0.006684
0.000000
0.000000
0.000000
0.006684
0.000000
0.000000
0.000000
0.006684
0.00000
0.00000
0.00000
Armstrong, S.R.
Cook, W.J.
Short, S.A.
Ealick, S.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
48
90.00
90.00
90.00
149.600
149.600
149.600
C10 H14 N2 O5
242.229
2'-deoxy-1-methyl-pseudouridine
5-METHYL-2'-DEOXYPSEUDOURIDINE
DNA linking
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
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
O
N
2
N
C
N
3
R
C
N
4
N
O
N
5
R
C
N
6
N
C
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
O
N
13
N
N
N
14
N
C
N
15
S
C
N
16
N
O
N
17
N
C
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
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
N
N
33
S
C
N
34
N
C
N
35
N
O
N
36
N
C
N
37
N
O
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
N
N
46
S
C
N
47
N
C
N
48
N
O
N
49
N
C
N
50
N
C
N
51
N
C
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
N
N
56
N
O
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
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
N
N
73
S
C
N
74
N
C
N
75
N
O
N
76
N
C
N
77
N
C
N
78
N
O
N
79
N
N
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
O
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
N
N
106
S
C
N
107
N
C
N
108
N
O
N
109
N
C
N
110
N
C
N
111
N
C
N
112
N
O
N
113
N
N
N
114
N
O
N
115
N
H
N
116
N
H
N
117
N
H
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
O
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
N
N
145
N
C
N
146
N
C
N
147
N
O
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
N
N
155
S
C
N
156
N
C
N
157
N
O
N
158
N
C
Y
159
N
C
Y
160
N
N
Y
161
N
C
Y
162
N
C
Y
163
N
N
N
164
N
O
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
O
N
176
N
H
N
177
N
H
N
178
N
N
N
179
S
C
N
180
N
C
N
181
N
O
N
182
S
C
N
183
N
C
N
184
N
C
N
185
N
C
N
186
N
O
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
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
N
N
201
S
C
N
202
N
C
N
203
N
O
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
O
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
H
N
221
N
H
N
222
N
N
N
223
S
C
N
224
N
C
N
225
N
O
N
226
N
C
N
227
N
C
N
228
N
C
N
229
N
C
N
230
N
N
N
231
N
O
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
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
N
252
N
C
N
253
N
S
N
254
N
C
N
255
N
O
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
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
N
278
N
O
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
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
C
N
296
N
C
N
297
N
O
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
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
R
C
N
326
N
O
N
327
N
C
N
328
N
O
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
N
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
N
376
N
O
N
377
N
O
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
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
N
N
390
S
C
N
391
N
C
N
392
N
O
N
393
N
C
N
394
N
C
N
395
N
C
N
396
N
O
N
397
N
H
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
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
sing
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
doub
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
doub
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
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
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
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
N
83
N
sing
N
84
N
sing
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
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
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
sing
N
116
N
doub
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
doub
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
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
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
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
Y
159
N
sing
Y
160
N
doub
Y
161
N
doub
N
162
N
sing
Y
163
N
sing
N
164
N
sing
Y
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
doub
N
178
N
sing
N
179
N
sing
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
doub
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
sing
N
219
N
doub
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
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
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
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
Y
267
N
doub
Y
268
N
sing
Y
269
N
sing
N
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
273
N
doub
N
274
N
sing
Y
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
sing
N
284
N
sing
N
285
N
doub
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
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
sing
N
301
N
sing
N
302
N
doub
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
doub
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
sing
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
doub
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
Y
336
N
doub
Y
337
N
sing
Y
338
N
sing
N
339
N
sing
Y
340
N
doub
Y
341
N
sing
Y
342
N
sing
N
343
N
sing
Y
344
N
sing
Y
345
N
doub
N
346
N
sing
Y
347
N
doub
N
348
N
sing
Y
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
doub
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
Y
364
N
doub
Y
365
N
sing
Y
366
N
sing
N
367
N
sing
Y
368
N
doub
N
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
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
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
doub
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
UK
Structure
STRUE6
2005
0969-2126
4
97
107
10.1016/S0969-2126(96)00013-5
8805514
Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
1996
10.2210/pdb1f8y/pdb
pdb_00001f8y
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
296
1
AREA DETECTOR
1992-01-01
SDMS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
18098.354
NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
2.4.2.6
2
nat
polymer
242.229
2'-deoxy-1-methyl-pseudouridine
2
syn
non-polymer
18.015
water
76
nat
water
no
no
MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND
IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY
MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND
IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Lactobacillus
sample
28039
Lactobacillus leichmannii
1
3.85
68.07
VAPOR DIFFUSION, HANGING DROP
5.4
Ammonium Sulfate, Citrate Buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
296
chem_comp
chem_comp_atom
chem_comp_bond
database_2
entity
pdbx_entity_nonpoly
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Structure summary
1
0
2000-08-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_chem_comp.name
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1F8X contains the same protein in the uncomplexed form.
RCSB
Y
RCSB
2000-07-05
REL
5MD
2'-deoxy-1-methyl-pseudouridine
HOH
water
5MD
1
2
5MD
5MD
158
A
5MD
2
2
5MD
5MD
2
B
HOH
801
3
HOH
HOH
801
A
HOH
803
3
HOH
HOH
803
A
HOH
804
3
HOH
HOH
804
A
HOH
806
3
HOH
HOH
806
A
HOH
807
3
HOH
HOH
807
A
HOH
808
3
HOH
HOH
808
A
HOH
809
3
HOH
HOH
809
A
HOH
810
3
HOH
HOH
810
A
HOH
811
3
HOH
HOH
811
A
HOH
812
3
HOH
HOH
812
A
HOH
813
3
HOH
HOH
813
A
HOH
814
3
HOH
HOH
814
A
HOH
816
3
HOH
HOH
816
A
HOH
817
3
HOH
HOH
817
A
HOH
818
3
HOH
HOH
818
A
HOH
819
3
HOH
HOH
819
A
HOH
820
3
HOH
HOH
820
A
HOH
821
3
HOH
HOH
821
A
HOH
822
3
HOH
HOH
822
A
HOH
823
3
HOH
HOH
823
A
HOH
824
3
HOH
HOH
824
A
HOH
825
3
HOH
HOH
825
A
HOH
827
3
HOH
HOH
827
A
HOH
836
3
HOH
HOH
836
A
HOH
839
3
HOH
HOH
839
A
HOH
841
3
HOH
HOH
841
A
HOH
842
3
HOH
HOH
842
A
HOH
843
3
HOH
HOH
843
A
HOH
844
3
HOH
HOH
844
A
HOH
848
3
HOH
HOH
848
A
HOH
849
3
HOH
HOH
849
A
HOH
850
3
HOH
HOH
850
A
HOH
852
3
HOH
HOH
852
A
HOH
853
3
HOH
HOH
853
A
HOH
855
3
HOH
HOH
855
A
HOH
856
3
HOH
HOH
856
A
HOH
857
3
HOH
HOH
857
A
HOH
858
3
HOH
HOH
858
A
HOH
859
3
HOH
HOH
859
A
HOH
860
3
HOH
HOH
860
A
HOH
867
3
HOH
HOH
867
A
HOH
868
3
HOH
HOH
868
A
HOH
869
3
HOH
HOH
869
A
HOH
870
3
HOH
HOH
870
A
HOH
874
3
HOH
HOH
874
A
HOH
875
3
HOH
HOH
875
A
HOH
876
3
HOH
HOH
876
A
HOH
802
3
HOH
HOH
802
B
HOH
805
3
HOH
HOH
805
B
HOH
815
3
HOH
HOH
815
B
HOH
826
3
HOH
HOH
826
B
HOH
828
3
HOH
HOH
828
B
HOH
829
3
HOH
HOH
829
B
HOH
830
3
HOH
HOH
830
B
HOH
831
3
HOH
HOH
831
B
HOH
832
3
HOH
HOH
832
B
HOH
833
3
HOH
HOH
833
B
HOH
834
3
HOH
HOH
834
B
HOH
835
3
HOH
HOH
835
B
HOH
837
3
HOH
HOH
837
B
HOH
838
3
HOH
HOH
838
B
HOH
840
3
HOH
HOH
840
B
HOH
845
3
HOH
HOH
845
B
HOH
846
3
HOH
HOH
846
B
HOH
847
3
HOH
HOH
847
B
HOH
851
3
HOH
HOH
851
B
HOH
854
3
HOH
HOH
854
B
HOH
861
3
HOH
HOH
861
B
HOH
862
3
HOH
HOH
862
B
HOH
863
3
HOH
HOH
863
B
HOH
864
3
HOH
HOH
864
B
HOH
865
3
HOH
HOH
865
B
HOH
866
3
HOH
HOH
866
B
HOH
871
3
HOH
HOH
871
B
HOH
872
3
HOH
HOH
872
B
HOH
873
3
HOH
HOH
873
B
n
1
1
A
PRO
2
n
2
PRO
2
A
LYS
3
n
3
LYS
3
A
LYS
4
n
4
LYS
4
A
THR
5
n
5
THR
5
A
ILE
6
n
6
ILE
6
A
TYR
7
n
7
TYR
7
A
PHE
8
n
8
PHE
8
A
GLY
9
n
9
GLY
9
A
ALA
10
n
10
ALA
10
A
GLY
11
n
11
GLY
11
A
TRP
12
n
12
TRP
12
A
PHE
13
n
13
PHE
13
A
THR
14
n
14
THR
14
A
ASP
15
n
15
ASP
15
A
ARG
16
n
16
ARG
16
A
GLN
17
n
17
GLN
17
A
ASN
18
n
18
ASN
18
A
LYS
19
n
19
LYS
19
A
ALA
20
n
20
ALA
20
A
TYR
21
n
21
TYR
21
A
LYS
22
n
22
LYS
22
A
GLU
23
n
23
GLU
23
A
ALA
24
n
24
ALA
24
A
MET
25
n
25
MET
25
A
GLU
26
n
26
GLU
26
A
ALA
27
n
27
ALA
27
A
LEU
28
n
28
LEU
28
A
LYS
29
n
29
LYS
29
A
GLU
30
n
30
GLU
30
A
ASN
31
n
31
ASN
31
A
PRO
32
n
32
PRO
32
A
THR
33
n
33
THR
33
A
ILE
34
n
34
ILE
34
A
ASP
35
n
35
ASP
35
A
LEU
36
n
36
LEU
36
A
GLU
37
n
37
GLU
37
A
ASN
38
n
38
ASN
38
A
SER
39
n
39
SER
39
A
TYR
40
n
40
TYR
40
A
VAL
41
n
41
VAL
41
A
PRO
42
n
42
PRO
42
A
LEU
43
n
43
LEU
43
A
ASP
44
n
44
ASP
44
A
ASN
45
n
45
ASN
45
A
GLN
46
n
46
GLN
46
A
TYR
47
n
47
TYR
47
A
LYS
48
n
48
LYS
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
ARG
51
n
51
ARG
51
A
VAL
52
n
52
VAL
52
A
ASP
53
n
53
ASP
53
A
GLU
54
n
54
GLU
54
A
HIS
55
n
55
HIS
55
A
PRO
56
n
56
PRO
56
A
GLU
57
n
57
GLU
57
A
TYR
58
n
58
TYR
58
A
LEU
59
n
59
LEU
59
A
HIS
60
n
60
HIS
60
A
ASP
61
n
61
ASP
61
A
LYS
62
n
62
LYS
62
A
VAL
63
n
63
VAL
63
A
TRP
64
n
64
TRP
64
A
ALA
65
n
65
ALA
65
A
THR
66
n
66
THR
66
A
ALA
67
n
67
ALA
67
A
THR
68
n
68
THR
68
A
TYR
69
n
69
TYR
69
A
ASN
70
n
70
ASN
70
A
ASN
71
n
71
ASN
71
A
ASP
72
n
72
ASP
72
A
LEU
73
n
73
LEU
73
A
ASN
74
n
74
ASN
74
A
GLY
75
n
75
GLY
75
A
ILE
76
n
76
ILE
76
A
LYS
77
n
77
LYS
77
A
THR
78
n
78
THR
78
A
ASN
79
n
79
ASN
79
A
ASP
80
n
80
ASP
80
A
ILE
81
n
81
ILE
81
A
MET
82
n
82
MET
82
A
LEU
83
n
83
LEU
83
A
GLY
84
n
84
GLY
84
A
VAL
85
n
85
VAL
85
A
TYR
86
n
86
TYR
86
A
ILE
87
n
87
ILE
87
A
PRO
88
n
88
PRO
88
A
ASP
89
n
89
ASP
89
A
GLU
90
n
90
GLU
90
A
GLU
91
n
91
GLU
91
A
ASP
92
n
92
ASP
92
A
VAL
93
n
93
VAL
93
A
GLY
94
n
94
GLY
94
A
LEU
95
n
95
LEU
95
A
GLY
96
n
96
GLY
96
A
MET
97
n
97
MET
97
A
GLU
98
n
98
GLU
98
A
LEU
99
n
99
LEU
99
A
GLY
100
n
100
GLY
100
A
TYR
101
n
101
TYR
101
A
ALA
102
n
102
ALA
102
A
LEU
103
n
103
LEU
103
A
SER
104
n
104
SER
104
A
GLN
105
n
105
GLN
105
A
GLY
106
n
106
GLY
106
A
LYS
107
n
107
LYS
107
A
TYR
108
n
108
TYR
108
A
VAL
109
n
109
VAL
109
A
LEU
110
n
110
LEU
110
A
LEU
111
n
111
LEU
111
A
VAL
112
n
112
VAL
112
A
ILE
113
n
113
ILE
113
A
PRO
114
n
114
PRO
114
A
ASP
115
n
115
ASP
115
A
GLU
116
n
116
GLU
116
A
ASP
117
n
117
ASP
117
A
TYR
118
n
118
TYR
118
A
GLY
119
n
119
GLY
119
A
LYS
120
n
120
LYS
120
A
PRO
121
n
121
PRO
121
A
ILE
122
n
122
ILE
122
A
ASN
123
n
123
ASN
123
A
LEU
124
n
124
LEU
124
A
MET
125
n
125
MET
125
A
SER
126
n
126
SER
126
A
TRP
127
n
127
TRP
127
A
GLY
128
n
128
GLY
128
A
VAL
129
n
129
VAL
129
A
SER
130
n
130
SER
130
A
ASP
131
n
131
ASP
131
A
ASN
132
n
132
ASN
132
A
VAL
133
n
133
VAL
133
A
ILE
134
n
134
ILE
134
A
LYS
135
n
135
LYS
135
A
MET
136
n
136
MET
136
A
SER
137
n
137
SER
137
A
GLN
138
n
138
GLN
138
A
LEU
139
n
139
LEU
139
A
LYS
140
n
140
LYS
140
A
ASP
141
n
141
ASP
141
A
PHE
142
n
142
PHE
142
A
ASN
143
n
143
ASN
143
A
PHE
144
n
144
PHE
144
A
ASN
145
n
145
ASN
145
A
LYS
146
n
146
LYS
146
A
PRO
147
n
147
PRO
147
A
ARG
148
n
148
ARG
148
A
PHE
149
n
149
PHE
149
A
ASP
150
n
150
ASP
150
A
PHE
151
n
151
PHE
151
A
TYR
152
n
152
TYR
152
A
GLU
153
n
153
GLU
153
A
GLY
154
n
154
GLY
154
A
ALA
155
n
155
ALA
155
A
VAL
156
n
156
VAL
156
A
TYR
157
n
157
TYR
157
A
n
1
201
B
PRO
202
n
2
PRO
202
B
LYS
203
n
3
LYS
203
B
LYS
204
n
4
LYS
204
B
THR
205
n
5
THR
205
B
ILE
206
n
6
ILE
206
B
TYR
207
n
7
TYR
207
B
PHE
208
n
8
PHE
208
B
GLY
209
n
9
GLY
209
B
ALA
210
n
10
ALA
210
B
GLY
211
n
11
GLY
211
B
TRP
212
n
12
TRP
212
B
PHE
213
n
13
PHE
213
B
THR
214
n
14
THR
214
B
ASP
215
n
15
ASP
215
B
ARG
216
n
16
ARG
216
B
GLN
217
n
17
GLN
217
B
ASN
218
n
18
ASN
218
B
LYS
219
n
19
LYS
219
B
ALA
220
n
20
ALA
220
B
TYR
221
n
21
TYR
221
B
LYS
222
n
22
LYS
222
B
GLU
223
n
23
GLU
223
B
ALA
224
n
24
ALA
224
B
MET
225
n
25
MET
225
B
GLU
226
n
26
GLU
226
B
ALA
227
n
27
ALA
227
B
LEU
228
n
28
LEU
228
B
LYS
229
n
29
LYS
229
B
GLU
230
n
30
GLU
230
B
ASN
231
n
31
ASN
231
B
PRO
232
n
32
PRO
232
B
THR
233
n
33
THR
233
B
ILE
234
n
34
ILE
234
B
ASP
235
n
35
ASP
235
B
LEU
236
n
36
LEU
236
B
GLU
237
n
37
GLU
237
B
ASN
238
n
38
ASN
238
B
SER
239
n
39
SER
239
B
TYR
240
n
40
TYR
240
B
VAL
241
n
41
VAL
241
B
PRO
242
n
42
PRO
242
B
LEU
243
n
43
LEU
243
B
ASP
244
n
44
ASP
244
B
ASN
245
n
45
ASN
245
B
GLN
246
n
46
GLN
246
B
TYR
247
n
47
TYR
247
B
LYS
248
n
48
LYS
248
B
GLY
249
n
49
GLY
249
B
ILE
250
n
50
ILE
250
B
ARG
251
n
51
ARG
251
B
VAL
252
n
52
VAL
252
B
ASP
253
n
53
ASP
253
B
GLU
254
n
54
GLU
254
B
HIS
255
n
55
HIS
255
B
PRO
256
n
56
PRO
256
B
GLU
257
n
57
GLU
257
B
TYR
258
n
58
TYR
258
B
LEU
259
n
59
LEU
259
B
HIS
260
n
60
HIS
260
B
ASP
261
n
61
ASP
261
B
LYS
262
n
62
LYS
262
B
VAL
263
n
63
VAL
263
B
TRP
264
n
64
TRP
264
B
ALA
265
n
65
ALA
265
B
THR
266
n
66
THR
266
B
ALA
267
n
67
ALA
267
B
THR
268
n
68
THR
268
B
TYR
269
n
69
TYR
269
B
ASN
270
n
70
ASN
270
B
ASN
271
n
71
ASN
271
B
ASP
272
n
72
ASP
272
B
LEU
273
n
73
LEU
273
B
ASN
274
n
74
ASN
274
B
GLY
275
n
75
GLY
275
B
ILE
276
n
76
ILE
276
B
LYS
277
n
77
LYS
277
B
THR
278
n
78
THR
278
B
ASN
279
n
79
ASN
279
B
ASP
280
n
80
ASP
280
B
ILE
281
n
81
ILE
281
B
MET
282
n
82
MET
282
B
LEU
283
n
83
LEU
283
B
GLY
284
n
84
GLY
284
B
VAL
285
n
85
VAL
285
B
TYR
286
n
86
TYR
286
B
ILE
287
n
87
ILE
287
B
PRO
288
n
88
PRO
288
B
ASP
289
n
89
ASP
289
B
GLU
290
n
90
GLU
290
B
GLU
291
n
91
GLU
291
B
ASP
292
n
92
ASP
292
B
VAL
293
n
93
VAL
293
B
GLY
294
n
94
GLY
294
B
LEU
295
n
95
LEU
295
B
GLY
296
n
96
GLY
296
B
MET
297
n
97
MET
297
B
GLU
298
n
98
GLU
298
B
LEU
299
n
99
LEU
299
B
GLY
300
n
100
GLY
300
B
TYR
301
n
101
TYR
301
B
ALA
302
n
102
ALA
302
B
LEU
303
n
103
LEU
303
B
SER
304
n
104
SER
304
B
GLN
305
n
105
GLN
305
B
GLY
306
n
106
GLY
306
B
LYS
307
n
107
LYS
307
B
TYR
308
n
108
TYR
308
B
VAL
309
n
109
VAL
309
B
LEU
310
n
110
LEU
310
B
LEU
311
n
111
LEU
311
B
VAL
312
n
112
VAL
312
B
ILE
313
n
113
ILE
313
B
PRO
314
n
114
PRO
314
B
ASP
315
n
115
ASP
315
B
GLU
316
n
116
GLU
316
B
ASP
317
n
117
ASP
317
B
TYR
318
n
118
TYR
318
B
GLY
319
n
119
GLY
319
B
LYS
320
n
120
LYS
320
B
PRO
321
n
121
PRO
321
B
ILE
322
n
122
ILE
322
B
ASN
323
n
123
ASN
323
B
LEU
324
n
124
LEU
324
B
MET
325
n
125
MET
325
B
SER
326
n
126
SER
326
B
TRP
327
n
127
TRP
327
B
GLY
328
n
128
GLY
328
B
VAL
329
n
129
VAL
329
B
SER
330
n
130
SER
330
B
ASP
331
n
131
ASP
331
B
ASN
332
n
132
ASN
332
B
VAL
333
n
133
VAL
333
B
ILE
334
n
134
ILE
334
B
LYS
335
n
135
LYS
335
B
MET
336
n
136
MET
336
B
SER
337
n
137
SER
337
B
GLN
338
n
138
GLN
338
B
LEU
339
n
139
LEU
339
B
LYS
340
n
140
LYS
340
B
ASP
341
n
141
ASP
341
B
PHE
342
n
142
PHE
342
B
ASN
343
n
143
ASN
343
B
PHE
344
n
144
PHE
344
B
ASN
345
n
145
ASN
345
B
LYS
346
n
146
LYS
346
B
PRO
347
n
147
PRO
347
B
ARG
348
n
148
ARG
348
B
PHE
349
n
149
PHE
349
B
ASP
350
n
150
ASP
350
B
PHE
351
n
151
PHE
351
B
TYR
352
n
152
TYR
352
B
GLU
353
n
153
GLU
353
B
GLY
354
n
154
GLY
354
B
ALA
355
n
155
ALA
355
B
VAL
356
n
156
VAL
356
B
TYR
357
n
157
TYR
357
B
author_defined_assembly
6
hexameric
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
0.0000000000
0.0000000000
1.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
6_555
z+1/2,-x+1/2,-y
crystal symmetry operation
74.8000000000
74.8000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
1.0000000000
0.0000000000
0.0000000000
12_554
-y+1/2,-z,x-1/2
crystal symmetry operation
74.8000000000
0.0000000000
-74.8000000000
A
N
TYR
7
A
N
TYR
7
A
O
ILE
81
A
O
ILE
81
A
N
MET
82
A
N
MET
82
A
O
TYR
108
A
O
TYR
108
A
N
LEU
111
A
N
LEU
111
A
O
ASN
132
A
O
ASN
132
B
N
TYR
207
B
N
TYR
7
B
O
ILE
281
B
O
ILE
81
B
N
MET
282
B
N
MET
82
B
O
TYR
308
B
O
TYR
108
B
N
LEU
311
B
N
LEU
111
B
O
ASN
332
B
O
ASN
132
1
A
MET
1
A
MET
1
1
Y
1
B
MET
201
B
MET
1
1
Y
1
A
TRP
12
-146.41
40.46
1
B
TRP
212
-152.05
33.87
1
B
HIS
255
-155.65
72.19
1
B
PRO
256
-52.98
-7.26
1
B
ASN
332
-173.70
147.27
0.218
0.16
0.16
2.40
5.00
1792
17921
17921
RANDOM
1
2.000
0
Engh & Huber
2.40
5.00
76
2646
34
0
2536
.008
1.56
2.4
100
1F8Y
21897
21897
0
0
0.075
1
4.6
93
model building
X-PLOR
refinement
X-PLOR
data reduction
SDMS
data scaling
SDMS
phasing
X-PLOR
CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
The biological assembly is a hexamer. Each pair of monomers is related by a noncrystallographic twofold symmetry axis.
A
THR
14
A
THR
14
HELX_P
A
ASN
31
A
ASN
31
1
1
18
A
VAL
41
A
VAL
41
HELX_P
A
ASN
45
A
ASN
45
5
2
5
A
GLN
46
A
GLN
46
HELX_P
A
ILE
50
A
ILE
50
5
3
5
A
HIS
55
A
HIS
55
HELX_P
A
HIS
60
A
HIS
60
5
4
6
A
ASP
61
A
ASP
61
HELX_P
A
THR
78
A
THR
78
1
5
18
A
ILE
87
A
ILE
87
HELX_P
A
GLU
91
A
GLU
91
5
6
5
A
ASP
92
A
ASP
92
HELX_P
A
GLN
105
A
GLN
105
1
7
14
A
PRO
114
A
PRO
114
HELX_P
A
TYR
118
A
TYR
118
5
8
5
A
ASN
123
A
ASN
123
HELX_P
A
SER
130
A
SER
130
1
9
8
A
SER
137
A
SER
137
HELX_P
A
LEU
139
A
LEU
139
5
10
3
B
THR
214
B
THR
14
HELX_P
B
ASN
231
B
ASN
31
1
11
18
B
VAL
241
B
VAL
41
HELX_P
B
ASN
245
B
ASN
45
5
12
5
B
GLN
246
B
GLN
46
HELX_P
B
ILE
250
B
ILE
50
5
13
5
B
ARG
251
B
ARG
51
HELX_P
B
HIS
255
B
HIS
55
5
14
5
B
HIS
255
B
HIS
55
HELX_P
B
HIS
260
B
HIS
60
5
15
6
B
ASP
261
B
ASP
61
HELX_P
B
THR
278
B
THR
78
1
16
18
B
ASP
292
B
ASP
92
HELX_P
B
GLN
305
B
GLN
105
1
17
14
B
ASN
323
B
ASN
123
HELX_P
B
SER
330
B
SER
130
1
18
8
B
SER
337
B
SER
137
HELX_P
B
LEU
339
B
LEU
139
5
19
3
TRANSFERASE
active site, alpha/beta protein, biocatalyst, nucleoside, TRANSFERASE
NTD_LACLE
UNP
1
1
Q9R5V5
MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND
IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY
1
157
1F8Y
1
157
Q9R5V5
A
1
1
157
1
157
1F8Y
201
357
Q9R5V5
B
1
1
157
4
4
parallel
parallel
parallel
parallel
parallel
parallel
A
ILE
6
A
ILE
6
A
GLY
9
A
GLY
9
A
ILE
81
A
ILE
81
A
VAL
85
A
VAL
85
A
TYR
108
A
TYR
108
A
ILE
113
A
ILE
113
A
ASN
132
A
ASN
132
A
LYS
135
A
LYS
135
B
ILE
206
B
ILE
6
B
GLY
209
B
GLY
9
B
ILE
281
B
ILE
81
B
VAL
285
B
VAL
85
B
TYR
308
B
TYR
108
B
ILE
313
B
ILE
113
B
ASN
332
B
ASN
132
B
LYS
335
B
LYS
135
BINDING SITE FOR RESIDUE 5MD A 158
A
5MD
158
Software
12
BINDING SITE FOR RESIDUE 5MD B 2
B
5MD
2
Software
11
A
TYR
7
A
TYR
7
12
1_555
A
GLY
9
A
GLY
9
12
1_555
A
ALA
10
A
ALA
10
12
1_555
A
TRP
12
A
TRP
12
12
1_555
A
PHE
13
A
PHE
13
12
1_555
A
GLN
46
A
GLN
46
12
1_555
A
ASP
72
A
ASP
72
12
1_555
A
ASP
92
A
ASP
92
12
1_555
A
GLY
94
A
GLY
94
12
1_555
A
GLU
98
A
GLU
98
12
1_555
B
ASN
323
B
ASN
123
12
1_555
B
TYR
357
B
TYR
157
12
1_555
A
ASN
123
A
ASN
123
11
1_555
A
MET
125
A
MET
125
11
1_555
A
TYR
157
A
TYR
157
11
1_555
B
TYR
207
B
TYR
7
11
1_555
B
GLY
209
B
GLY
9
11
1_555
B
TRP
212
B
TRP
12
11
1_555
B
PRO
242
B
PRO
42
11
1_555
B
GLN
246
B
GLN
46
11
1_555
B
ASP
272
B
ASP
72
11
1_555
B
ASP
292
B
ASP
92
11
1_555
B
GLU
298
B
GLU
98
11
1_555
199
I 21 3