SER
205
n
206
SER
205
A
PRO
206
n
207
PRO
206
A
VAL
207
n
208
VAL
207
A
THR
208
n
209
THR
208
A
LYS
209
n
210
LYS
209
A
SER
210
n
211
SER
210
A
PHE
211
n
212
PHE
211
A
ASN
212
n
213
ASN
212
A
ARG
213
n
214
ARG
213
A
GLY
214
n
215
GLY
214
A
n
216
215
A
n
217
216
A
n
1
-2
B
n
2
-1
B
n
3
0
B
GLU
1
n
4
GLU
1
B
VAL
2
n
5
VAL
2
B
GLN
3
n
6
GLN
3
B
LEU
4
n
7
LEU
4
B
VAL
5
n
8
VAL
5
B
GLU
6
n
9
GLU
6
B
SER
7
n
10
SER
7
B
GLY
8
n
11
GLY
8
B
GLY
9
n
12
GLY
9
B
GLY
10
n
13
GLY
10
B
LEU
11
n
14
LEU
11
B
VAL
12
n
15
VAL
12
B
GLN
13
n
16
GLN
13
B
PRO
14
n
17
PRO
14
B
GLY
15
n
18
GLY
15
B
GLY
16
n
19
GLY
16
B
SER
17
n
20
SER
17
B
LEU
18
n
21
LEU
18
B
ARG
19
n
22
ARG
19
B
LEU
20
n
23
LEU
20
B
SER
21
n
24
SER
21
B
CYS
22
n
25
CYS
22
B
ALA
23
n
26
ALA
23
B
ALA
24
n
27
ALA
24
B
SER
25
n
28
SER
25
B
GLY
26
n
29
GLY
26
B
PHE
27
n
30
PHE
27
B
ASN
28
n
31
ASN
28
B
VAL
29
n
32
VAL
29
B
LYS
30
n
33
LYS
30
B
THR
31
n
34
THR
31
B
GLY
32
n
35
GLY
32
B
LEU
33
n
36
LEU
33
B
ILE
34
n
37
ILE
34
B
HIS
35
n
38
HIS
35
B
TRP
36
n
39
TRP
36
B
VAL
37
n
40
VAL
37
B
ARG
38
n
41
ARG
38
B
GLN
39
n
42
GLN
39
B
ALA
40
n
43
ALA
40
B
PRO
41
n
44
PRO
41
B
GLY
42
n
45
GLY
42
B
LYS
43
n
46
LYS
43
B
GLY
44
n
47
GLY
44
B
LEU
45
n
48
LEU
45
B
GLU
46
n
49
GLU
46
B
TRP
47
n
50
TRP
47
B
VAL
48
n
51
VAL
48
B
ALA
49
n
52
ALA
49
B
TYR
50
n
53
TYR
50
B
ILE
51
n
54
ILE
51
B
THR
52
n
55
THR
52
B
PRO
53
n
56
PRO
53
B
TYR
54
n
57
TYR
54
B
TYR
55
n
58
TYR
55
B
GLY
56
n
59
GLY
56
B
SER
57
n
60
SER
57
B
THR
58
n
61
THR
58
B
SER
59
n
62
SER
59
B
TYR
60
n
63
TYR
60
B
ALA
61
n
64
ALA
61
B
ASP
62
n
65
ASP
62
B
SER
63
n
66
SER
63
B
VAL
64
n
67
VAL
64
B
LYS
65
n
68
LYS
65
B
GLY
66
n
69
GLY
66
B
ARG
67
n
70
ARG
67
B
PHE
68
n
71
PHE
68
B
THR
69
n
72
THR
69
B
ILE
70
n
73
ILE
70
B
SER
71
n
74
SER
71
B
ALA
72
n
75
ALA
72
B
ASP
73
n
76
ASP
73
B
THR
74
n
77
THR
74
B
SER
75
n
78
SER
75
B
LYS
76
n
79
LYS
76
B
ASN
77
n
80
ASN
77
B
THR
78
n
81
THR
78
B
ALA
79
n
82
ALA
79
B
TYR
80
n
83
TYR
80
B
LEU
81
n
84
LEU
81
B
GLN
82
n
85
GLN
82
B
MET
83
n
86
MET
83
B
ASN
84
n
87
ASN
84
B
SER
85
n
88
SER
85
B
LEU
86
n
89
LEU
86
B
ARG
87
n
90
ARG
87
B
ALA
88
n
91
ALA
88
B
GLU
89
n
92
GLU
89
B
ASP
90
n
93
ASP
90
B
THR
91
n
94
THR
91
B
ALA
92
n
95
ALA
92
B
VAL
93
n
96
VAL
93
B
TYR
94
n
97
TYR
94
B
TYR
95
n
98
TYR
95
B
CYS
96
n
99
CYS
96
B
ALA
97
n
100
ALA
97
B
ARG
98
n
101
ARG
98
B
GLU
99
n
102
GLU
99
B
TYR
100
n
103
TYR
100
B
TYR
101
n
104
TYR
101
B
ARG
102
n
105
ARG
102
B
TRP
103
n
106
TRP
103
B
TYR
104
n
107
TYR
104
B
THR
105
n
108
THR
105
B
ALA
106
n
109
ALA
106
B
ILE
107
n
110
ILE
107
B
ASP
108
n
111
ASP
108
B
TYR
109
n
112
TYR
109
B
TRP
110
n
113
TRP
110
B
GLY
111
n
114
GLY
111
B
GLN
112
n
115
GLN
112
B
GLY
113
n
116
GLY
113
B
THR
114
n
117
THR
114
B
LEU
115
n
118
LEU
115
B
VAL
116
n
119
VAL
116
B
THR
117
n
120
THR
117
B
VAL
118
n
121
VAL
118
B
SER
119
n
122
SER
119
B
SER
120
n
123
SER
120
B
ALA
121
n
124
ALA
121
B
SER
122
n
125
SER
122
B
THR
123
n
126
THR
123
B
LYS
124
n
127
LYS
124
B
GLY
125
n
128
GLY
125
B
PRO
126
n
129
PRO
126
B
SER
127
n
130
SER
127
B
VAL
128
n
131
VAL
128
B
PHE
129
n
132
PHE
129
B
PRO
130
n
133
PRO
130
B
LEU
131
n
134
LEU
131
B
ALA
132
n
135
ALA
132
B
PRO
133
n
136
PRO
133
B
SER
134
n
137
SER
134
B
SER
135
n
138
SER
135
B
LYS
136
n
139
LYS
136
B
SER
137
n
140
SER
137
B
THR
138
n
141
THR
138
B
SER
139
n
142
SER
139
B
GLY
140
n
143
GLY
140
B
GLY
141
n
144
GLY
141
B
THR
142
n
145
THR
142
B
ALA
143
n
146
ALA
143
B
ALA
144
n
147
ALA
144
B
LEU
145
n
148
LEU
145
B
GLY
146
n
149
GLY
146
B
CYS
147
n
150
CYS
147
B
LEU
148
n
151
LEU
148
B
VAL
149
n
152
VAL
149
B
LYS
150
n
153
LYS
150
B
ASP
151
n
154
ASP
151
B
TYR
152
n
155
TYR
152
B
PHE
153
n
156
PHE
153
B
PRO
154
n
157
PRO
154
B
GLU
155
n
158
GLU
155
B
PRO
156
n
159
PRO
156
B
VAL
157
n
160
VAL
157
B
THR
158
n
161
THR
158
B
VAL
159
n
162
VAL
159
B
SER
160
n
163
SER
160
B
TRP
161
n
164
TRP
161
B
ASN
162
n
165
ASN
162
B
SER
163
n
166
SER
163
B
GLY
164
n
167
GLY
164
B
ALA
165
n
168
ALA
165
B
LEU
166
n
169
LEU
166
B
THR
167
n
170
THR
167
B
SER
168
n
171
SER
168
B
GLY
169
n
172
GLY
169
B
VAL
170
n
173
VAL
170
B
HIS
171
n
174
HIS
171
B
THR
172
n
175
THR
172
B
PHE
173
n
176
PHE
173
B
PRO
174
n
177
PRO
174
B
ALA
175
n
178
ALA
175
B
VAL
176
n
179
VAL
176
B
LEU
177
n
180
LEU
177
B
GLN
178
n
181
GLN
178
B
SER
179
n
182
SER
179
B
SER
180
n
183
SER
180
B
GLY
181
n
184
GLY
181
B
LEU
182
n
185
LEU
182
B
TYR
183
n
186
TYR
183
B
SER
184
n
187
SER
184
B
LEU
185
n
188
LEU
185
B
SER
186
n
189
SER
186
B
SER
187
n
190
SER
187
B
VAL
188
n
191
VAL
188
B
VAL
189
n
192
VAL
189
B
THR
190
n
193
THR
190
B
VAL
191
n
194
VAL
191
B
PRO
192
n
195
PRO
192
B
SER
193
n
196
SER
193
B
SER
194
n
197
SER
194
B
SER
195
n
198
SER
195
B
LEU
196
n
199
LEU
196
B
GLY
197
n
200
GLY
197
B
THR
198
n
201
THR
198
B
GLN
199
n
202
GLN
199
B
THR
200
n
203
THR
200
B
TYR
201
n
204
TYR
201
B
ILE
202
n
205
ILE
202
B
CYS
203
n
206
CYS
203
B
ASN
204
n
207
ASN
204
B
VAL
205
n
208
VAL
205
B
ASN
206
n
209
ASN
206
B
HIS
207
n
210
HIS
207
B
LYS
208
n
211
LYS
208
B
PRO
209
n
212
PRO
209
B
SER
210
n
213
SER
210
B
ASN
211
n
214
ASN
211
B
THR
212
n
215
THR
212
B
LYS
213
n
216
LYS
213
B
VAL
214
n
217
VAL
214
B
ASP
215
n
218
ASP
215
B
LYS
216
n
219
LYS
216
B
LYS
217
n
220
LYS
217
B
VAL
218
n
221
VAL
218
B
GLU
219
n
222
GLU
219
B
PRO
220
n
223
PRO
220
B
ALA
221
n
224
LYS
221
B
n
225
222
B
n
226
223
B
n
227
224
B
n
228
225
B
n
229
226
B
n
230
227
B
n
1
-2
X
ALA
-1
n
2
SER
-1
X
MET
0
n
3
HIS
0
X
MET
1
n
4
MET
1
X
GLN
2
n
5
GLN
2
X
ILE
3
n
6
ILE
3
X
PHE
4
n
7
PHE
4
X
VAL
5
n
8
VAL
5
X
LYS
6
n
9
LYS
6
X
THR
7
n
10
THR
7
X
LEU
8
n
11
LEU
8
X
THR
9
n
12
THR
9
X
GLY
10
n
13
GLY
10
X
LYS
11
n
14
LYS
11
X
THR
12
n
15
THR
12
X
ILE
13
n
16
ILE
13
X
THR
14
n
17
THR
14
X
LEU
15
n
18
LEU
15
X
GLU
16
n
19
GLU
16
X
VAL
17
n
20
VAL
17
X
GLU
18
n
21
GLU
18
X
PRO
19
n
22
PRO
19
X
SER
20
n
23
SER
20
X
ASP
21
n
24
ASP
21
X
THR
22
n
25
THR
22
X
ILE
23
n
26
ILE
23
X
GLU
24
n
27
GLU
24
X
ASN
25
n
28
ASN
25
X
VAL
26
n
29
VAL
26
X
LYS
27
n
30
LYS
27
X
ALA
28
n
31
ALA
28
X
LYS
29
n
32
LYS
29
X
ILE
30
n
33
ILE
30
X
GLN
31
n
34
GLN
31
X
ASP
32
n
35
ASP
32
X
LYS
33
n
36
LYS
33
X
GLU
34
n
37
GLU
34
X
GLY
35
n
38
GLY
35
X
ILE
36
n
39
ILE
36
X
PRO
37
n
40
PRO
37
X
PRO
38
n
41
PRO
38
X
ASP
39
n
42
ASP
39
X
GLN
40
n
43
GLN
40
X
GLN
41
n
44
GLN
41
X
ARG
42
n
45
ARG
42
X
LEU
43
n
46
LEU
43
X
ILE
44
n
47
ILE
44
X
PHE
45
n
48
PHE
45
X
ALA
46
n
49
ALA
46
X
GLY
47
n
50
GLY
47
X
LYS
48
n
51
LYS
48
X
GLN
49
n
52
GLN
49
X
LEU
50
n
53
LEU
50
X
GLU
51
n
54
GLU
51
X
ASP
52
n
55
ASP
52
X
GLY
53
n
56
GLY
53
X
ARG
54
n
57
ARG
54
X
THR
55
n
58
THR
55
X
LEU
56
n
59
LEU
56
X
SER
57
n
60
SER
57
X
ASP
58
n
61
ASP
58
X
TYR
59
n
62
TYR
59
X
ASN
60
n
63
ASN
60
X
ILE
61
n
64
ILE
61
X
GLN
62
n
65
GLN
62
X
LYS
63
n
66
LYS
63
X
GLU
64
n
67
GLU
64
X
SER
65
n
68
SER
65
X
THR
66
n
69
THR
66
X
LEU
67
n
70
LEU
67
X
HIS
68
n
71
HIS
68
X
LEU
69
n
72
LEU
69
X
VAL
70
n
73
VAL
70
X
LEU
71
n
74
LEU
71
X
ARG
72
n
75
ARG
72
X
LEU
73
n
76
LEU
73
X
n
77
74
X
n
78
75
X
n
79
76
X
n
80
77
X
n
1
-2
Y
n
2
-1
Y
n
3
0
Y
MET
1
n
4
MET
1
Y
GLN
2
n
5
GLN
2
Y
ILE
3
n
6
ILE
3
Y
PHE
4
n
7
PHE
4
Y
VAL
5
n
8
VAL
5
Y
LYS
6
n
9
LYS
6
Y
THR
7
n
10
THR
7
Y
LEU
8
n
11
LEU
8
Y
THR
9
n
12
THR
9
Y
GLY
10
n
13
GLY
10
Y
LYS
11
n
14
LYS
11
Y
THR
12
n
15
THR
12
Y
ILE
13
n
16
ILE
13
Y
THR
14
n
17
THR
14
Y
LEU
15
n
18
LEU
15
Y
GLU
16
n
19
GLU
16
Y
VAL
17
n
20
VAL
17
Y
GLU
18
n
21
GLU
18
Y
PRO
19
n
22
PRO
19
Y
SER
20
n
23
SER
20
Y
ASP
21
n
24
ASP
21
Y
THR
22
n
25
THR
22
Y
ILE
23
n
26
ILE
23
Y
GLU
24
n
27
GLU
24
Y
ASN
25
n
28
ASN
25
Y
VAL
26
n
29
VAL
26
Y
LYS
27
n
30
LYS
27
Y
ALA
28
n
31
ALA
28
Y
LYS
29
n
32
LYS
29
Y
ILE
30
n
33
ILE
30
Y
GLN
31
n
34
GLN
31
Y
ASP
32
n
35
ASP
32
Y
LYS
33
n
36
LYS
33
Y
GLU
34
n
37
GLU
34
Y
GLY
35
n
38
GLY
35
Y
ILE
36
n
39
ILE
36
Y
PRO
37
n
40
PRO
37
Y
PRO
38
n
41
PRO
38
Y
ASP
39
n
42
ASP
39
Y
GLN
40
n
43
GLN
40
Y
GLN
41
n
44
GLN
41
Y
ARG
42
n
45
ARG
42
Y
LEU
43
n
46
LEU
43
Y
ILE
44
n
47
ILE
44
Y
PHE
45
n
48
PHE
45
Y
ALA
46
n
49
ALA
46
Y
GLY
47
n
50
GLY
47
Y
LYS
48
n
51
LYS
48
Y
GLN
49
n
52
GLN
49
Y
LEU
50
n
53
LEU
50
Y
GLU
51
n
54
GLU
51
Y
ASP
52
n
55
ASP
52
Y
GLY
53
n
56
GLY
53
Y
ARG
54
n
57
ARG
54
Y
THR
55
n
58
THR
55
Y
LEU
56
n
59
LEU
56
Y
SER
57
n
60
SER
57
Y
ASP
58
n
61
ASP
58
Y
TYR
59
n
62
TYR
59
Y
ASN
60
n
63
ASN
60
Y
ILE
61
n
64
ILE
61
Y
GLN
62
n
65
GLN
62
Y
ARG
63
n
66
ARG
63
Y
GLU
64
n
67
GLU
64
Y
SER
65
n
68
SER
65
Y
THR
66
n
69
THR
66
Y
LEU
67
n
70
LEU
67
Y
HIS
68
n
71
HIS
68
Y
LEU
69
n
72
LEU
69
Y
VAL
70
n
73
VAL
70
Y
LEU
71
n
74
LEU
71
Y
ARG
72
n
75
ARG
72
Y
LEU
73
n
76
LEU
73
Y
ARG
74
n
77
ARG
74
Y
GLY
75
n
78
GLY
75
Y
GLY
76
n
79
GLY
76
Y
2.7630
-0.0205
0.7631
5.0940
-0.1715
1.4026
0.0515
-0.1077
0.1945
0.0562
0.0475
0.3214
-0.0832
0.1254
-0.0990
-0.4661
-0.1367
-0.1498
0.0236
0.0439
-0.2159
refined
7.1176
40.5591
19.1880
X-RAY DIFFRACTION
2.8373
1.2816
-0.1652
3.4934
-0.1708
2.4087
0.1232
0.0070
0.0329
0.1583
-0.3056
0.2486
0.1058
-0.2329
0.1823
-0.5061
-0.1088
-0.1956
-0.0205
-0.0137
-0.0942
refined
-19.5631
21.8648
7.4817
X-RAY DIFFRACTION
5.7950
-1.3352
-1.0324
7.9342
1.8272
5.4564
0.1045
-0.8064
0.5003
0.8926
0.3367
-0.7035
-0.6018
0.5376
-0.4412
-0.1063
-0.2677
-0.3387
0.4029
-0.0667
-0.1200
refined
29.6096
51.1761
35.3372
X-RAY DIFFRACTION
A
5
A
109
X-RAY DIFFRACTION
1
B
1
B
112
X-RAY DIFFRACTION
1
A
110
A
214
X-RAY DIFFRACTION
2
B
113
B
221
X-RAY DIFFRACTION
2
X
1
X
73
X-RAY DIFFRACTION
3
Y
1
Y
76
X-RAY DIFFRACTION
3
author_defined_assembly
4
tetrameric
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
LEU
11
A
N
LEU
12
A
O
LYS
105
A
O
LYS
106
A
O
THR
104
A
O
THR
105
A
N
TYR
86
A
N
TYR
87
A
O
THR
85
A
O
THR
86
A
N
GLN
38
A
N
GLN
39
A
N
TRP
35
A
N
TRP
36
A
O
LEU
47
A
O
LEU
48
A
N
TYR
49
A
N
TYR
50
A
O
SER
53
A
O
SER
54
A
N
LEU
11
A
N
LEU
12
A
O
LYS
105
A
O
LYS
106
A
O
THR
104
A
O
THR
105
A
N
TYR
86
A
N
TYR
87
A
N
GLN
90
A
N
GLN
91
A
O
THR
99
A
O
THR
100
A
N
CYS
23
A
N
CYS
24
A
O
PHE
71
A
O
PHE
72
A
O
THR
72
A
O
THR
73
A
N
SER
65
A
N
SER
66
A
N
PHE
118
A
N
PHE
119
A
O
LEU
137
A
O
LEU
138
A
N
LEU
138
A
N
LEU
139
A
O
LEU
177
A
O
LEU
178
A
O
THR
180
A
O
THR
181
A
N
GLN
162
A
N
GLN
163
A
O
ALA
155
A
O
ALA
156
A
N
VAL
152
A
N
VAL
153
A
N
GLN
149
A
N
GLN
150
A
O
GLU
197
A
O
GLU
198
A
N
CYS
196
A
N
CYS
197
A
O
LYS
209
A
O
LYS
210
B
N
SER
7
B
N
SER
10
B
O
SER
21
B
O
SER
24
B
N
LEU
18
B
N
LEU
21
B
O
MET
83
B
O
MET
86
B
O
TYR
80
B
O
TYR
83
B
N
SER
71
B
N
SER
74
B
N
GLY
10
B
N
GLY
13
B
O
THR
117
B
O
THR
120
B
O
VAL
116
B
O
VAL
119
B
N
ALA
92
B
N
ALA
95
B
O
TYR
95
B
O
TYR
98
B
N
VAL
37
B
N
VAL
40
B
N
ARG
38
B
N
ARG
41
B
O
GLU
46
B
O
GLU
49
B
N
TYR
50
B
N
TYR
53
B
O
SER
59
B
O
SER
62
B
N
GLY
10
B
N
GLY
13
B
O
THR
117
B
O
THR
120
B
O
VAL
116
B
O
VAL
119
B
N
ALA
92
B
N
ALA
95
B
N
ARG
98
B
N
ARG
101
B
O
ASP
108
B
O
ASP
111
B
N
PHE
129
B
N
PHE
132
B
O
LEU
148
B
O
LEU
151
B
N
ALA
143
B
N
ALA
146
B
O
VAL
191
B
O
VAL
194
B
O
VAL
188
B
O
VAL
191
B
N
HIS
171
B
N
HIS
174
B
N
SER
139
B
N
SER
142
B
O
THR
142
B
O
THR
145
B
N
ALA
143
B
N
ALA
146
B
O
VAL
191
B
O
VAL
194
B
O
SER
184
B
O
SER
187
B
N
VAL
176
B
N
VAL
179
B
N
SER
160
B
N
SER
163
B
O
ASN
204
B
O
ASN
207
B
N
VAL
205
B
N
VAL
208
B
O
VAL
214
B
O
VAL
217
X
O
VAL
17
C
O
VAL
20
X
N
MET
1
C
N
MET
4
X
N
LYS
6
C
N
LYS
9
X
O
LEU
67
C
O
LEU
70
X
O
HIS
68
C
O
HIS
71
X
N
ILE
44
C
N
ILE
47
X
N
PHE
45
C
N
PHE
48
X
O
LYS
48
C
O
LYS
51
Y
O
ILE
13
D
O
ILE
16
Y
N
VAL
5
D
N
VAL
8
Y
N
LYS
6
D
N
LYS
9
Y
O
LEU
67
D
O
LEU
70
Y
O
VAL
70
D
O
VAL
73
Y
N
ARG
42
D
N
ARG
45
Y
N
PHE
45
D
N
PHE
48
Y
O
LYS
48
D
O
LYS
51
1
B
CG
LYS
221
B
CG
LYS
224
1
Y
1
B
CD
LYS
221
B
CD
LYS
224
1
Y
1
B
CE
LYS
221
B
CE
LYS
224
1
Y
1
B
NZ
LYS
221
B
NZ
LYS
224
1
Y
1
X
OG
SER
-1
C
OG
SER
2
1
Y
1
X
CG
HIS
0
C
CG
HIS
3
1
Y
1
X
ND1
HIS
0
C
ND1
HIS
3
1
Y
1
X
CD2
HIS
0
C
CD2
HIS
3
1
Y
1
X
CE1
HIS
0
C
CE1
HIS
3
1
Y
1
X
NE2
HIS
0
C
NE2
HIS
3
1
Y
1
A
SER
0
A
SER
1
1
Y
1
A
ASP
1
A
ASP
2
1
Y
1
A
ILE
2
A
ILE
3
1
Y
1
A
GLN
3
A
GLN
4
1
Y
1
A
MET
4
A
MET
5
1
Y
1
A
GLU
215
A
GLU
216
1
Y
1
A
CYS
216
A
CYS
217
1
Y
1
B
GLU
-2
B
GLU
1
1
Y
1
B
ILE
-1
B
ILE
2
1
Y
1
B
SER
0
B
SER
3
1
Y
1
B
SER
222
B
SER
225
1
Y
1
B
CYS
223
B
CYS
226
1
Y
1
B
ASP
224
B
ASP
227
1
Y
1
B
LYS
225
B
LYS
228
1
Y
1
B
THR
226
B
THR
229
1
Y
1
B
HIS
227
B
HIS
230
1
Y
1
X
GLY
-2
C
GLY
1
1
Y
1
X
ARG
74
C
ARG
77
1
Y
1
X
GLY
75
C
GLY
78
1
Y
1
X
GLY
76
C
GLY
79
1
Y
1
X
ASP
77
C
ASP
80
1
Y
1
Y
GLY
-2
D
GLY
1
1
Y
1
Y
SER
-1
D
SER
2
1
Y
1
Y
HIS
0
D
HIS
3
1
Y
1
X
X
C
O
GLY
GLY
10
10
0.173
0.016
1.232
1.405
N
1
X
X
C
N
GLY
LYS
10
11
0.157
0.023
1.336
1.493
Y
1
X
X
C
O
LEU
LEU
73
73
0.125
0.019
1.229
1.354
N
1
A
ALA
51
70.14
-45.08
1
A
ARG
52
-141.64
21.61
1
A
ALA
84
-165.51
-162.26
1
A
ARG
213
-32.99
111.75
1
B
SER
63
-67.04
2.26
1
B
VAL
64
-141.04
-22.56
1
B
THR
105
100.14
-22.72
1
B
SER
134
-171.80
-179.74
1
B
LYS
136
-62.68
6.31
1
B
SER
137
-145.34
20.30
1
B
ASP
151
63.44
61.43
1
B
SER
163
56.26
17.51
1
B
THR
198
-134.43
-46.09
1
Y
THR
7
-91.18
-138.87
1
Y
ALA
46
60.41
-2.28
1
Y
ASP
52
-73.95
34.17
1
Y
ASN
60
49.15
73.41
64.091
0.939
0.913
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.26079
0.21917
0.22355
2.60
48.00
2441
21569
21569
10.2
97.91
29.626
0.287
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0
-3
MOLECULAR REPLACEMENT
0.666
0.323
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.60
48.00
25
4491
0
0
4466
0.009
0.022
4564
1.131
1.963
6196
5.592
5.000
578
35.827
24.309
181
18.512
15.000
772
17.486
15.000
22
0.078
0.200
711
0.003
0.020
3388
0.193
0.200
1693
0.302
0.200
3017
0.120
0.200
152
0.173
0.200
40
0.097
0.200
5
2.141
2.500
2977
3.357
5.000
4686
2.159
2.500
1821
3.124
5.000
1510
0.425
0.317
2.655
139
1231
25
94.16
2.6
50
3DVG
24012
24012
0
-3
0.051
1
3.8
98.1
2.60
2.69
1.8
2380
0.58
1
3.9
97.9
refinement
REFMAC
5.2.0019
data collection
Blu-Ice
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHASER
Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
A
GLN
79
A
GLN
80
HELX_P
A
PHE
83
A
PHE
84
5
1
5
A
SER
123
A
SER
124
HELX_P
A
LYS
128
A
LYS
129
1
2
6
A
LYS
185
A
LYS
186
HELX_P
A
LYS
190
A
LYS
191
1
3
6
B
ASN
28
B
ASN
31
HELX_P
B
GLY
32
B
GLY
35
5
4
5
B
ARG
87
B
ARG
90
HELX_P
B
THR
91
B
THR
94
5
5
5
B
TYR
101
B
TYR
104
HELX_P
B
TYR
104
B
TYR
107
5
6
4
B
SER
134
B
SER
137
HELX_P
B
LYS
136
B
LYS
139
5
7
3
B
SER
163
B
SER
166
HELX_P
B
ALA
165
B
ALA
168
5
8
3
B
SER
194
B
SER
197
HELX_P
B
LEU
196
B
LEU
199
5
9
3
B
LYS
208
B
LYS
211
HELX_P
B
ASN
211
B
ASN
214
5
10
4
X
THR
22
C
THR
25
HELX_P
X
GLY
35
C
GLY
38
1
11
14
X
PRO
37
C
PRO
40
HELX_P
X
ASP
39
C
ASP
42
5
12
3
X
LEU
56
C
LEU
59
HELX_P
X
ASN
60
C
ASN
63
5
13
5
Y
THR
22
D
THR
25
HELX_P
Y
GLY
35
D
GLY
38
1
14
14
Y
PRO
37
D
PRO
40
HELX_P
Y
ASP
39
D
ASP
42
5
15
3
disulf
2.064
A
CYS
23
A
SG
CYS
24
1_555
A
CYS
88
A
SG
CYS
89
1_555
disulf
2.034
A
CYS
136
A
SG
CYS
137
1_555
A
CYS
196
A
SG
CYS
197
1_555
disulf
2.040
B
CYS
22
B
SG
CYS
25
1_555
B
CYS
96
B
SG
CYS
99
1_555
disulf
2.047
B
CYS
147
B
SG
CYS
150
1_555
B
CYS
203
B
SG
CYS
206
1_555
covale
1.488
one
X
LYS
63
C
NZ
LYS
66
1_555
Y
GLY
76
D
C
GLY
79
1_555
IMMUNE SYSTEM
di-ubiquitin, fab fragment, antibody, Nucleus, Phosphoprotein, Ribosomal protein, IMMUNE SYSTEM
A
TYR
142
A
TYR
143
1
A
PRO
143
A
PRO
144
-1.06
B
PHE
153
B
PHE
156
1
B
PRO
154
B
PRO
157
-9.98
B
GLU
155
B
GLU
158
1
B
PRO
156
B
PRO
159
-3.29
3DVG
PDB
1
1
3DVG
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSARSLYSGVPSRFSGSRSGTDFTLTISSLQ
PEDFATYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG
NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
3DVG
PDB
2
1
3DVG
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQAPGKGLEWVAYITPYYGSTSYADSVKGRFTISADTSKN
TAYLQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
UBIQ_HUMAN
UNP
3
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
UBIQ_HUMAN
UNP
4
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
0
216
3DVG
0
216
3DVG
A
1
1
217
-2
227
3DVG
-2
227
3DVG
B
2
1
230
1
76
3DVG
1
76
P62988
X
3
4
79
1
76
3DVG
1
76
P62988
Y
4
4
79
3
expression tag
GLY
-2
3DVG
X
P62988
UNP
1
3
expression tag
SER
-1
3DVG
X
P62988
UNP
2
3
expression tag
HIS
0
3DVG
X
P62988
UNP
3
3
engineered mutation
ASP
77
3DVG
X
P62988
UNP
80
4
expression tag
GLY
-2
3DVG
Y
P62988
UNP
1
4
expression tag
SER
-1
3DVG
Y
P62988
UNP
2
4
expression tag
HIS
0
3DVG
Y
P62988
UNP
3
4
LYS
engineered mutation
ARG
63
3DVG
Y
P62988
UNP
63
66
6
4
3
4
4
4
6
4
4
4
3
5
5
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
SER
9
A
SER
10
A
ALA
13
A
ALA
14
A
THR
104
A
THR
105
A
ILE
108
A
ILE
109
A
THR
85
A
THR
86
A
TYR
91
A
TYR
92
A
ALA
34
A
ALA
35
A
GLN
38
A
GLN
39
A
LYS
45
A
LYS
46
A
TYR
49
A
TYR
50
A
SER
53
A
SER
54
A
LEU
54
A
LEU
55
A
SER
9
A
SER
10
A
ALA
13
A
ALA
14
A
THR
104
A
THR
105
A
ILE
108
A
ILE
109
A
THR
85
A
THR
86
A
TYR
91
A
TYR
92
A
PHE
98
A
PHE
99
A
PHE
100
A
PHE
101
A
VAL
19
A
VAL
20
A
CYS
23
A
CYS
24
A
ASP
70
A
ASP
71
A
ILE
75
A
ILE
76
A
PHE
62
A
PHE
63
A
SER
67
A
SER
68
A
SER
116
A
SER
117
A
PHE
120
A
PHE
121
A
THR
131
A
THR
132
A
PHE
141
A
PHE
142
A
TYR
175
A
TYR
176
A
SER
184
A
SER
185
A
SER
161
A
SER
162
A
VAL
165
A
VAL
166
A
ALA
155
A
ALA
156
A
LEU
156
A
LEU
157
A
LYS
147
A
LYS
148
A
VAL
152
A
VAL
153
A
VAL
193
A
VAL
194
A
THR
199
A
THR
200
A
VAL
207
A
VAL
208
A
ASN
212
A
ASN
213
B
GLN
3
B
GLN
6
B
SER
7
B
SER
10
B
LEU
18
B
LEU
21
B
SER
25
B
SER
28
B
THR
78
B
THR
81
B
MET
83
B
MET
86
B
PHE
68
B
PHE
71
B
ASP
73
B
ASP
76
B
GLY
10
B
GLY
13
B
VAL
12
B
VAL
15
B
THR
114
B
THR
117
B
VAL
118
B
VAL
121
B
ALA
92
B
ALA
95
B
GLU
99
B
GLU
102
B
LEU
33
B
LEU
36
B
GLN
39
B
GLN
42
B
LEU
45
B
LEU
48
B
ILE
51
B
ILE
54
B
THR
58
B
THR
61
B
TYR
60
B
TYR
63
B
GLY
10
B
GLY
13
B
VAL
12
B
VAL
15
B
THR
114
B
THR
117
B
VAL
118
B
VAL
121
B
ALA
92
B
ALA
95
B
GLU
99
B
GLU
102
B
ILE
107
B
ILE
110
B
TRP
110
B
TRP
113
B
SER
127
B
SER
130
B
LEU
131
B
LEU
134
B
THR
142
B
THR
145
B
TYR
152
B
TYR
155
B
TYR
183
B
TYR
186
B
PRO
192
B
PRO
195
B
VAL
170
B
VAL
173
B
THR
172
B
THR
175
B
THR
138
B
THR
141
B
SER
139
B
SER
142
B
THR
142
B
THR
145
B
TYR
152
B
TYR
155
B
TYR
183
B
TYR
186
B
PRO
192
B
PRO
195
B
VAL
176
B
VAL
179
B
LEU
177
B
LEU
180
B
THR
158
B
THR
161
B
TRP
161
B
TRP
164
B
ILE
202
B
ILE
205
B
HIS
207
B
HIS
210
B
THR
212
B
THR
215
B
LYS
217
B
LYS
220
X
THR
12
C
THR
15
X
VAL
17
C
VAL
20
X
MET
1
C
MET
4
X
THR
7
C
THR
10
X
THR
66
C
THR
69
X
LEU
71
C
LEU
74
X
GLN
41
C
GLN
44
X
PHE
45
C
PHE
48
X
LYS
48
C
LYS
51
X
GLN
49
C
GLN
52
Y
ILE
13
D
ILE
16
Y
GLU
16
D
GLU
19
Y
GLN
2
D
GLN
5
Y
LYS
6
D
LYS
9
Y
THR
66
D
THR
69
Y
LEU
71
D
LEU
74
Y
GLN
41
D
GLN
44
Y
PHE
45
D
PHE
48
Y
LYS
48
D
LYS
51
Y
GLN
49
D
GLN
52
5
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