0.010982
0.000000
0.000000
0.000000
0.016509
0.000000
0.000000
0.000000
0.014231
0.00000
0.00000
0.00000
Odell, M.
Malinina, L.
Teplova, M.
Shuman, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
91.059
60.574
70.268
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C10 H14 N5 O7 P
347.221
ADENOSINE MONOPHOSPHATE
non-polymer
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
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
P
N
15
N
O
N
16
N
O
N
17
N
O
N
18
N
O
N
19
N
C
N
20
R
C
N
21
N
O
N
22
S
C
N
23
N
O
N
24
R
C
N
25
N
O
N
26
R
C
Y
27
N
N
Y
28
N
C
Y
29
N
N
Y
30
N
C
Y
31
N
C
N
32
N
N
Y
33
N
N
Y
34
N
C
Y
35
N
N
Y
36
N
C
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
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
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
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
N
N
112
R
C
N
113
N
C
N
114
N
O
N
115
N
C
N
116
N
S
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
H
N
124
N
H
N
125
N
N
N
126
S
C
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
C
N
131
N
C
N
132
N
O
N
133
N
N
N
134
N
O
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
H
N
145
N
N
N
146
S
C
N
147
N
C
N
148
N
O
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
O
N
153
N
O
N
154
N
O
N
155
N
H
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
N
N
165
N
C
N
166
N
C
N
167
N
O
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
N
N
175
S
C
N
176
N
C
N
177
N
O
N
178
N
C
Y
179
N
C
Y
180
N
N
Y
181
N
C
Y
182
N
C
Y
183
N
N
N
184
N
O
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
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
O
N
196
N
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
S
C
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
O
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
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
N
N
221
S
C
N
222
N
C
N
223
N
O
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
O
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
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
N
N
243
S
C
N
244
N
C
N
245
N
O
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
C
N
250
N
N
N
251
N
O
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
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
N
272
N
C
N
273
N
S
N
274
N
C
N
275
N
O
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
Y
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
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
N
N
311
S
C
N
312
N
C
N
313
N
O
N
314
N
C
N
315
N
C
N
316
N
C
N
317
N
O
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
N
332
N
O
N
333
N
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
R
C
N
346
N
O
N
347
N
C
N
348
N
O
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
355
N
H
N
356
N
H
N
357
N
H
N
358
N
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
N
Y
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
N
372
N
O
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
N
396
N
O
N
397
N
O
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
N
N
410
S
C
N
411
N
C
N
412
N
O
N
413
N
C
N
414
N
C
N
415
N
C
N
416
N
O
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
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
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
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
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
Y
37
N
sing
Y
38
N
sing
Y
39
N
doub
N
40
N
sing
Y
41
N
sing
Y
42
N
sing
Y
43
N
doub
N
44
N
sing
Y
45
N
doub
N
46
N
sing
N
47
N
sing
Y
48
N
sing
Y
49
N
doub
N
50
N
sing
Y
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
doub
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
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
sing
N
114
N
sing
N
115
N
doub
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
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
sing
N
146
N
sing
N
147
N
doub
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
doub
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
doub
N
166
N
sing
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
doub
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
sing
N
186
N
sing
N
187
N
sing
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
doub
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
sing
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
doub
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
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
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
sing
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
doub
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
sing
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
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
doub
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
Y
287
N
doub
Y
288
N
sing
Y
289
N
sing
N
290
N
sing
Y
291
N
doub
N
292
N
sing
Y
293
N
doub
N
294
N
sing
Y
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
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
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
doub
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
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
doub
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
Y
356
N
doub
Y
357
N
sing
Y
358
N
sing
N
359
N
sing
Y
360
N
doub
Y
361
N
sing
Y
362
N
sing
N
363
N
sing
Y
364
N
sing
Y
365
N
doub
N
366
N
sing
Y
367
N
doub
N
368
N
sing
Y
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
Y
384
N
doub
Y
385
N
sing
Y
386
N
sing
N
387
N
sing
Y
388
N
doub
N
389
N
sing
Y
390
N
doub
N
391
N
sing
Y
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
doub
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
31
5090
5100
10.1093/nar/gkg665
12930960
Analysis of the DNA Joining Repertoire of Chlorella Virus DNA ligase and a New Crystal Structure of the Ligase-Adenylate Intermediate
2003
10.2210/pdb1p8l/pdb
pdb_00001p8l
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
2002-01-25
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RUH3R
35128.270
PBCV-1 DNA ligase
1
man
polymer
347.221
ADENOSINE MONOPHOSPHATE
1
syn
non-polymer
18.015
water
2
nat
water
no
no
HHHHHHMAITKPLLAATLENIEDVQFPCLATPKIDGIRSVKQTQMLSRTFKPIRNSVMNRLLTELLPEGSDGEISIEGAT
FQDTTSAVMTGHKMYNAKFSYYWFDYVTDDPLKKYIDRVEDMKNYITVHPHILEHAQVKIIPLIPVEINNITELLQYERD
VLSKGFEGVMIRKPDGKYKFGRSTLKEGILLKMKQFKDAEATIISMTALFKNTNTKTKDNFGYSKRSTHKSGKVEEDVMG
SIEVDYDGVVFSIGTGFDADQRRDFWQNKESYIGKMVKFKYFEMGSKDCPRFPVFIGIRHEEDR
HHHHHHMAITKPLLAATLENIEDVQFPCLATPKIDGIRSVKQTQMLSRTFKPIRNSVMNRLLTELLPEGSDGEISIEGAT
FQDTTSAVMTGHKMYNAKFSYYWFDYVTDDPLKKYIDRVEDMKNYITVHPHILEHAQVKIIPLIPVEINNITELLQYERD
VLSKGFEGVMIRKPDGKYKFGRSTLKEGILLKMKQFKDAEATIISMTALFKNTNTKTKDNFGYSKRSTHKSGKVEEDVMG
SIEVDYDGVVFSIGTGFDADQRRDFWQNKESYIGKMVKFKYFEMGSKDCPRFPVFIGIRHEEDR
A
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
Chlorovirus
Escherichia
Escherichia coli
sample
10506
Paramecium bursaria Chlorella virus 1
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
1
2.76
55.39
hanging drops
7.5
4-6% PEG 4000, 50 mM HEPES, 50 mM sodium acetate, pH 7.5, hanging drops, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Advisory
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-08-26
1
1
2008-04-29
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_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
2003-05-07
REL
REL
AMP
ADENOSINE MONOPHOSPHATE
HOH
water
1FVI
PDB ENTRY 1FVI
PDB
experimental model
AMP
301
2
AMP
AMP
301
A
HOH
311
3
HOH
HOH
311
A
HOH
325
3
HOH
HOH
325
A
n
1
-5
A
n
2
-4
A
n
3
-3
A
n
4
-2
A
n
5
-1
A
n
6
0
A
n
7
1
A
ALA
2
n
8
ALA
2
A
ILE
3
n
9
ILE
3
A
THR
4
n
10
THR
4
A
LYS
5
n
11
LYS
5
A
PRO
6
n
12
PRO
6
A
LEU
7
n
13
LEU
7
A
LEU
8
n
14
LEU
8
A
ALA
9
n
15
ALA
9
A
ALA
10
n
16
ALA
10
A
THR
11
n
17
THR
11
A
LEU
12
n
18
LEU
12
A
GLU
13
n
19
GLU
13
A
ASN
14
n
20
ASN
14
A
ILE
15
n
21
ILE
15
A
GLU
16
n
22
GLU
16
A
ASP
17
n
23
ASP
17
A
VAL
18
n
24
VAL
18
A
GLN
19
n
25
GLN
19
A
PHE
20
n
26
PHE
20
A
PRO
21
n
27
PRO
21
A
CYS
22
n
28
CYS
22
A
LEU
23
n
29
LEU
23
A
ALA
24
n
30
ALA
24
A
THR
25
n
31
THR
25
A
PRO
26
n
32
PRO
26
A
LYS
27
n
33
LYS
27
A
ILE
28
n
34
ILE
28
A
ASP
29
n
35
ASP
29
A
GLY
30
n
36
GLY
30
A
ILE
31
n
37
ILE
31
A
ARG
32
n
38
ARG
32
A
SER
33
n
39
SER
33
A
VAL
34
n
40
VAL
34
A
LYS
35
n
41
LYS
35
A
GLN
36
n
42
GLN
36
A
THR
37
n
43
THR
37
A
GLN
38
n
44
GLN
38
A
MET
39
n
45
MET
39
A
LEU
40
n
46
LEU
40
A
SER
41
n
47
SER
41
A
ARG
42
n
48
ARG
42
A
THR
43
n
49
THR
43
A
PHE
44
n
50
PHE
44
A
LYS
45
n
51
LYS
45
A
PRO
46
n
52
PRO
46
A
ILE
47
n
53
ILE
47
A
ARG
48
n
54
ARG
48
A
ASN
49
n
55
ASN
49
A
SER
50
n
56
SER
50
A
VAL
51
n
57
VAL
51
A
MET
52
n
58
MET
52
A
ASN
53
n
59
ASN
53
A
ARG
54
n
60
ARG
54
A
LEU
55
n
61
LEU
55
A
LEU
56
n
62
LEU
56
A
THR
57
n
63
THR
57
A
GLU
58
n
64
GLU
58
A
LEU
59
n
65
LEU
59
A
LEU
60
n
66
LEU
60
A
PRO
61
n
67
PRO
61
A
GLU
62
n
68
GLU
62
A
GLY
63
n
69
GLY
63
A
SER
64
n
70
SER
64
A
ASP
65
n
71
ASP
65
A
GLY
66
n
72
GLY
66
A
GLU
67
n
73
GLU
67
A
ILE
68
n
74
ILE
68
A
SER
69
n
75
SER
69
A
ILE
70
n
76
ILE
70
A
GLU
71
n
77
GLU
71
A
GLY
72
n
78
GLY
72
A
ALA
73
n
79
ALA
73
A
THR
74
n
80
THR
74
A
PHE
75
n
81
PHE
75
A
GLN
76
n
82
GLN
76
A
ASP
77
n
83
ASP
77
A
THR
78
n
84
THR
78
A
THR
79
n
85
THR
79
A
SER
80
n
86
SER
80
A
ALA
81
n
87
ALA
81
A
VAL
82
n
88
VAL
82
A
MET
83
n
89
MET
83
A
THR
84
n
90
THR
84
A
GLY
85
n
91
GLY
85
A
HIS
86
n
92
HIS
86
A
LYS
87
n
93
LYS
87
A
MET
88
n
94
MET
88
A
TYR
89
n
95
TYR
89
A
ASN
90
n
96
ASN
90
A
ALA
91
n
97
ALA
91
A
LYS
92
n
98
LYS
92
A
PHE
93
n
99
PHE
93
A
SER
94
n
100
SER
94
A
TYR
95
n
101
TYR
95
A
TYR
96
n
102
TYR
96
A
TRP
97
n
103
TRP
97
A
PHE
98
n
104
PHE
98
A
ASP
99
n
105
ASP
99
A
TYR
100
n
106
TYR
100
A
VAL
101
n
107
VAL
101
A
THR
102
n
108
THR
102
A
ASP
103
n
109
ASP
103
A
ASP
104
n
110
ASP
104
A
PRO
105
n
111
PRO
105
A
LEU
106
n
112
LEU
106
A
LYS
107
n
113
LYS
107
A
LYS
108
n
114
LYS
108
A
TYR
109
n
115
TYR
109
A
ILE
110
n
116
ILE
110
A
ASP
111
n
117
ASP
111
A
ARG
112
n
118
ARG
112
A
VAL
113
n
119
VAL
113
A
GLU
114
n
120
GLU
114
A
ASP
115
n
121
ASP
115
A
MET
116
n
122
MET
116
A
LYS
117
n
123
LYS
117
A
ASN
118
n
124
ASN
118
A
TYR
119
n
125
TYR
119
A
ILE
120
n
126
ILE
120
A
THR
121
n
127
THR
121
A
VAL
122
n
128
VAL
122
A
HIS
123
n
129
HIS
123
A
PRO
124
n
130
PRO
124
A
HIS
125
n
131
HIS
125
A
ILE
126
n
132
ILE
126
A
LEU
127
n
133
LEU
127
A
GLU
128
n
134
GLU
128
A
HIS
129
n
135
HIS
129
A
ALA
130
n
136
ALA
130
A
GLN
131
n
137
GLN
131
A
VAL
132
n
138
VAL
132
A
LYS
133
n
139
LYS
133
A
ILE
134
n
140
ILE
134
A
ILE
135
n
141
ILE
135
A
PRO
136
n
142
PRO
136
A
LEU
137
n
143
LEU
137
A
ILE
138
n
144
ILE
138
A
PRO
139
n
145
PRO
139
A
VAL
140
n
146
VAL
140
A
GLU
141
n
147
GLU
141
A
ILE
142
n
148
ILE
142
A
ASN
143
n
149
ASN
143
A
ASN
144
n
150
ASN
144
A
ILE
145
n
151
ILE
145
A
THR
146
n
152
THR
146
A
GLU
147
n
153
GLU
147
A
LEU
148
n
154
LEU
148
A
LEU
149
n
155
LEU
149
A
GLN
150
n
156
GLN
150
A
TYR
151
n
157
TYR
151
A
GLU
152
n
158
GLU
152
A
ARG
153
n
159
ARG
153
A
ASP
154
n
160
ASP
154
A
VAL
155
n
161
VAL
155
A
LEU
156
n
162
LEU
156
A
SER
157
n
163
SER
157
A
LYS
158
n
164
LYS
158
A
GLY
159
n
165
GLY
159
A
PHE
160
n
166
PHE
160
A
GLU
161
n
167
GLU
161
A
GLY
162
n
168
GLY
162
A
VAL
163
n
169
VAL
163
A
MET
164
n
170
MET
164
A
ILE
165
n
171
ILE
165
A
ARG
166
n
172
ARG
166
A
LYS
167
n
173
LYS
167
A
PRO
168
n
174
PRO
168
A
ASP
169
n
175
ASP
169
A
GLY
170
n
176
GLY
170
A
LYS
171
n
177
LYS
171
A
TYR
172
n
178
TYR
172
A
LYS
173
n
179
LYS
173
A
PHE
174
n
180
PHE
174
A
GLY
175
n
181
GLY
175
A
ARG
176
n
182
ARG
176
A
SER
177
n
183
SER
177
A
THR
178
n
184
THR
178
A
LEU
179
n
185
LEU
179
A
LYS
180
n
186
LYS
180
A
GLU
181
n
187
GLU
181
A
GLY
182
n
188
GLY
182
A
ILE
183
n
189
ILE
183
A
LEU
184
n
190
LEU
184
A
LEU
185
n
191
LEU
185
A
LYS
186
n
192
LYS
186
A
MET
187
n
193
MET
187
A
LYS
188
n
194
LYS
188
A
GLN
189
n
195
GLN
189
A
PHE
190
n
196
PHE
190
A
LYS
191
n
197
LYS
191
A
ASP
192
n
198
ASP
192
A
ALA
193
n
199
ALA
193
A
GLU
194
n
200
GLU
194
A
ALA
195
n
201
ALA
195
A
THR
196
n
202
THR
196
A
ILE
197
n
203
ILE
197
A
ILE
198
n
204
ILE
198
A
SER
199
n
205
SER
199
A
MET
200
n
206
MET
200
A
THR
201
n
207
THR
201
A
ALA
202
n
208
ALA
202
A
LEU
203
n
209
LEU
203
A
PHE
204
n
210
PHE
204
A
LYS
205
n
211
LYS
205
A
ASN
206
n
212
ASN
206
A
n
213
207
A
n
214
208
A
n
215
209
A
n
216
210
A
n
217
211
A
n
218
212
A
n
219
213
A
n
220
214
A
PHE
215
n
221
PHE
215
A
GLY
216
n
222
GLY
216
A
TYR
217
n
223
TYR
217
A
n
224
218
A
n
225
219
A
n
226
220
A
n
227
221
A
n
228
222
A
n
229
223
A
n
230
224
A
n
231
225
A
n
232
226
A
n
233
227
A
n
234
228
A
n
235
229
A
GLU
230
n
236
GLU
230
A
ASP
231
n
237
ASP
231
A
VAL
232
n
238
VAL
232
A
MET
233
n
239
MET
233
A
GLY
234
n
240
GLY
234
A
SER
235
n
241
SER
235
A
ILE
236
n
242
ILE
236
A
GLU
237
n
243
GLU
237
A
VAL
238
n
244
VAL
238
A
ASP
239
n
245
ASP
239
A
TYR
240
n
246
TYR
240
A
ASP
241
n
247
ASP
241
A
GLY
242
n
248
GLY
242
A
VAL
243
n
249
VAL
243
A
VAL
244
n
250
VAL
244
A
PHE
245
n
251
PHE
245
A
SER
246
n
252
SER
246
A
ILE
247
n
253
ILE
247
A
GLY
248
n
254
GLY
248
A
THR
249
n
255
THR
249
A
GLY
250
n
256
GLY
250
A
PHE
251
n
257
PHE
251
A
ASP
252
n
258
ASP
252
A
ALA
253
n
259
ALA
253
A
ASP
254
n
260
ASP
254
A
GLN
255
n
261
GLN
255
A
ARG
256
n
262
ARG
256
A
ARG
257
n
263
ARG
257
A
ASP
258
n
264
ASP
258
A
PHE
259
n
265
PHE
259
A
TRP
260
n
266
TRP
260
A
GLN
261
n
267
GLN
261
A
ASN
262
n
268
ASN
262
A
LYS
263
n
269
LYS
263
A
GLU
264
n
270
GLU
264
A
SER
265
n
271
SER
265
A
TYR
266
n
272
TYR
266
A
ILE
267
n
273
ILE
267
A
GLY
268
n
274
GLY
268
A
LYS
269
n
275
LYS
269
A
MET
270
n
276
MET
270
A
VAL
271
n
277
VAL
271
A
LYS
272
n
278
LYS
272
A
PHE
273
n
279
PHE
273
A
LYS
274
n
280
LYS
274
A
TYR
275
n
281
TYR
275
A
PHE
276
n
282
PHE
276
A
GLU
277
n
283
GLU
277
A
MET
278
n
284
MET
278
A
GLY
279
n
285
GLY
279
A
SER
280
n
286
SER
280
A
LYS
281
n
287
LYS
281
A
ASP
282
n
288
ASP
282
A
CYS
283
n
289
CYS
283
A
PRO
284
n
290
PRO
284
A
ARG
285
n
291
ARG
285
A
PHE
286
n
292
PHE
286
A
PRO
287
n
293
PRO
287
A
VAL
288
n
294
VAL
288
A
PHE
289
n
295
PHE
289
A
ILE
290
n
296
ILE
290
A
GLY
291
n
297
GLY
291
A
ILE
292
n
298
ILE
292
A
ARG
293
n
299
ARG
293
A
HIS
294
n
300
HIS
294
A
GLU
295
n
301
GLU
295
A
GLU
296
n
302
GLU
296
A
ASP
297
n
303
ASP
297
A
n
304
298
A
6.0108
-1.5044
0.7806
6.4808
-2.3871
5.4027
-0.8240
-1.1999
0.5272
-0.1165
0.6578
0.3541
-0.1738
-0.0729
0.1662
0.2637
0.3207
-0.1545
0.7539
-0.2123
1.2859
refined
24.4950
24.2870
16.8470
X-RAY DIFFRACTION
14.3359
-0.0653
1.5716
12.4733
2.8119
2.1521
-1.4240
-2.5066
1.3985
0.2895
1.3903
-1.1622
-0.4620
0.2360
0.0337
0.3075
0.4999
-0.2999
0.9925
-0.2886
1.2510
refined
51.0980
8.5120
21.6960
X-RAY DIFFRACTION
A
2
A
8
A
188
A
194
X-RAY DIFFRACTION
1
A
301
B
1
A
301
B
1
X-RAY DIFFRACTION
1
A
215
A
221
A
217
A
223
X-RAY DIFFRACTION
1
A
311
C
1
A
325
C
2
X-RAY DIFFRACTION
1
A
189
A
195
A
206
A
212
X-RAY DIFFRACTION
2
A
230
A
236
A
297
A
303
X-RAY DIFFRACTION
2
author_defined_assembly
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
N
ALA
10
A
N
ALA
16
A
O
LYS
186
A
O
LYS
192
A
O
LEU
185
A
O
LEU
191
A
N
ILE
165
A
N
ILE
171
A
O
ARG
166
A
O
ARG
172
A
N
LEU
23
A
N
LEU
29
A
N
ALA
24
A
N
ALA
30
A
O
VAL
140
A
O
VAL
146
A
O
LEU
40
A
O
LEU
46
A
N
VAL
34
A
N
VAL
40
A
N
ILE
31
A
N
ILE
37
A
O
ILE
68
A
O
ILE
74
A
N
SER
69
A
N
SER
75
A
O
SER
94
A
O
SER
100
A
N
TYR
95
A
N
TYR
101
A
O
LYS
133
A
O
LYS
139
A
O
PHE
245
A
O
PHE
251
A
N
VAL
238
A
N
VAL
244
A
O
GLY
234
A
O
GLY
240
A
N
THR
201
A
N
THR
207
A
N
ALA
193
A
N
ALA
199
A
O
PHE
273
A
O
PHE
279
A
N
LYS
272
A
N
LYS
278
A
O
ILE
290
A
O
ILE
296
1
A
CG
LYS
87
A
CG
LYS
93
1
Y
1
A
CD
LYS
87
A
CD
LYS
93
1
Y
1
A
CE
LYS
87
A
CE
LYS
93
1
Y
1
A
NZ
LYS
87
A
NZ
LYS
93
1
Y
1
A
HIS
-5
A
HIS
1
1
Y
1
A
HIS
-4
A
HIS
2
1
Y
1
A
HIS
-3
A
HIS
3
1
Y
1
A
HIS
-2
A
HIS
4
1
Y
1
A
HIS
-1
A
HIS
5
1
Y
1
A
HIS
0
A
HIS
6
1
Y
1
A
MET
1
A
MET
7
1
Y
1
A
THR
207
A
THR
213
1
Y
1
A
ASN
208
A
ASN
214
1
Y
1
A
THR
209
A
THR
215
1
Y
1
A
LYS
210
A
LYS
216
1
Y
1
A
THR
211
A
THR
217
1
Y
1
A
LYS
212
A
LYS
218
1
Y
1
A
ASP
213
A
ASP
219
1
Y
1
A
ASN
214
A
ASN
220
1
Y
1
A
SER
218
A
SER
224
1
Y
1
A
LYS
219
A
LYS
225
1
Y
1
A
ARG
220
A
ARG
226
1
Y
1
A
SER
221
A
SER
227
1
Y
1
A
THR
222
A
THR
228
1
Y
1
A
HIS
223
A
HIS
229
1
Y
1
A
LYS
224
A
LYS
230
1
Y
1
A
SER
225
A
SER
231
1
Y
1
A
GLY
226
A
GLY
232
1
Y
1
A
LYS
227
A
LYS
233
1
Y
1
A
VAL
228
A
VAL
234
1
Y
1
A
GLU
229
A
GLU
235
1
Y
1
A
ARG
298
A
ARG
304
1
Y
1
A
A
OD2
OH
ASP
TYR
65
172
2.15
1
A
A
PHE
PRO
20
21
-132.08
1
5.52
0.90
118.30
123.82
A
A
A
CB
CG
OD2
ASP
ASP
ASP
17
17
17
N
1
6.20
0.90
118.30
124.50
A
A
A
CB
CG
OD2
ASP
ASP
ASP
104
104
104
N
1
6.69
0.90
118.30
124.99
A
A
A
CB
CG
OD2
ASP
ASP
ASP
192
192
192
N
1
5.55
0.90
118.30
123.85
A
A
A
CB
CG
OD2
ASP
ASP
ASP
241
241
241
N
1
5.57
0.90
118.30
123.87
A
A
A
CB
CG
OD2
ASP
ASP
ASP
282
282
282
N
1
5.77
0.90
118.30
124.07
A
A
A
CB
CG
OD2
ASP
ASP
ASP
297
297
297
N
1
A
GLU
16
-71.62
39.75
1
A
PHE
20
-84.81
-143.43
1
A
PRO
21
-13.12
57.18
1
A
ASP
29
-105.81
69.32
1
A
THR
37
51.70
-79.57
1
A
GLN
38
-100.74
-168.50
1
A
THR
57
-37.84
-29.59
1
A
LEU
59
-100.12
-65.79
1
A
ASN
90
-153.04
3.74
1
A
THR
102
69.85
-67.76
1
A
ASP
103
-158.97
-94.90
1
A
ILE
126
-26.08
-38.69
1
A
ILE
183
-71.93
-71.41
1
A
ILE
198
-151.13
-29.40
1
A
LEU
203
-53.15
-78.22
1
A
PHE
204
158.65
94.55
1
A
ASP
239
-74.14
-89.45
1
A
TYR
240
58.03
101.92
1
A
ASP
241
13.11
92.23
1
A
ALA
253
-59.93
-9.95
1
A
MET
278
-88.70
-125.69
1
A
SER
280
-64.44
65.74
1
A
CYS
283
-178.23
97.90
1
A
PHE
286
16.20
93.14
26.237
4.92
0.00
0.00
0.37
0.00
-5.30
0.911
0.876
0.30351
0.26299
0.26641
2.95
15.00
680
8265
7585
8.2
96.86
35.010
0.560
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
0.507
0.80
0.80
1.40
PDB ENTRY 1FVI
MAXIMUM LIKELIHOOD
MASK
2.95
15.00
2
2252
22
0
2228
0.013
0.022
2300
1.575
1.971
3099
7.828
5.000
273
38.004
24.340
106
23.032
15.000
420
14.840
15.000
12
0.128
0.200
339
0.005
0.020
1708
0.251
0.200
1044
0.213
0.200
77
0.289
0.200
35
0.202
0.200
3
0.414
1.500
1371
0.777
2.000
2226
1.153
3.000
929
1.924
4.500
873
0.406
0.405
3.024
55
529
20
26.2
2.95
15
1P8L
8265
8265
0
0.092
1
3.5
96.9
refinement
REFMAC
5.1.06
data reduction
CrystalClear
(MSC/RIGAKU)
data scaling
SCALEPACK
phasing
AMoRE
New Crystal Structure of Chlorella Virus DNA Ligase-Adenylate
1
N
N
2
N
N
3
N
N
A
ASN
49
A
ASN
55
HELX_P
A
LEU
60
A
LEU
66
1
1
12
A
GLN
76
A
GLN
82
HELX_P
A
MET
83
A
MET
89
1
2
8
A
LYS
108
A
LYS
114
HELX_P
A
HIS
123
A
HIS
129
1
3
16
A
PRO
124
A
PRO
130
HELX_P
A
GLU
128
A
GLU
134
5
4
5
A
ASN
144
A
ASN
150
HELX_P
A
LYS
158
A
LYS
164
1
5
15
A
GLN
255
A
GLN
261
HELX_P
A
TRP
260
A
TRP
266
1
6
6
covale
1.670
one
A
LYS
27
A
NZ
LYS
33
1_555
A
AMP
301
B
P
AMP
1_555
LIGASE
ligase
O41026_CHVP1
UNP
1
1
O41026
MAITKPLLAATLENIEDVQFPCLATPKIDGIRSVKQTQMLSRTFKPIRNSVMNRLLTELLPEGSDGEISIEGATFQDTTS
AVMTGHKMYNAKFSYYWFDYVTDDPLKKYIDRVEDMKNYITVHPHILEHAQVKIIPLIPVEINNITELLQYERDVLSKGF
EGVMIRKPDGKYKFGRSTLKEGILLKMKQFKDAEATIISMTALFKNTNTKTKDNFGYSKRSTHKSGKVEEDVMGSIEVDY
DGVVFSIGTGFDADQRRDFWQNKESYIGKMVKFKYFEMGSKDCPRFPVFIGIRHEEDR
1
298
1P8L
1
298
O41026
A
1
7
304
1
expression tag
HIS
-5
1P8L
A
O41026
UNP
1
1
expression tag
HIS
-4
1P8L
A
O41026
UNP
2
1
expression tag
HIS
-3
1P8L
A
O41026
UNP
3
1
expression tag
HIS
-2
1P8L
A
O41026
UNP
4
1
expression tag
HIS
-1
1P8L
A
O41026
UNP
5
1
expression tag
HIS
0
1P8L
A
O41026
UNP
6
5
5
5
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ALA
10
A
ALA
16
A
THR
11
A
THR
17
A
LEU
185
A
LEU
191
A
MET
187
A
MET
193
A
VAL
163
A
VAL
169
A
ARG
166
A
ARG
172
A
LEU
23
A
LEU
29
A
PRO
26
A
PRO
32
A
VAL
140
A
VAL
146
A
GLU
141
A
GLU
147
A
MET
39
A
MET
45
A
LEU
40
A
LEU
46
A
ILE
31
A
ILE
37
A
LYS
35
A
LYS
41
A
SER
64
A
SER
70
A
SER
69
A
SER
75
A
PHE
93
A
PHE
99
A
TYR
100
A
TYR
106
A
VAL
132
A
VAL
138
A
PRO
136
A
PRO
142
A
PHE
245
A
PHE
251
A
ILE
247
A
ILE
253
A
MET
233
A
MET
239
A
VAL
238
A
VAL
244
A
LYS
191
A
LYS
197
A
ALA
202
A
ALA
208
A
MET
270
A
MET
276
A
PHE
276
A
PHE
282
A
ARG
285
A
ARG
291
A
ILE
292
A
ILE
298
BINDING SITE FOR RESIDUE AMP A 301
A
AMP
301
Software
11
A
THR
25
A
THR
31
11
1_555
A
PRO
26
A
PRO
32
11
1_555
A
LYS
27
A
LYS
33
11
1_555
A
ILE
28
A
ILE
34
11
1_555
A
ASP
29
A
ASP
35
11
1_555
A
ARG
32
A
ARG
38
11
1_555
A
GLU
67
A
GLU
73
11
1_555
A
PHE
98
A
PHE
104
11
1_555
A
MET
164
A
MET
170
11
1_555
A
LEU
184
A
LEU
190
11
1_555
A
LYS
186
A
LYS
192
11
1_555
18
P 21 21 2