0.007321
0.000000
0.006151
0.000000
0.017124
0.000000
0.000000
0.000000
0.014228
0.000000
0.000000
0.000000
Otomo, C.
Metlagel, Z.
Takaesu, G.
Otomo, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
130.040
90.000
136.601
58.399
91.802
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
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
Na 1
22.990
SODIUM ION
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
Nat.Struct.Mol.Biol.
1545-9993
20
59
66
10.1038/nsmb.2431
23202584
Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy.
2013
100
1
CCD
2009-11-06
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.0092
1.0
5.0.2
ALS
1.0092
SYNCHROTRON
ALS BEAMLINE 5.0.2
10282.029
Ubiquitin-like protein ATG12
1
man
polymer
32489.195
Autophagy protein 5
1
man
polymer
4657.435
Autophagy-related protein 16-1
1
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
Autophagy-related protein 12, APG12-like
APG5-like, Apoptosis-specific protein
APG16-like 1
no
no
GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKL
VLHYCKSQAWG
GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKL
VLHYCKSQAWG
A
polypeptide(L)
no
no
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH
YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND
RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH
YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND
RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
B
polypeptide(L)
no
no
SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
C
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
human
sample
APG12, APG12L, ATG12
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
plasmid
pACYC Duet-1
human
sample
APG5L, ASP, ATG5
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
plasmid
pACYC Duet-1
human
sample
APG16L, ATG16L1, UNQ9393/PRO34307
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
plasmid
pET
1
2.96
58.38
VAPOR DIFFUSION, HANGING DROP
6.5
PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
293
software
repository
Initial release
Database references
Database references
Refinement description
1
0
2012-12-05
1
1
2013-01-02
1
2
2013-01-16
1
3
2017-11-15
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.language
_software.location
_software.name
_software.type
_software.version
The structure of the same complex in a different space group.
RCSB
Y
RCSB
2012-07-31
REL
REL
NA
SODIUM ION
THERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUE GLY140 OF ATG12 AND LYS130 OF ATG5. THE ATG12~ATG5 CONJUGATE WAS GENERATED BY CO-EXPRESSING ATG12 AND ATG5 FROM PACYC DUET-1 AND ATG7 AND ATG10 FROM PCDF DUET-1 IN E. COLI
NA
1
4
NA
NA
301
B
n
1
50
A
n
2
51
A
n
3
52
A
LYS
53
n
4
LYS
53
A
LYS
54
n
5
LYS
54
A
ILE
55
n
6
ILE
55
A
ASP
56
n
7
ASP
56
A
ILE
57
n
8
ILE
57
A
LEU
58
n
9
LEU
58
A
LEU
59
n
10
LEU
59
A
LYS
60
n
11
LYS
60
A
ALA
61
n
12
ALA
61
A
VAL
62
n
13
VAL
62
A
GLY
63
n
14
GLY
63
A
ASP
64
n
15
ASP
64
A
THR
65
n
16
THR
65
A
PRO
66
n
17
PRO
66
A
ILE
67
n
18
ILE
67
A
MET
68
n
19
MET
68
A
LYS
69
n
20
LYS
69
A
THR
70
n
21
THR
70
A
LYS
71
n
22
LYS
71
A
LYS
72
n
23
LYS
72
A
TRP
73
n
24
TRP
73
A
ALA
74
n
25
ALA
74
A
VAL
75
n
26
VAL
75
A
GLU
76
n
27
GLU
76
A
ARG
77
n
28
ARG
77
A
THR
78
n
29
THR
78
A
ARG
79
n
30
ARG
79
A
THR
80
n
31
THR
80
A
ILE
81
n
32
ILE
81
A
GLN
82
n
33
GLN
82
A
GLY
83
n
34
GLY
83
A
LEU
84
n
35
LEU
84
A
ILE
85
n
36
ILE
85
A
ASP
86
n
37
ASP
86
A
PHE
87
n
38
PHE
87
A
ILE
88
n
39
ILE
88
A
LYS
89
n
40
LYS
89
A
LYS
90
n
41
LYS
90
A
PHE
91
n
42
PHE
91
A
LEU
92
n
43
LEU
92
A
LYS
93
n
44
LYS
93
A
LEU
94
n
45
LEU
94
A
VAL
95
n
46
VAL
95
A
ALA
96
n
47
ALA
96
A
SER
97
n
48
SER
97
A
GLU
98
n
49
GLU
98
A
GLN
99
n
50
GLN
99
A
LEU
100
n
51
LEU
100
A
PHE
101
n
52
PHE
101
A
ILE
102
n
53
ILE
102
A
TYR
103
n
54
TYR
103
A
VAL
104
n
55
VAL
104
A
ASN
105
n
56
ASN
105
A
GLN
106
n
57
GLN
106
A
SER
107
n
58
SER
107
A
PHE
108
n
59
PHE
108
A
ALA
109
n
60
ALA
109
A
PRO
110
n
61
PRO
110
A
SER
111
n
62
SER
111
A
PRO
112
n
63
PRO
112
A
ASP
113
n
64
ASP
113
A
GLN
114
n
65
GLN
114
A
GLU
115
n
66
GLU
115
A
VAL
116
n
67
VAL
116
A
GLY
117
n
68
GLY
117
A
THR
118
n
69
THR
118
A
LEU
119
n
70
LEU
119
A
TYR
120
n
71
TYR
120
A
GLU
121
n
72
GLU
121
A
CYS
122
n
73
CYS
122
A
PHE
123
n
74
PHE
123
A
GLY
124
n
75
GLY
124
A
SER
125
n
76
SER
125
A
ASP
126
n
77
ASP
126
A
GLY
127
n
78
GLY
127
A
LYS
128
n
79
LYS
128
A
LEU
129
n
80
LEU
129
A
VAL
130
n
81
VAL
130
A
LEU
131
n
82
LEU
131
A
HIS
132
n
83
HIS
132
A
TYR
133
n
84
TYR
133
A
CYS
134
n
85
CYS
134
A
LYS
135
n
86
LYS
135
A
SER
136
n
87
SER
136
A
GLN
137
n
88
GLN
137
A
ALA
138
n
89
ALA
138
A
TRP
139
n
90
TRP
139
A
GLY
140
n
91
GLY
140
A
n
1
1
B
n
2
2
B
ASP
3
n
3
ASP
3
B
ASP
4
n
4
ASP
4
B
LYS
5
n
5
LYS
5
B
ASP
6
n
6
ASP
6
B
VAL
7
n
7
VAL
7
B
LEU
8
n
8
LEU
8
B
ARG
9
n
9
ARG
9
B
ASP
10
n
10
ASP
10
B
VAL
11
n
11
VAL
11
B
TRP
12
n
12
TRP
12
B
PHE
13
n
13
PHE
13
B
GLY
14
n
14
GLY
14
B
ARG
15
n
15
ARG
15
B
ILE
16
n
16
ILE
16
B
PRO
17
n
17
PRO
17
B
THR
18
n
18
THR
18
B
CYS
19
n
19
CYS
19
B
PHE
20
n
20
PHE
20
B
THR
21
n
21
THR
21
B
LEU
22
n
22
LEU
22
B
TYR
23
n
23
TYR
23
B
GLN
24
n
24
GLN
24
B
ASP
25
n
25
ASP
25
B
GLU
26
n
26
GLU
26
B
ILE
27
n
27
ILE
27
B
THR
28
n
28
THR
28
B
GLU
29
n
29
GLU
29
B
ARG
30
n
30
ARG
30
B
GLU
31
n
31
GLU
31
B
ALA
32
n
32
ALA
32
B
GLU
33
n
33
GLU
33
B
PRO
34
n
34
PRO
34
B
TYR
35
n
35
TYR
35
B
TYR
36
n
36
TYR
36
B
LEU
37
n
37
LEU
37
B
LEU
38
n
38
LEU
38
B
LEU
39
n
39
LEU
39
B
PRO
40
n
40
PRO
40
B
ARG
41
n
41
ARG
41
B
VAL
42
n
42
VAL
42
B
SER
43
n
43
SER
43
B
TYR
44
n
44
TYR
44
B
LEU
45
n
45
LEU
45
B
THR
46
n
46
THR
46
B
LEU
47
n
47
LEU
47
B
VAL
48
n
48
VAL
48
B
THR
49
n
49
THR
49
B
ASP
50
n
50
ASP
50
B
LYS
51
n
51
LYS
51
B
VAL
52
n
52
VAL
52
B
LYS
53
n
53
LYS
53
B
LYS
54
n
54
LYS
54
B
HIS
55
n
55
HIS
55
B
PHE
56
n
56
PHE
56
B
GLN
57
n
57
GLN
57
B
LYS
58
n
58
LYS
58
B
VAL
59
n
59
VAL
59
B
MET
60
n
60
MET
60
B
ARG
61
n
61
ARG
61
B
GLN
62
n
62
GLN
62
B
GLU
63
n
63
GLU
63
B
ASP
64
n
64
ASP
64
B
ILE
65
n
65
ILE
65
B
SER
66
n
66
SER
66
B
GLU
67
n
67
GLU
67
B
ILE
68
n
68
ILE
68
B
TRP
69
n
69
TRP
69
B
PHE
70
n
70
PHE
70
B
GLU
71
n
71
GLU
71
B
TYR
72
n
72
TYR
72
B
GLU
73
n
73
GLU
73
B
GLY
74
n
74
GLY
74
B
THR
75
n
75
THR
75
B
PRO
76
n
76
PRO
76
B
LEU
77
n
77
LEU
77
B
LYS
78
n
78
LYS
78
B
TRP
79
n
79
TRP
79
B
HIS
80
n
80
HIS
80
B
TYR
81
n
81
TYR
81
B
PRO
82
n
82
PRO
82
B
ILE
83
n
83
ILE
83
B
GLY
84
n
84
GLY
84
B
LEU
85
n
85
LEU
85
B
LEU
86
n
86
LEU
86
B
PHE
87
n
87
PHE
87
B
ASP
88
n
88
ASP
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
ALA
91
n
91
ALA
91
B
SER
92
n
92
SER
92
B
SER
93
n
93
SER
93
B
SER
94
n
94
SER
94
B
ALA
95
n
95
ALA
95
B
LEU
96
n
96
LEU
96
B
PRO
97
n
97
PRO
97
B
TRP
98
n
98
TRP
98
B
ASN
99
n
99
ASN
99
B
ILE
100
n
100
ILE
100
B
THR
101
n
101
THR
101
B
VAL
102
n
102
VAL
102
B
HIS
103
n
103
HIS
103
B
PHE
104
n
104
PHE
104
B
LYS
105
n
105
LYS
105
B
SER
106
n
106
SER
106
B
PHE
107
n
107
PHE
107
B
PRO
108
n
108
PRO
108
B
GLU
109
n
109
GLU
109
B
LYS
110
n
110
LYS
110
B
ASP
111
n
111
ASP
111
B
LEU
112
n
112
LEU
112
B
LEU
113
n
113
LEU
113
B
HIS
114
n
114
HIS
114
B
CYS
115
n
115
CYS
115
B
PRO
116
n
116
PRO
116
B
SER
117
n
117
SER
117
B
LYS
118
n
118
LYS
118
B
ASP
119
n
119
ASP
119
B
ALA
120
n
120
ALA
120
B
ILE
121
n
121
ILE
121
B
GLU
122
n
122
GLU
122
B
ALA
123
n
123
ALA
123
B
HIS
124
n
124
HIS
124
B
PHE
125
n
125
PHE
125
B
MET
126
n
126
MET
126
B
SER
127
n
127
SER
127
B
CYS
128
n
128
CYS
128
B
MET
129
n
129
MET
129
B
LYS
130
n
130
LYS
130
B
GLU
131
n
131
GLU
131
B
ALA
132
n
132
ALA
132
B
ASP
133
n
133
ASP
133
B
ALA
134
n
134
ALA
134
B
LEU
135
n
135
LEU
135
B
LYS
136
n
136
LYS
136
B
HIS
137
n
137
HIS
137
B
LYS
138
n
138
LYS
138
B
SER
139
n
139
SER
139
B
GLN
140
n
140
GLN
140
B
VAL
141
n
141
VAL
141
B
ILE
142
n
142
ILE
142
B
ASN
143
n
143
ASN
143
B
GLU
144
n
144
GLU
144
B
MET
145
n
145
MET
145
B
GLN
146
n
146
GLN
146
B
LYS
147
n
147
LYS
147
B
LYS
148
n
148
LYS
148
B
ASP
149
n
149
ASP
149
B
HIS
150
n
150
HIS
150
B
LYS
151
n
151
LYS
151
B
GLN
152
n
152
GLN
152
B
LEU
153
n
153
LEU
153
B
TRP
154
n
154
TRP
154
B
MET
155
n
155
MET
155
B
GLY
156
n
156
GLY
156
B
LEU
157
n
157
LEU
157
B
GLN
158
n
158
GLN
158
B
ASN
159
n
159
ASN
159
B
ASP
160
n
160
ASP
160
B
ARG
161
n
161
ARG
161
B
PHE
162
n
162
PHE
162
B
ASP
163
n
163
ASP
163
B
GLN
164
n
164
GLN
164
B
PHE
165
n
165
PHE
165
B
TRP
166
n
166
TRP
166
B
ALA
167
n
167
ALA
167
B
ILE
168
n
168
ILE
168
B
ASN
169
n
169
ASN
169
B
ARG
170
n
170
ARG
170
B
LYS
171
n
171
LYS
171
B
LEU
172
n
172
LEU
172
B
MET
173
n
173
MET
173
B
GLU
174
n
174
GLU
174
B
TYR
175
n
175
TYR
175
B
PRO
176
n
176
PRO
176
B
ALA
177
n
177
ALA
177
B
GLU
178
n
178
GLU
178
B
GLU
179
n
179
GLU
179
B
ASN
180
n
180
ASN
180
B
GLY
181
n
181
GLY
181
B
PHE
182
n
182
PHE
182
B
ARG
183
n
183
ARG
183
B
TYR
184
n
184
TYR
184
B
ILE
185
n
185
ILE
185
B
PRO
186
n
186
PRO
186
B
PHE
187
n
187
PHE
187
B
ARG
188
n
188
ARG
188
B
ILE
189
n
189
ILE
189
B
TYR
190
n
190
TYR
190
B
GLN
191
n
191
GLN
191
B
THR
192
n
192
THR
192
B
THR
193
n
193
THR
193
B
THR
194
n
194
THR
194
B
GLU
195
n
195
GLU
195
B
ARG
196
n
196
ARG
196
B
PRO
197
n
197
PRO
197
B
PHE
198
n
198
PHE
198
B
ILE
199
n
199
ILE
199
B
GLN
200
n
200
GLN
200
B
LYS
201
n
201
LYS
201
B
LEU
202
n
202
LEU
202
B
PHE
203
n
203
PHE
203
B
ARG
204
n
204
ARG
204
B
PRO
205
n
205
PRO
205
B
VAL
206
n
206
VAL
206
B
ALA
207
n
207
ALA
207
B
ALA
208
n
208
ALA
208
B
ASP
209
n
209
ASP
209
B
GLY
210
n
210
GLY
210
B
GLN
211
n
211
GLN
211
B
LEU
212
n
212
LEU
212
B
HIS
213
n
213
HIS
213
B
THR
214
n
214
THR
214
B
LEU
215
n
215
LEU
215
B
GLY
216
n
216
GLY
216
B
ASP
217
n
217
ASP
217
B
LEU
218
n
218
LEU
218
B
LEU
219
n
219
LEU
219
B
LYS
220
n
220
LYS
220
B
GLU
221
n
221
GLU
221
B
VAL
222
n
222
VAL
222
B
CYS
223
n
223
CYS
223
B
PRO
224
n
224
PRO
224
B
SER
225
n
225
SER
225
B
ALA
226
n
226
ALA
226
B
ILE
227
n
227
ILE
227
B
n
228
228
B
n
229
229
B
n
230
230
B
n
231
231
B
n
232
232
B
n
233
233
B
n
234
234
B
LYS
235
n
235
LYS
235
B
ASN
236
n
236
ASN
236
B
GLN
237
n
237
GLN
237
B
VAL
238
n
238
VAL
238
B
MET
239
n
239
MET
239
B
ILE
240
n
240
ILE
240
B
HIS
241
n
241
HIS
241
B
GLY
242
n
242
GLY
242
B
ILE
243
n
243
ILE
243
B
GLU
244
n
244
GLU
244
B
PRO
245
n
245
PRO
245
B
MET
246
n
246
MET
246
B
LEU
247
n
247
LEU
247
B
GLU
248
n
248
GLU
248
B
THR
249
n
249
THR
249
B
PRO
250
n
250
PRO
250
B
LEU
251
n
251
LEU
251
B
GLN
252
n
252
GLN
252
B
TRP
253
n
253
TRP
253
B
LEU
254
n
254
LEU
254
B
SER
255
n
255
SER
255
B
GLU
256
n
256
GLU
256
B
HIS
257
n
257
HIS
257
B
LEU
258
n
258
LEU
258
B
SER
259
n
259
SER
259
B
TYR
260
n
260
TYR
260
B
PRO
261
n
261
PRO
261
B
ASP
262
n
262
ASP
262
B
ASN
263
n
263
ASN
263
B
PHE
264
n
264
PHE
264
B
LEU
265
n
265
LEU
265
B
HIS
266
n
266
HIS
266
B
ILE
267
n
267
ILE
267
B
SER
268
n
268
SER
268
B
ILE
269
n
269
ILE
269
B
ILE
270
n
270
ILE
270
B
PRO
271
n
271
PRO
271
B
GLN
272
n
272
GLN
272
B
PRO
273
n
273
PRO
273
B
THR
274
n
274
THR
274
B
n
275
275
B
n
1
8
C
n
2
9
C
MET
10
n
3
MET
10
C
PRO
11
n
4
PRO
11
C
ARG
12
n
5
ARG
12
C
TRP
13
n
6
TRP
13
C
LYS
14
n
7
LYS
14
C
ARG
15
n
8
ARG
15
C
HIS
16
n
9
HIS
16
C
ILE
17
n
10
ILE
17
C
SER
18
n
11
SER
18
C
GLU
19
n
12
GLU
19
C
GLN
20
n
13
GLN
20
C
LEU
21
n
14
LEU
21
C
ARG
22
n
15
ARG
22
C
ARG
23
n
16
ARG
23
C
ARG
24
n
17
ARG
24
C
ASP
25
n
18
ASP
25
C
ARG
26
n
19
ARG
26
C
LEU
27
n
20
LEU
27
C
GLN
28
n
21
GLN
28
C
ARG
29
n
22
ARG
29
C
GLN
30
n
23
GLN
30
C
ALA
31
n
24
ALA
31
C
PHE
32
n
25
PHE
32
C
GLU
33
n
26
GLU
33
C
GLU
34
n
27
GLU
34
C
ILE
35
n
28
ILE
35
C
ILE
36
n
29
ILE
36
C
LEU
37
n
30
LEU
37
C
GLN
38
n
31
GLN
38
C
TYR
39
n
32
TYR
39
C
ASN
40
n
33
ASN
40
C
LYS
41
n
34
LYS
41
C
LEU
42
n
35
LEU
42
C
LEU
43
n
36
LEU
43
C
3.6238
2.7977
0.6736
3.2452
0.8570
6.0662
-0.9306
1.6393
1.6291
-1.4487
0.1603
1.6733
-0.2069
-1.6583
0.8281
0.8731
0.5559
0.1543
1.5639
0.5159
1.5721
refined
131.9098
14.7466
14.7212
X-RAY DIFFRACTION
7.2938
-3.3147
-4.1637
3.7272
-0.7557
5.8908
0.3887
1.6713
-0.3986
-0.4764
-0.5727
0.9357
-0.0244
-2.8717
0.0498
0.6716
0.1147
-0.2917
1.8883
-0.1696
1.1547
refined
129.9928
6.0654
15.7652
X-RAY DIFFRACTION
6.5054
4.9979
-2.7965
3.8222
-1.8131
3.2700
-1.4633
0.6937
-2.0906
-1.9660
1.1251
-0.2622
1.6633
0.6728
0.3787
1.1311
-0.1251
0.0261
1.3008
-0.1878
1.5979
refined
133.6834
-2.2909
12.3846
X-RAY DIFFRACTION
9.7311
7.6172
-0.5108
8.8877
2.8401
3.3538
-0.3554
1.6975
0.9582
-1.0900
0.8627
0.3778
-1.1970
0.2940
-0.6039
0.9782
0.2414
-0.1224
1.6464
0.1838
1.2002
refined
140.0424
11.9384
13.0095
X-RAY DIFFRACTION
3.7752
5.6888
-0.1132
9.6962
1.3887
2.3201
0.0168
2.3705
0.7689
-1.8665
0.8880
0.5925
-0.1597
-1.8648
0.0609
1.5600
0.3194
-0.2346
2.3461
-0.1557
1.7240
refined
140.1161
-0.3734
4.6258
X-RAY DIFFRACTION
7.0139
-1.4957
1.3425
6.3927
-2.9860
7.1094
0.2765
0.2747
-1.2077
-0.3156
-0.0774
0.9176
0.7319
-0.3263
0.0475
0.6411
-0.0160
0.0173
0.9328
-0.2245
0.9535
refined
158.9248
-6.7631
28.9032
X-RAY DIFFRACTION
4.2388
-2.2128
0.0823
3.7026
-3.8407
6.3635
0.3081
3.5878
-0.2294
-0.8773
-0.0315
0.2101
0.2615
1.0743
-0.4028
1.1155
0.0125
-0.1655
2.5459
-0.2036
0.9501
refined
157.4494
3.1499
6.6807
X-RAY DIFFRACTION
6.8884
-0.0630
1.7123
4.0508
1.5365
2.8113
-0.4282
1.7108
2.1212
-0.3057
0.1234
0.0233
-0.6817
0.4777
0.2267
0.8807
-0.0844
-0.0671
0.9552
0.4015
1.0515
refined
158.9984
18.7852
20.0348
X-RAY DIFFRACTION
7.7345
-4.1351
4.4435
3.2343
-2.2397
4.4717
0.0006
0.9326
1.0446
-0.1225
-0.4194
-0.4746
-0.1523
0.8516
0.7474
0.7444
-0.0613
0.2367
1.4281
0.0818
0.7622
refined
175.8442
3.7178
25.6581
X-RAY DIFFRACTION
A
53
A
61
X-RAY DIFFRACTION
1
chain 'A' and (resseq 53:61)
A
62
A
91
X-RAY DIFFRACTION
2
chain 'A' and (resseq 62:91)
A
92
A
104
X-RAY DIFFRACTION
3
chain 'A' and (resseq 92:104)
A
105
A
134
X-RAY DIFFRACTION
4
chain 'A' and (resseq 105:134)
A
135
A
140
X-RAY DIFFRACTION
5
chain 'A' and (resseq 135:140)
B
3
B
117
X-RAY DIFFRACTION
6
chain 'B' and (resseq 3:117)
B
118
B
173
X-RAY DIFFRACTION
7
chain 'B' and (resseq 118:173)
B
174
B
274
X-RAY DIFFRACTION
8
chain 'B' and (resseq 174:274)
C
10
C
43
X-RAY DIFFRACTION
9
chain 'C' and (resseq 10:43)
author_defined_assembly
3
trimeric
B
ALA
95
B
O
ALA
95
1_555
B
NA
301
D
NA
NA
1_555
B
ASN
99
B
OD1
ASN
99
1_555
152.4
B
ALA
95
B
O
ALA
95
1_555
B
NA
301
D
NA
NA
1_555
B
PRO
97
B
O
PRO
97
1_555
82.7
B
ASN
99
B
OD1
ASN
99
1_555
B
NA
301
D
NA
NA
1_555
B
PRO
97
B
O
PRO
97
1_555
92.8
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
TRP
73
A
O
TRP
24
A
N
ILE
57
A
N
ILE
8
A
N
LEU
58
A
N
LEU
9
A
O
LEU
131
A
O
LEU
82
A
O
CYS
134
A
O
CYS
85
A
N
PHE
101
A
N
PHE
52
B
O
TYR
35
B
O
TYR
35
B
N
PHE
20
B
N
PHE
20
B
N
PRO
17
B
N
PRO
17
B
O
TRP
98
B
O
TRP
98
B
O
THR
101
B
O
THR
101
B
N
GLU
71
B
N
GLU
71
B
N
TYR
72
B
N
TYR
72
B
O
THR
75
B
O
THR
75
B
N
TYR
190
B
N
TYR
190
B
O
ILE
267
B
O
ILE
267
B
O
ILE
270
B
O
ILE
270
B
N
GLN
237
B
N
GLN
237
1
A
GLY
50
A
GLY
1
1
Y
1
A
SER
51
A
SER
2
1
Y
1
A
LYS
52
A
LYS
3
1
Y
1
B
MET
1
B
MET
1
1
Y
1
B
THR
2
B
THR
2
1
Y
1
B
ASP
228
B
ASP
228
1
Y
1
B
PRO
229
B
PRO
229
1
Y
1
B
GLU
230
B
GLU
230
1
Y
1
B
ASP
231
B
ASP
231
1
Y
1
B
GLY
232
B
GLY
232
1
Y
1
B
GLU
233
B
GLU
233
1
Y
1
B
LYS
234
B
LYS
234
1
Y
1
B
ASP
275
B
ASP
275
1
Y
1
C
SER
8
C
SER
1
1
Y
1
C
HIS
9
C
HIS
2
1
Y
1
A
SER
107
-133.91
-60.10
1
B
SER
43
-107.38
-164.54
1
B
SER
66
-146.50
-144.37
1
B
PHE
104
-140.11
-38.90
1
B
GLN
191
-166.06
118.20
1
B
CYS
223
-156.28
65.91
1
B
ALA
226
-159.42
17.75
1
B
LEU
265
-101.67
75.59
1
B
PRO
273
-61.62
-163.49
1
C
GLN
28
-108.70
-67.83
283.770
138.7687
64.410
0.2540
0.2146
0.2186
2.8750
36.2240
1263
12465
10.1300
97.4100
1.000
1.000
0.7275
0.3200
RANDOM
1
1.340
MOLECULAR REPLACEMENT
32.8400
0.8000
1.0000
ML
FLAT BULK SOLVENT MODEL
2.8750
36.2240
0
3227
1
0
3226
0.006
3316
0.510
4482
0.037
479
0.003
566
9.914
1256
0.4281
0.3301
2.9903
126
1081
1207
9
86.0000
0.3126
0.3040
3.1264
136
1222
1358
9
97.0000
0.2864
0.2506
3.2911
141
1257
1398
9
98.0000
0.2919
0.2514
3.4971
133
1253
1386
9
99.0000
0.3062
0.2354
3.7669
145
1258
1403
9
99.0000
0.2620
0.2207
4.1455
141
1269
1410
9
99.0000
0.2081
0.1802
4.7442
142
1267
1409
9
100.0000
0.2265
0.2030
5.9729
148
1287
1435
9
100.0000
0.2450
0.2006
36.2267
151
1308
1459
9
99.0000
2.8750
50.000
4GDL
12548
0.056
1.044
1
14.900
4.400
98.600
0.541
2.900
3.000
1174
1.042
1
3.700
92.400
0.467
3.000
3.120
1253
1.092
1
4.300
98.400
0.287
3.120
3.270
1232
1.139
1
4.500
99.000
0.208
3.270
3.440
1253
1.122
1
4.600
99.300
0.138
3.440
3.650
1256
1.092
1
4.600
99.600
0.092
3.650
3.940
1268
0.979
1
4.500
99.700
0.065
3.940
4.330
1244
0.929
1
4.500
99.500
0.055
4.330
4.960
1285
0.971
1
4.500
99.700
0.046
4.960
6.240
1281
0.955
1
4.300
99.800
0.031
6.240
50.000
1302
1.118
1
4.400
98.900
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_1069
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
Atg12, Atg5, Atg16L1
Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1
1
N
N
2
N
N
3
N
N
4
N
N
A
THR
80
A
THR
31
HELX_P
A
LEU
92
A
LEU
43
1
1
13
A
GLU
115
A
GLU
66
HELX_P
A
GLY
124
A
GLY
75
1
2
10
B
ASP
4
B
ASP
4
HELX_P
B
PHE
13
B
PHE
13
1
3
10
B
TYR
44
B
TYR
44
HELX_P
B
VAL
48
B
VAL
48
5
4
5
B
ASP
50
B
ASP
50
HELX_P
B
LYS
58
B
LYS
58
1
5
9
B
PRO
82
B
PRO
82
HELX_P
B
ALA
91
B
ALA
91
1
6
10
B
SER
117
B
SER
117
HELX_P
B
LYS
138
B
LYS
138
1
7
22
B
GLN
146
B
GLN
146
HELX_P
B
ASN
159
B
ASN
159
1
8
14
B
ARG
161
B
ARG
161
HELX_P
B
ARG
170
B
ARG
170
1
9
10
B
LYS
171
B
LYS
171
HELX_P
B
GLU
174
B
GLU
174
5
10
4
B
THR
214
B
THR
214
HELX_P
B
CYS
223
B
CYS
223
1
11
10
B
PRO
250
B
PRO
250
HELX_P
B
LEU
258
B
LEU
258
1
12
9
C
PRO
11
C
PRO
4
HELX_P
C
GLN
28
C
GLN
21
1
13
18
C
GLN
28
C
GLN
21
HELX_P
C
LEU
42
C
LEU
35
1
14
15
metalc
2.245
B
ALA
95
B
O
ALA
95
1_555
B
NA
301
D
NA
NA
1_555
metalc
2.407
B
ASN
99
B
OD1
ASN
99
1_555
B
NA
301
D
NA
NA
1_555
metalc
2.680
B
PRO
97
B
O
PRO
97
1_555
B
NA
301
D
NA
NA
1_555
covale
1.329
A
GLY
140
A
C
GLY
91
1_555
B
LYS
130
B
NZ
LYS
130
1_555
PROTEIN BINDING
protein-protein conjugate, protein-protein complex, ubiquitin-like protein, autophagy, E3 ligase, ubiquitin-like fold, structural protein, isopeptide bond, Cytoplasm and autophagosomal membranes, protein binding
A
GLY
63
A
GLY
14
1
A
ASP
64
A
ASP
15
2.84
B
LEU
96
B
LEU
96
1
B
PRO
97
B
PRO
97
-4.26
ATG12_HUMAN
UNP
1
52
O94817
KKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVL
HYCKSQAWG
ATG5_HUMAN
UNP
2
1
Q9H1Y0
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH
YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND
RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
A16L1_HUMAN
UNP
3
11
Q676U5
PRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
52
140
4GDL
52
140
O94817
A
1
3
91
1
275
4GDL
1
275
Q9H1Y0
B
2
1
275
11
43
4GDL
11
43
Q676U5
C
3
4
36
1
EXPRESSION TAG
GLY
50
4GDL
A
O94817
UNP
1
1
EXPRESSION TAG
SER
51
4GDL
A
O94817
UNP
2
3
EXPRESSION TAG
SER
8
4GDL
C
Q676U5
UNP
1
3
EXPRESSION TAG
HIS
9
4GDL
C
Q676U5
UNP
2
3
EXPRESSION TAG
MET
10
4GDL
C
Q676U5
UNP
3
4
5
3
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
LYS
72
A
LYS
23
A
GLU
76
A
GLU
27
A
LYS
54
A
LYS
5
A
ALA
61
A
ALA
12
A
LYS
128
A
LYS
79
A
CYS
134
A
CYS
85
A
PHE
101
A
PHE
52
A
VAL
104
A
VAL
55
B
TYR
35
B
TYR
35
B
PRO
40
B
PRO
40
B
ARG
15
B
ARG
15
B
LEU
22
B
LEU
22
B
TRP
98
B
TRP
98
B
HIS
103
B
HIS
103
B
TRP
69
B
TRP
69
B
TYR
72
B
TYR
72
B
THR
75
B
THR
75
B
PRO
76
B
PRO
76
B
PHE
187
B
PHE
187
B
TYR
190
B
TYR
190
B
LEU
265
B
LEU
265
B
PRO
271
B
PRO
271
B
ASN
236
B
ASN
236
B
MET
239
B
MET
239
BINDING SITE FOR RESIDUE NA B 301
Software
3
B
ALA
95
B
ALA
95
3
1_555
B
PRO
97
B
PRO
97
3
1_555
B
ASN
99
B
ASN
99
3
1_555
5
C 1 2 1