0.008114
0.004685
0.000000
0.000000
0.009369
0.000000
0.000000
0.000000
0.022297
0.00000
0.00000
0.00000
Imamura, K.
Wallace, S.
Doublie, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
123.241
123.241
44.849
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
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
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
C
N
124
N
O
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
O
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
S
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
O
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
R
C
N
314
N
O
N
315
N
C
N
316
N
O
N
317
N
H
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
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
N
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
N
364
N
O
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
N
N
378
S
C
N
379
N
C
N
380
N
O
N
381
N
C
N
382
N
C
N
383
N
C
N
384
N
O
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
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
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
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
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
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
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
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
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
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
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
doub
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
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
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
sing
N
335
N
sing
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
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
doub
N
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
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
284
26174
26183
10.1074/jbc.M109.021907
19625256
Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA
2009
10.2210/pdb3a42/pdb
pdb_00003a42
100
1
IMAGE PLATE
2006-10-11
MARRESEARCH
MAR mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
34582.352
Formamidopyrimidine-DNA glycosylase
3.2.2.23
1
man
polymer
92.094
GLYCEROL
3
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
82
nat
water
Fapy-DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase, AP lyase, Endonuclease VIII MvNei1
no
no
MPEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWN
TFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVAL
LMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPN
IHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLEHHHHHH
MPEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWN
TFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVAL
LMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPN
IHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLEHHHHHH
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
APMV
sample
L315, MIMI_L315
212035
Acanthamoeba polyphaga mimivirus
562
Escherichia coli
Rosetta(DE3)pLys
plasmid
pET22b
1
2.84
56.74
VAPOR DIFFUSION, HANGING DROP
6.3
PEG2000MME, ammonium sulfate, pH6.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K
285
software
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Non-polymer description
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
1
0
2009-07-21
1
1
2011-07-13
1
2
2017-10-11
1
3
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PDBJ
Y
PDBJ
2009-06-30
REL
REL
GOL
GLYCEROL
SO4
SULFATE ION
HOH
water
GOL
401
2
GOL
GOL
401
A
GOL
402
2
GOL
GOL
402
A
GOL
403
2
GOL
GOL
403
A
SO4
504
3
SO4
SO4
504
A
HOH
1
4
HOH
HOH
296
A
HOH
2
4
HOH
HOH
297
A
HOH
3
4
HOH
HOH
298
A
HOH
4
4
HOH
HOH
299
A
HOH
5
4
HOH
HOH
300
A
HOH
6
4
HOH
HOH
301
A
HOH
7
4
HOH
HOH
302
A
HOH
8
4
HOH
HOH
303
A
HOH
9
4
HOH
HOH
304
A
HOH
10
4
HOH
HOH
305
A
HOH
11
4
HOH
HOH
306
A
HOH
12
4
HOH
HOH
307
A
HOH
13
4
HOH
HOH
308
A
HOH
14
4
HOH
HOH
309
A
HOH
15
4
HOH
HOH
310
A
HOH
16
4
HOH
HOH
311
A
HOH
17
4
HOH
HOH
312
A
HOH
18
4
HOH
HOH
313
A
HOH
19
4
HOH
HOH
314
A
HOH
20
4
HOH
HOH
315
A
HOH
21
4
HOH
HOH
316
A
HOH
22
4
HOH
HOH
317
A
HOH
23
4
HOH
HOH
318
A
HOH
24
4
HOH
HOH
319
A
HOH
25
4
HOH
HOH
320
A
HOH
26
4
HOH
HOH
321
A
HOH
27
4
HOH
HOH
322
A
HOH
28
4
HOH
HOH
323
A
HOH
29
4
HOH
HOH
324
A
HOH
30
4
HOH
HOH
325
A
HOH
31
4
HOH
HOH
326
A
HOH
32
4
HOH
HOH
327
A
HOH
33
4
HOH
HOH
328
A
HOH
34
4
HOH
HOH
329
A
HOH
35
4
HOH
HOH
330
A
HOH
36
4
HOH
HOH
331
A
HOH
37
4
HOH
HOH
332
A
HOH
38
4
HOH
HOH
333
A
HOH
39
4
HOH
HOH
334
A
HOH
40
4
HOH
HOH
335
A
HOH
41
4
HOH
HOH
336
A
HOH
42
4
HOH
HOH
337
A
HOH
43
4
HOH
HOH
338
A
HOH
44
4
HOH
HOH
339
A
HOH
45
4
HOH
HOH
340
A
HOH
46
4
HOH
HOH
341
A
HOH
47
4
HOH
HOH
342
A
HOH
48
4
HOH
HOH
343
A
HOH
49
4
HOH
HOH
344
A
HOH
50
4
HOH
HOH
345
A
HOH
51
4
HOH
HOH
346
A
HOH
52
4
HOH
HOH
347
A
HOH
53
4
HOH
HOH
348
A
HOH
54
4
HOH
HOH
349
A
HOH
55
4
HOH
HOH
350
A
HOH
56
4
HOH
HOH
351
A
HOH
57
4
HOH
HOH
352
A
HOH
58
4
HOH
HOH
353
A
HOH
59
4
HOH
HOH
354
A
HOH
60
4
HOH
HOH
355
A
HOH
61
4
HOH
HOH
356
A
HOH
62
4
HOH
HOH
357
A
HOH
63
4
HOH
HOH
358
A
HOH
64
4
HOH
HOH
359
A
HOH
65
4
HOH
HOH
360
A
HOH
66
4
HOH
HOH
361
A
HOH
67
4
HOH
HOH
362
A
HOH
68
4
HOH
HOH
363
A
HOH
69
4
HOH
HOH
364
A
HOH
70
4
HOH
HOH
365
A
HOH
71
4
HOH
HOH
366
A
HOH
72
4
HOH
HOH
367
A
HOH
73
4
HOH
HOH
368
A
HOH
74
4
HOH
HOH
369
A
HOH
75
4
HOH
HOH
370
A
HOH
76
4
HOH
HOH
371
A
HOH
77
4
HOH
HOH
372
A
HOH
78
4
HOH
HOH
373
A
HOH
79
4
HOH
HOH
374
A
HOH
80
4
HOH
HOH
375
A
HOH
81
4
HOH
HOH
376
A
HOH
82
4
HOH
HOH
377
A
n
1
1
A
PRO
2
n
2
PRO
2
A
GLU
3
n
3
GLU
3
A
GLY
4
n
4
GLY
4
A
PRO
5
n
5
PRO
5
A
GLU
6
n
6
GLU
6
A
VAL
7
n
7
VAL
7
A
ALA
8
n
8
ALA
8
A
LEU
9
n
9
LEU
9
A
THR
10
n
10
THR
10
A
ALA
11
n
11
ALA
11
A
ASP
12
n
12
ASP
12
A
ILE
13
n
13
ILE
13
A
LEU
14
n
14
LEU
14
A
GLU
15
n
15
GLU
15
A
LYS
16
n
16
LYS
16
A
TYR
17
n
17
TYR
17
A
PHE
18
n
18
PHE
18
A
LYS
19
n
19
LYS
19
A
GLY
20
n
20
GLY
20
A
LYS
21
n
21
LYS
21
A
THR
22
n
22
THR
22
A
LEU
23
n
23
LEU
23
A
GLU
24
n
24
GLU
24
A
TYR
25
n
25
TYR
25
A
ILE
26
n
26
ILE
26
A
ASP
27
n
27
ASP
27
A
PHE
28
n
28
PHE
28
A
ILE
29
n
29
ILE
29
A
SER
30
n
30
SER
30
A
GLY
31
n
31
GLY
31
A
ARG
32
n
32
ARG
32
A
TYR
33
n
33
TYR
33
A
SER
34
n
34
SER
34
A
LYS
35
n
35
LYS
35
A
SER
36
n
36
SER
36
A
GLU
37
n
37
GLU
37
A
PRO
38
n
38
PRO
38
A
GLU
39
n
39
GLU
39
A
GLY
40
n
40
GLY
40
A
TYR
41
n
41
TYR
41
A
ASP
42
n
42
ASP
42
A
ASP
43
n
43
ASP
43
A
PHE
44
n
44
PHE
44
A
ILE
45
n
45
ILE
45
A
ALA
46
n
46
ALA
46
A
ASN
47
n
47
ASN
47
A
LEU
48
n
48
LEU
48
A
PRO
49
n
49
PRO
49
A
LEU
50
n
50
LEU
50
A
LYS
51
n
51
LYS
51
A
VAL
52
n
52
VAL
52
A
SER
53
n
53
SER
53
A
ASN
54
n
54
ASN
54
A
VAL
55
n
55
VAL
55
A
ASP
56
n
56
ASP
56
A
THR
57
n
57
THR
57
A
LYS
58
n
58
LYS
58
A
GLY
59
n
59
GLY
59
A
LYS
60
n
60
LYS
60
A
PHE
61
n
61
PHE
61
A
LEU
62
n
62
LEU
62
A
TRP
63
n
63
TRP
63
A
PHE
64
n
64
PHE
64
A
GLU
65
n
65
GLU
65
A
LEU
66
n
66
LEU
66
A
PHE
67
n
67
PHE
67
A
ASP
68
n
68
ASP
68
A
PRO
69
n
69
PRO
69
A
ASN
70
n
70
ASN
70
A
ASP
71
n
71
ASP
71
A
LYS
72
n
72
LYS
72
A
SER
73
n
73
SER
73
A
ASN
74
n
74
ASN
74
A
LYS
75
n
75
LYS
75
A
TRP
76
n
76
TRP
76
A
TYR
77
n
77
TYR
77
A
ILE
78
n
78
ILE
78
A
TRP
79
n
79
TRP
79
A
ASN
80
n
80
ASN
80
A
THR
81
n
81
THR
81
A
PHE
82
n
82
PHE
82
A
GLY
83
n
83
GLY
83
A
LEU
84
n
84
LEU
84
A
THR
85
n
85
THR
85
A
GLY
86
n
86
GLY
86
A
MET
87
n
87
MET
87
A
TRP
88
n
88
TRP
88
A
SER
89
n
89
SER
89
A
LEU
90
n
90
LEU
90
A
PHE
91
n
91
PHE
91
A
GLU
92
n
92
GLU
92
A
ALA
93
n
93
ALA
93
A
LYS
94
n
94
LYS
94
A
TYR
95
n
95
TYR
95
A
THR
96
n
96
THR
96
A
ARG
97
n
97
ARG
97
A
ALA
98
n
98
ALA
98
A
VAL
99
n
99
VAL
99
A
LEU
100
n
100
LEU
100
A
SER
101
n
101
SER
101
A
PHE
102
n
102
PHE
102
A
ASP
103
n
103
ASP
103
A
ASN
104
n
104
ASN
104
A
GLU
105
n
105
GLU
105
A
LEU
106
n
106
LEU
106
A
MET
107
n
107
MET
107
A
ALA
108
n
108
ALA
108
A
TYR
109
n
109
TYR
109
A
PHE
110
n
110
PHE
110
A
SER
111
n
111
SER
111
A
ASP
112
n
112
ASP
112
A
MET
113
n
113
MET
113
A
ARG
114
n
114
ARG
114
A
ASN
115
n
115
ASN
115
A
PHE
116
n
116
PHE
116
A
GLY
117
n
117
GLY
117
A
THR
118
n
118
THR
118
A
PHE
119
n
119
PHE
119
A
LYS
120
n
120
LYS
120
A
PHE
121
n
121
PHE
121
A
SER
122
n
122
SER
122
A
ASN
123
n
123
ASN
123
A
SER
124
n
124
SER
124
A
GLU
125
n
125
GLU
125
A
LYS
126
n
126
LYS
126
A
GLU
127
n
127
GLU
127
A
LEU
128
n
128
LEU
128
A
LYS
129
n
129
LYS
129
A
ARG
130
n
130
ARG
130
A
LYS
131
n
131
LYS
131
A
LEU
132
n
132
LEU
132
A
ASN
133
n
133
ASN
133
A
GLU
134
n
134
GLU
134
A
LEU
135
n
135
LEU
135
A
GLY
136
n
136
GLY
136
A
PRO
137
n
137
PRO
137
A
ASP
138
n
138
ASP
138
A
PHE
139
n
139
PHE
139
A
LEU
140
n
140
LEU
140
A
LYS
141
n
141
LYS
141
A
ASN
142
n
142
ASN
142
A
ASP
143
n
143
ASP
143
A
ASP
144
n
144
ASP
144
A
ILE
145
n
145
ILE
145
A
ASP
146
n
146
ASP
146
A
ILE
147
n
147
ILE
147
A
SER
148
n
148
SER
148
A
LYS
149
n
149
LYS
149
A
ILE
150
n
150
ILE
150
A
LYS
151
n
151
LYS
151
A
LYS
152
n
152
LYS
152
A
TYR
153
n
153
TYR
153
A
LYS
154
n
154
LYS
154
A
GLN
155
n
155
GLN
155
A
PRO
156
n
156
PRO
156
A
ILE
157
n
157
ILE
157
A
VAL
158
n
158
VAL
158
A
ALA
159
n
159
ALA
159
A
LEU
160
n
160
LEU
160
A
LEU
161
n
161
LEU
161
A
MET
162
n
162
MET
162
A
ASP
163
n
163
ASP
163
A
GLN
164
n
164
GLN
164
A
LYS
165
n
165
LYS
165
A
LYS
166
n
166
LYS
166
A
ILE
167
n
167
ILE
167
A
GLY
168
n
168
GLY
168
A
SER
169
n
169
SER
169
A
GLY
170
n
170
GLY
170
A
LEU
171
n
171
LEU
171
A
GLY
172
n
172
GLY
172
A
ASN
173
n
173
ASN
173
A
TYR
174
n
174
TYR
174
A
LEU
175
n
175
LEU
175
A
VAL
176
n
176
VAL
176
A
ALA
177
n
177
ALA
177
A
GLU
178
n
178
GLU
178
A
ILE
179
n
179
ILE
179
A
LEU
180
n
180
LEU
180
A
TYR
181
n
181
TYR
181
A
ARG
182
n
182
ARG
182
A
ALA
183
n
183
ALA
183
A
LYS
184
n
184
LYS
184
A
ILE
185
n
185
ILE
185
A
ASP
186
n
186
ASP
186
A
PRO
187
n
187
PRO
187
A
HIS
188
n
188
HIS
188
A
LYS
189
n
189
LYS
189
A
LEU
190
n
190
LEU
190
A
GLY
191
n
191
GLY
191
A
SER
192
n
192
SER
192
A
ASN
193
n
193
ASN
193
A
LEU
194
n
194
LEU
194
A
THR
195
n
195
THR
195
A
ASP
196
n
196
ASP
196
A
GLN
197
n
197
GLN
197
A
GLU
198
n
198
GLU
198
A
ILE
199
n
199
ILE
199
A
GLU
200
n
200
GLU
200
A
ASN
201
n
201
ASN
201
A
LEU
202
n
202
LEU
202
A
TRP
203
n
203
TRP
203
A
TYR
204
n
204
TYR
204
A
TRP
205
n
205
TRP
205
A
ILE
206
n
206
ILE
206
A
LYS
207
n
207
LYS
207
A
TYR
208
n
208
TYR
208
A
GLU
209
n
209
GLU
209
A
THR
210
n
210
THR
210
A
LYS
211
n
211
LYS
211
A
LEU
212
n
212
LEU
212
A
ALA
213
n
213
ALA
213
A
TYR
214
n
214
TYR
214
A
ASP
215
n
215
ASP
215
A
SER
216
n
216
SER
216
A
ASN
217
n
217
ASN
217
A
HIS
218
n
218
HIS
218
A
ILE
219
n
219
ILE
219
A
GLY
220
n
220
GLY
220
A
TYR
221
n
221
TYR
221
A
MET
222
n
222
MET
222
A
VAL
223
n
223
VAL
223
A
ASN
224
n
224
ASN
224
A
LEU
225
n
225
LEU
225
A
GLU
226
n
226
GLU
226
A
ASN
227
n
227
ASN
227
A
GLU
228
n
228
GLU
228
A
SER
229
n
229
SER
229
A
SER
230
n
230
SER
230
A
LYS
231
n
231
LYS
231
A
ILE
232
n
232
ILE
232
A
GLY
233
n
233
GLY
233
A
ARG
234
n
234
ARG
234
A
LYS
235
n
235
LYS
235
A
ASN
236
n
236
ASN
236
A
TYR
237
n
237
TYR
237
A
HIS
238
n
238
HIS
238
A
PRO
239
n
239
PRO
239
A
ASN
240
n
240
ASN
240
A
ILE
241
n
241
ILE
241
A
HIS
242
n
242
HIS
242
A
PRO
243
n
243
PRO
243
A
THR
244
n
244
THR
244
A
GLU
245
n
245
GLU
245
A
LYS
246
n
246
LYS
246
A
GLU
247
n
247
GLU
247
A
PHE
248
n
248
PHE
248
A
ASP
249
n
249
ASP
249
A
PHE
250
n
250
PHE
250
A
LEU
251
n
251
LEU
251
A
VAL
252
n
252
VAL
252
A
TYR
253
n
253
TYR
253
A
ARG
254
n
254
ARG
254
A
LYS
255
n
255
LYS
255
A
LYS
256
n
256
LYS
256
A
LYS
257
n
257
LYS
257
A
ASP
258
n
258
ASP
258
A
PRO
259
n
259
PRO
259
A
ASN
260
n
260
ASN
260
A
GLY
261
n
261
GLY
261
A
ASN
262
n
262
ASN
262
A
LYS
263
n
263
LYS
263
A
VAL
264
n
264
VAL
264
A
ILE
265
n
265
ILE
265
A
ALA
266
n
266
ALA
266
A
ASP
267
n
267
ASP
267
A
LYS
268
n
268
LYS
268
A
ILE
269
n
269
ILE
269
A
ILE
270
n
270
ILE
270
A
n
271
271
A
n
272
272
A
n
273
273
A
n
274
274
A
n
275
275
A
n
276
276
A
ARG
277
n
277
ARG
277
A
THR
278
n
278
THR
278
A
THR
279
n
279
THR
279
A
TYR
280
n
280
TYR
280
A
TRP
281
n
281
TRP
281
A
ALA
282
n
282
ALA
282
A
PRO
283
n
283
PRO
283
A
ALA
284
n
284
ALA
284
A
ILE
285
n
285
ILE
285
A
GLN
286
n
286
GLN
286
A
LYS
287
n
287
LYS
287
A
LEU
288
n
288
LEU
288
A
GLU
289
n
289
GLU
289
A
n
290
290
A
n
291
291
A
n
292
292
A
n
293
293
A
n
294
294
A
n
295
295
A
author_and_software_defined_assembly
PISA
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
SER
89
A
N
SER
89
A
O
TYR
109
A
O
TYR
109
A
O
ALA
108
A
O
ALA
108
A
N
LEU
100
A
N
LEU
100
A
O
SER
101
A
O
SER
101
A
N
TYR
25
A
N
TYR
25
A
N
LEU
23
A
N
LEU
23
A
O
LEU
50
A
O
LEU
50
A
N
SER
53
A
N
SER
53
A
O
GLU
65
A
O
GLU
65
A
N
LEU
66
A
N
LEU
66
A
O
TRP
76
A
O
TRP
76
A
N
TRP
79
A
N
TRP
79
A
O
LYS
120
A
O
LYS
120
1
A
MET
1
A
MET
1
1
Y
1
A
GLY
271
A
GLY
271
1
Y
1
A
SER
272
A
SER
272
1
Y
1
A
GLY
273
A
GLY
273
1
Y
1
A
LYS
274
A
LYS
274
1
Y
1
A
ASN
275
A
ASN
275
1
Y
1
A
LYS
276
A
LYS
276
1
Y
1
A
HIS
290
A
HIS
290
1
Y
1
A
HIS
291
A
HIS
291
1
Y
1
A
HIS
292
A
HIS
292
1
Y
1
A
HIS
293
A
HIS
293
1
Y
1
A
HIS
294
A
HIS
294
1
Y
1
A
HIS
295
A
HIS
295
1
Y
1
A
GLU
37
-38.86
156.34
1
A
LYS
72
-66.74
0.31
1
A
ASP
112
-165.23
79.71
1
A
LYS
120
-170.42
133.51
1
A
ASP
144
-153.81
48.26
1
A
ASP
146
-105.31
79.37
1
A
LYS
149
-59.47
3.17
1
A
LYS
154
-92.92
49.45
1
A
MET
222
81.23
-2.06
1
A
PRO
239
-59.68
-1.83
1
A
ASN
260
-66.20
10.46
1
A
ALA
266
-90.80
49.88
protein_rep.param
protein.top
dna-rna_rep.param
dna-rna.top
water_rep.param
water.top
ion.param
ion.top
gol_xplor_param
gol_xplor_top
106.95
54.731
21.32
0.653
0.000
0.000
0.653
0.000
-1.307
0.268
0.209
2.600
15.000
1256
12144
10.300
99.900
1.00
0.80
random
1
0.00
MIR
Engh & Huber
49.071
0.43
0.33
5.00
0.49
0.39
2.600
15.000
82
2442
23
0
2337
0.007
1.335
1.510
1.500
1.876
2.000
2.618
2.000
2.953
2.500
0.393
0.031
0.326
2.72
1507
99.9
66.5
2.6
15
3A42
12173
0.059
1
44.4
11.8
100
0.27
2.60
2.69
4.8
1209
1
100
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
program
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
phasing
Tom Terwilliger
terwilliger@LANL.gov
http://www.solve.lanl.gov/
SOLVE
program
phasing
Thomas C. Terwilliger
terwilliger@lanl.gov
http://www.solve.lanl.gov/
RESOLVE
program
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns-online.org/
CNS
package
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
MAR345dtb
Crystal structure of MvNei1
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
GLU
3
A
GLU
3
HELX_P
A
LYS
19
A
LYS
19
1
1
17
A
GLY
31
A
GLY
31
HELX_P
A
SER
36
A
SER
36
1
2
6
A
GLY
40
A
GLY
40
HELX_P
A
ALA
46
A
ALA
46
1
3
7
A
GLU
125
A
GLU
125
HELX_P
A
ASN
133
A
ASN
133
1
4
9
A
ASP
146
A
ASP
146
HELX_P
A
LYS
151
A
LYS
151
5
5
6
A
PRO
156
A
PRO
156
HELX_P
A
ASP
163
A
ASP
163
1
6
8
A
GLY
172
A
GLY
172
HELX_P
A
LYS
184
A
LYS
184
1
7
13
A
LEU
190
A
LEU
190
HELX_P
A
LEU
194
A
LEU
194
5
8
5
A
THR
195
A
THR
195
HELX_P
A
SER
216
A
SER
216
1
9
22
A
MET
222
A
MET
222
HELX_P
A
ASN
224
A
ASN
224
5
10
3
A
LEU
225
A
LEU
225
HELX_P
A
SER
230
A
SER
230
1
11
6
HYDROLASE
helix two turns helix, zinc-less finger, HYDROLASE, DNA damage, DNA repair, DNA-binding, Glycosidase, Lyase, Multifunctional enzyme
A
LEU
48
A
LEU
48
1
A
PRO
49
A
PRO
49
0.40
FPG_MIMIV
UNP
1
1
Q5UQ00
MPEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWN
TFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVAL
LMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPN
IHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQK
1
287
3A42
1
287
Q5UQ00
A
1
1
287
1
expression tag
LEU
288
3A42
A
Q5UQ00
UNP
288
1
expression tag
GLU
289
3A42
A
Q5UQ00
UNP
289
1
expression tag
HIS
290
3A42
A
Q5UQ00
UNP
290
1
expression tag
HIS
291
3A42
A
Q5UQ00
UNP
291
1
expression tag
HIS
292
3A42
A
Q5UQ00
UNP
292
1
expression tag
HIS
293
3A42
A
Q5UQ00
UNP
293
1
expression tag
HIS
294
3A42
A
Q5UQ00
UNP
294
1
expression tag
HIS
295
3A42
A
Q5UQ00
UNP
295
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
86
A
GLY
86
A
SER
89
A
SER
89
A
MET
107
A
MET
107
A
ASP
112
A
ASP
112
A
THR
96
A
THR
96
A
PHE
102
A
PHE
102
A
THR
22
A
THR
22
A
PHE
28
A
PHE
28
A
LEU
50
A
LEU
50
A
LYS
58
A
LYS
58
A
PHE
61
A
PHE
61
A
PHE
67
A
PHE
67
A
LYS
75
A
LYS
75
A
THR
81
A
THR
81
A
THR
118
A
THR
118
A
SER
122
A
SER
122
BINDING SITE FOR RESIDUE GOL A 401
A
GOL
401
Software
5
BINDING SITE FOR RESIDUE GOL A 402
A
GOL
402
Software
3
BINDING SITE FOR RESIDUE GOL A 403
A
GOL
403
Software
3
BINDING SITE FOR RESIDUE SO4 A 504
A
SO4
504
Software
5
A
LYS
16
A
LYS
16
5
1_555
A
TYR
17
A
TYR
17
5
1_555
A
LYS
94
A
LYS
94
5
4_664
A
TYR
95
A
TYR
95
5
4_664
A
LYS
231
A
LYS
231
5
1_555
A
SER
124
A
SER
124
3
1_555
A
GLU
125
A
GLU
125
3
1_555
A
LYS
126
A
LYS
126
3
1_555
A
ASN
201
A
ASN
201
3
1_555
A
TYR
204
A
TYR
204
3
1_555
A
TRP
205
A
TRP
205
3
1_555
A
TRP
79
A
TRP
79
5
1_555
A
LYS
120
A
LYS
120
5
1_555
A
ARG
130
A
ARG
130
5
1_555
A
LYS
131
A
LYS
131
5
1_555
A
HOH
341
F
HOH
5
1_555
170
P 65