0.024510
0.000000
0.000000
0.000000
0.024510
0.000000
0.000000
0.000000
0.006031
0.00000
0.00000
0.00000
Lim, K.
Zhang, H.
Tempczyk, A.
Bonander, N.
Toedt, J.
Howard, A.
Eisenstein, E.
Herzberg, O.
Structure 2 Function Project (S2F)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90
90
90
40.8
40.8
165.8
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
I -1
126.904
IODIDE ION
non-polymer
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
C14 H20 N6 O5 S
384.411
n
S-ADENOSYL-L-HOMOCYSTEINE
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
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
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
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
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
I
N
184
N
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
O
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
H
N
206
N
N
N
207
S
C
N
208
N
C
N
209
N
O
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
N
N
215
N
O
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
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
S
N
238
N
C
N
239
N
O
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
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
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
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
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
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
C
N
295
N
S
N
296
N
C
N
297
N
O
N
298
N
O
N
299
N
C
N
300
S
C
N
301
N
O
N
302
S
C
N
303
N
O
N
304
R
C
N
305
N
O
N
306
R
C
Y
307
N
N
Y
308
N
C
Y
309
N
N
Y
310
N
C
Y
311
N
C
N
312
N
N
Y
313
N
N
Y
314
N
C
Y
315
N
N
Y
316
N
C
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
H
N
327
N
H
N
328
N
H
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
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
N
C
N
342
N
O
N
343
N
O
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
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
R
C
N
356
N
O
N
357
N
C
N
358
N
O
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
H
N
366
N
H
N
367
N
H
N
368
N
N
N
369
S
C
N
370
N
C
N
371
N
O
N
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
N
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
Y
381
N
C
N
382
N
O
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
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
N
N
396
S
C
N
397
N
C
N
398
N
O
N
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
N
406
N
O
N
407
N
O
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
N
424
N
C
N
425
N
C
N
426
N
O
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
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
sing
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
doub
N
98
N
sing
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
doub
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
sing
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
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
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
Y
310
N
sing
Y
311
N
sing
Y
312
N
doub
N
313
N
sing
Y
314
N
sing
Y
315
N
sing
Y
316
N
doub
N
317
N
sing
Y
318
N
doub
N
319
N
sing
N
320
N
sing
Y
321
N
sing
Y
322
N
doub
N
323
N
sing
Y
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
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
N
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
sing
N
360
N
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
Y
365
N
doub
Y
366
N
sing
Y
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
sing
Y
374
N
doub
N
375
N
sing
Y
376
N
doub
N
377
N
sing
Y
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
doub
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
Y
393
N
doub
Y
394
N
sing
Y
395
N
sing
N
396
N
sing
Y
397
N
doub
N
398
N
sing
Y
399
N
doub
N
400
N
sing
Y
401
N
sing
N
402
N
sing
N
403
N
sing
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
doub
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
US
Proteins
PSFGEY
0867
0887-3585
51
56
67
10.1002/prot.10323
12596263
Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a Cofactor Bound at a Site Formed by a Knot
2003
10.2210/pdb1mxi/pdb
pdb_00001mxi
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
CCD
2001-10-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.00
1.0
17-ID
APS
1.00
SYNCHROTRON
APS BEAMLINE 17-ID
18427.414
Hypothetical tRNA/rRNA methyltransferase HI0766
2.1.1.-
1
man
polymer
126.904
IODIDE ION
1
syn
non-polymer
384.411
S-ADENOSYL-L-HOMOCYSTEINE
1
syn
non-polymer
18.015
water
153
nat
water
yibK
no
no
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT
KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT
KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK
A
HI0766
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
Haemophilus
Escherichia
Escherichia coli
sample
HI0766
727
Haemophilus influenzae
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
PET17B
1
1.87
34.27
Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH
4.6
20% PMME 2000, 0.1 M sodium acetate, 0.2 M ammonium acetate, 3 % ethylene glycol, pH 4.6, Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH, temperature 298K
298
Structure 2 Function Project
S2F
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-02-25
1
1
2008-04-28
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1J85 IS YibK methyltransferase from Haemophilius influenzae (HI0766), apo-methyltransferase with a knot-containing fold
Y
RCSB
Y
RCSB
2002-10-02
REL
REL
IOD
IODIDE ION
SAH
S-ADENOSYL-L-HOMOCYSTEINE
HOH
water
1J85
PDB 1j85
PDB
experimental model
I1
2001
2
IOD
IOD
2001
A
SAH
302
3
SAH
SAH
302
A
WAT
1001
4
HOH
HOH
1001
A
WAT
1002
4
HOH
HOH
1002
A
WAT
1003
4
HOH
HOH
1003
A
WAT
1004
4
HOH
HOH
1004
A
WAT
1005
4
HOH
HOH
1005
A
WAT
1006
4
HOH
HOH
1006
A
WAT
1007
4
HOH
HOH
1007
A
WAT
1008
4
HOH
HOH
1008
A
WAT
1009
4
HOH
HOH
1009
A
WAT
1010
4
HOH
HOH
1010
A
WAT
1011
4
HOH
HOH
1011
A
WAT
1012
4
HOH
HOH
1012
A
WAT
1013
4
HOH
HOH
1013
A
WAT
1014
4
HOH
HOH
1014
A
WAT
1015
4
HOH
HOH
1015
A
WAT
1016
4
HOH
HOH
1016
A
WAT
1017
4
HOH
HOH
1017
A
WAT
1018
4
HOH
HOH
1018
A
WAT
1019
4
HOH
HOH
1019
A
WAT
1020
4
HOH
HOH
1020
A
WAT
1021
4
HOH
HOH
1021
A
WAT
1022
4
HOH
HOH
1022
A
WAT
1023
4
HOH
HOH
1023
A
WAT
1024
4
HOH
HOH
1024
A
WAT
1025
4
HOH
HOH
1025
A
WAT
1026
4
HOH
HOH
1026
A
WAT
1027
4
HOH
HOH
1027
A
WAT
1028
4
HOH
HOH
1028
A
WAT
1029
4
HOH
HOH
1029
A
WAT
1030
4
HOH
HOH
1030
A
WAT
1031
4
HOH
HOH
1031
A
WAT
1032
4
HOH
HOH
1032
A
WAT
1033
4
HOH
HOH
1033
A
WAT
1034
4
HOH
HOH
1034
A
WAT
1035
4
HOH
HOH
1035
A
WAT
1036
4
HOH
HOH
1036
A
WAT
1037
4
HOH
HOH
1037
A
WAT
1038
4
HOH
HOH
1038
A
WAT
1039
4
HOH
HOH
1039
A
WAT
1040
4
HOH
HOH
1040
A
WAT
1041
4
HOH
HOH
1041
A
WAT
1042
4
HOH
HOH
1042
A
WAT
1043
4
HOH
HOH
1043
A
WAT
1044
4
HOH
HOH
1044
A
WAT
1045
4
HOH
HOH
1045
A
WAT
1046
4
HOH
HOH
1046
A
WAT
1047
4
HOH
HOH
1047
A
WAT
1048
4
HOH
HOH
1048
A
WAT
1049
4
HOH
HOH
1049
A
WAT
1050
4
HOH
HOH
1050
A
WAT
1051
4
HOH
HOH
1051
A
WAT
1052
4
HOH
HOH
1052
A
WAT
1053
4
HOH
HOH
1053
A
WAT
1054
4
HOH
HOH
1054
A
WAT
1055
4
HOH
HOH
1055
A
WAT
1056
4
HOH
HOH
1056
A
WAT
1057
4
HOH
HOH
1057
A
WAT
1058
4
HOH
HOH
1058
A
WAT
1059
4
HOH
HOH
1059
A
WAT
1060
4
HOH
HOH
1060
A
WAT
1061
4
HOH
HOH
1061
A
WAT
1062
4
HOH
HOH
1062
A
WAT
1063
4
HOH
HOH
1063
A
WAT
1064
4
HOH
HOH
1064
A
WAT
1065
4
HOH
HOH
1065
A
WAT
1066
4
HOH
HOH
1066
A
WAT
1067
4
HOH
HOH
1067
A
WAT
1068
4
HOH
HOH
1068
A
WAT
1069
4
HOH
HOH
1069
A
WAT
1070
4
HOH
HOH
1070
A
WAT
1071
4
HOH
HOH
1071
A
WAT
1072
4
HOH
HOH
1072
A
WAT
1073
4
HOH
HOH
1073
A
WAT
1074
4
HOH
HOH
1074
A
WAT
1075
4
HOH
HOH
1075
A
WAT
1076
4
HOH
HOH
1076
A
WAT
1077
4
HOH
HOH
1077
A
WAT
1078
4
HOH
HOH
1078
A
WAT
1079
4
HOH
HOH
1079
A
WAT
1080
4
HOH
HOH
1080
A
WAT
1081
4
HOH
HOH
1081
A
WAT
1082
4
HOH
HOH
1082
A
WAT
1083
4
HOH
HOH
1083
A
WAT
1084
4
HOH
HOH
1084
A
WAT
1085
4
HOH
HOH
1085
A
WAT
1086
4
HOH
HOH
1086
A
WAT
1087
4
HOH
HOH
1087
A
WAT
1088
4
HOH
HOH
1088
A
WAT
1089
4
HOH
HOH
1089
A
WAT
1090
4
HOH
HOH
1090
A
WAT
1091
4
HOH
HOH
1091
A
WAT
1092
4
HOH
HOH
1092
A
WAT
1093
4
HOH
HOH
1093
A
WAT
1094
4
HOH
HOH
1094
A
WAT
1095
4
HOH
HOH
1095
A
WAT
1096
4
HOH
HOH
1096
A
WAT
1097
4
HOH
HOH
1097
A
WAT
1098
4
HOH
HOH
1098
A
WAT
1099
4
HOH
HOH
1099
A
WAT
1100
4
HOH
HOH
1100
A
WAT
1101
4
HOH
HOH
1101
A
WAT
1102
4
HOH
HOH
1102
A
WAT
1103
4
HOH
HOH
1103
A
WAT
1104
4
HOH
HOH
1104
A
WAT
1105
4
HOH
HOH
1105
A
WAT
1106
4
HOH
HOH
1106
A
WAT
1107
4
HOH
HOH
1107
A
WAT
1108
4
HOH
HOH
1108
A
WAT
1109
4
HOH
HOH
1109
A
WAT
1110
4
HOH
HOH
1110
A
WAT
1111
4
HOH
HOH
1111
A
WAT
1112
4
HOH
HOH
1112
A
WAT
1113
4
HOH
HOH
1113
A
WAT
1114
4
HOH
HOH
1114
A
WAT
1115
4
HOH
HOH
1115
A
WAT
1116
4
HOH
HOH
1116
A
WAT
1117
4
HOH
HOH
1117
A
WAT
1118
4
HOH
HOH
1118
A
WAT
1119
4
HOH
HOH
1119
A
WAT
1120
4
HOH
HOH
1120
A
WAT
1121
4
HOH
HOH
1121
A
WAT
1122
4
HOH
HOH
1122
A
WAT
1123
4
HOH
HOH
1123
A
WAT
1124
4
HOH
HOH
1124
A
WAT
1125
4
HOH
HOH
1125
A
WAT
1126
4
HOH
HOH
1126
A
WAT
1127
4
HOH
HOH
1127
A
WAT
1128
4
HOH
HOH
1128
A
WAT
1129
4
HOH
HOH
1129
A
WAT
1130
4
HOH
HOH
1130
A
WAT
1131
4
HOH
HOH
1131
A
WAT
1132
4
HOH
HOH
1132
A
WAT
1133
4
HOH
HOH
1133
A
WAT
1134
4
HOH
HOH
1134
A
WAT
1135
4
HOH
HOH
1135
A
WAT
1136
4
HOH
HOH
1136
A
WAT
1137
4
HOH
HOH
1137
A
WAT
1138
4
HOH
HOH
1138
A
WAT
1139
4
HOH
HOH
1139
A
WAT
1140
4
HOH
HOH
1140
A
WAT
1141
4
HOH
HOH
1141
A
WAT
1142
4
HOH
HOH
1142
A
WAT
1143
4
HOH
HOH
1143
A
WAT
1144
4
HOH
HOH
1144
A
WAT
1145
4
HOH
HOH
1145
A
WAT
1146
4
HOH
HOH
1146
A
WAT
1147
4
HOH
HOH
1147
A
WAT
1148
4
HOH
HOH
1148
A
WAT
1149
4
HOH
HOH
1149
A
WAT
1150
4
HOH
HOH
1150
A
WAT
1151
4
HOH
HOH
1151
A
WAT
1152
4
HOH
HOH
1152
A
WAT
1153
4
HOH
HOH
1153
A
MET
1
n
1
MET
1
A
LEU
2
n
2
LEU
2
A
ASP
3
n
3
ASP
3
A
ILE
4
n
4
ILE
4
A
VAL
5
n
5
VAL
5
A
LEU
6
n
6
LEU
6
A
TYR
7
n
7
TYR
7
A
GLU
8
n
8
GLU
8
A
PRO
9
n
9
PRO
9
A
GLU
10
n
10
GLU
10
A
ILE
11
n
11
ILE
11
A
PRO
12
n
12
PRO
12
A
GLN
13
n
13
GLN
13
A
ASN
14
n
14
ASN
14
A
THR
15
n
15
THR
15
A
GLY
16
n
16
GLY
16
A
ASN
17
n
17
ASN
17
A
ILE
18
n
18
ILE
18
A
ILE
19
n
19
ILE
19
A
ARG
20
n
20
ARG
20
A
LEU
21
n
21
LEU
21
A
CYS
22
n
22
CYS
22
A
ALA
23
n
23
ALA
23
A
ASN
24
n
24
ASN
24
A
THR
25
n
25
THR
25
A
GLY
26
n
26
GLY
26
A
PHE
27
n
27
PHE
27
A
ARG
28
n
28
ARG
28
A
LEU
29
n
29
LEU
29
A
HIS
30
n
30
HIS
30
A
LEU
31
n
31
LEU
31
A
ILE
32
n
32
ILE
32
A
GLU
33
n
33
GLU
33
A
PRO
34
n
34
PRO
34
A
LEU
35
n
35
LEU
35
A
GLY
36
n
36
GLY
36
A
PHE
37
n
37
PHE
37
A
THR
38
n
38
THR
38
A
TRP
39
n
39
TRP
39
A
ASP
40
n
40
ASP
40
A
ASP
41
n
41
ASP
41
A
LYS
42
n
42
LYS
42
A
ARG
43
n
43
ARG
43
A
LEU
44
n
44
LEU
44
A
ARG
45
n
45
ARG
45
A
ARG
46
n
46
ARG
46
A
SER
47
n
47
SER
47
A
GLY
48
n
48
GLY
48
A
LEU
49
n
49
LEU
49
A
ASP
50
n
50
ASP
50
A
TYR
51
n
51
TYR
51
A
HIS
52
n
52
HIS
52
A
GLU
53
n
53
GLU
53
A
PHE
54
n
54
PHE
54
A
ALA
55
n
55
ALA
55
A
GLU
56
n
56
GLU
56
A
ILE
57
n
57
ILE
57
A
LYS
58
n
58
LYS
58
A
ARG
59
n
59
ARG
59
A
HIS
60
n
60
HIS
60
A
LYS
61
n
61
LYS
61
A
THR
62
n
62
THR
62
A
PHE
63
n
63
PHE
63
A
GLU
64
n
64
GLU
64
A
ALA
65
n
65
ALA
65
A
PHE
66
n
66
PHE
66
A
LEU
67
n
67
LEU
67
A
GLU
68
n
68
GLU
68
A
SER
69
n
69
SER
69
A
GLU
70
n
70
GLU
70
A
LYS
71
n
71
LYS
71
A
PRO
72
n
72
PRO
72
A
LYS
73
n
73
LYS
73
A
ARG
74
n
74
ARG
74
A
LEU
75
n
75
LEU
75
A
PHE
76
n
76
PHE
76
A
ALA
77
n
77
ALA
77
A
LEU
78
n
78
LEU
78
A
THR
79
n
79
THR
79
A
THR
80
n
80
THR
80
A
LYS
81
n
81
LYS
81
A
GLY
82
n
82
GLY
82
A
CYS
83
n
83
CYS
83
A
PRO
84
n
84
PRO
84
A
ALA
85
n
85
ALA
85
A
HIS
86
n
86
HIS
86
A
SER
87
n
87
SER
87
A
GLN
88
n
88
GLN
88
A
VAL
89
n
89
VAL
89
A
LYS
90
n
90
LYS
90
A
PHE
91
n
91
PHE
91
A
LYS
92
n
92
LYS
92
A
LEU
93
n
93
LEU
93
A
GLY
94
n
94
GLY
94
A
ASP
95
n
95
ASP
95
A
TYR
96
n
96
TYR
96
A
LEU
97
n
97
LEU
97
A
MET
98
n
98
MET
98
A
PHE
99
n
99
PHE
99
A
GLY
100
n
100
GLY
100
A
PRO
101
n
101
PRO
101
A
GLU
102
n
102
GLU
102
A
THR
103
n
103
THR
103
A
ARG
104
n
104
ARG
104
A
GLY
105
n
105
GLY
105
A
ILE
106
n
106
ILE
106
A
PRO
107
n
107
PRO
107
A
MET
108
n
108
MET
108
A
SER
109
n
109
SER
109
A
ILE
110
n
110
ILE
110
A
LEU
111
n
111
LEU
111
A
ASN
112
n
112
ASN
112
A
GLU
113
n
113
GLU
113
A
MET
114
n
114
MET
114
A
PRO
115
n
115
PRO
115
A
MET
116
n
116
MET
116
A
GLU
117
n
117
GLU
117
A
GLN
118
n
118
GLN
118
A
LYS
119
n
119
LYS
119
A
ILE
120
n
120
ILE
120
A
ARG
121
n
121
ARG
121
A
ILE
122
n
122
ILE
122
A
PRO
123
n
123
PRO
123
A
MET
124
n
124
MET
124
A
THR
125
n
125
THR
125
A
ALA
126
n
126
ALA
126
A
ASN
127
n
127
ASN
127
A
SER
128
n
128
SER
128
A
ARG
129
n
129
ARG
129
A
SER
130
n
130
SER
130
A
MET
131
n
131
MET
131
A
ASN
132
n
132
ASN
132
A
LEU
133
n
133
LEU
133
A
SER
134
n
134
SER
134
A
ASN
135
n
135
ASN
135
A
SER
136
n
136
SER
136
A
VAL
137
n
137
VAL
137
A
ALA
138
n
138
ALA
138
A
VAL
139
n
139
VAL
139
A
THR
140
n
140
THR
140
A
VAL
141
n
141
VAL
141
A
TYR
142
n
142
TYR
142
A
GLU
143
n
143
GLU
143
A
ALA
144
n
144
ALA
144
A
TRP
145
n
145
TRP
145
A
ARG
146
n
146
ARG
146
A
GLN
147
n
147
GLN
147
A
LEU
148
n
148
LEU
148
A
GLY
149
n
149
GLY
149
A
TYR
150
n
150
TYR
150
A
LYS
151
n
151
LYS
151
A
GLY
152
n
152
GLY
152
A
ALA
153
n
153
ALA
153
A
VAL
154
n
154
VAL
154
A
ASN
155
n
155
ASN
155
A
LEU
156
n
156
LEU
156
A
n
157
157
A
n
158
158
A
n
159
159
A
n
160
160
A
author_defined_assembly
2
dimeric
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
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
HIS
60
A
O
HIS
60
A
N
LEU
31
A
N
LEU
31
A
O
ARG
28
A
O
ARG
28
A
N
ILE
4
A
N
ILE
4
A
N
VAL
5
A
N
VAL
5
A
O
LEU
97
A
O
LEU
97
A
O
TYR
96
A
O
TYR
96
A
N
PHE
76
A
N
PHE
76
A
N
ALA
77
A
N
ALA
77
A
O
ILE
120
A
O
ILE
120
1
A
PRO
157
A
PRO
157
1
Y
1
A
GLU
158
A
GLU
158
1
Y
1
A
VAL
159
A
VAL
159
1
Y
1
A
LYS
160
A
LYS
160
1
Y
1
A
ARG
43
-59.09
12.82
1
A
PHE
54
-104.51
-162.81
1
A
ALA
55
63.34
-16.30
1
A
ARG
104
-152.98
-12.25
1
A
SER
130
B
176.58
173.08
29
0.254
0.196
1.7
20.0
1593
14742
random
1
isotropic
THROUGHOUT
2
MOLECULAR REPLACEMENT
PDB 1j85
Engh & Huber
1.7
20.0
153
1479
27
0
1299
0.017
1.8
0.273
0.215
1.78
1.7
50
1MXI
15394
15394
0
0
0.04
1
18.5
93.7
0.223
1.7
1.78
69.2
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot
1
N
N
2
N
N
3
N
N
4
N
N
A
ILE
11
A
ILE
11
HELX_P
A
GLY
26
A
GLY
26
1
1
16
A
ASP
41
A
ASP
41
HELX_P
A
ARG
46
A
ARG
46
1
2
6
A
ASP
50
A
ASP
50
HELX_P
A
PHE
54
A
PHE
54
5
3
5
A
THR
62
A
THR
62
HELX_P
A
LYS
71
A
LYS
71
1
4
10
A
ALA
85
A
ALA
85
HELX_P
A
VAL
89
A
VAL
89
5
5
5
A
PRO
107
A
PRO
107
HELX_P
A
ASN
112
A
ASN
112
1
6
6
A
GLU
113
A
GLU
113
HELX_P
A
MET
114
A
MET
114
5
7
2
A
PRO
115
A
PRO
115
HELX_P
A
GLU
117
A
GLU
117
5
8
3
A
ASN
132
A
ASN
132
HELX_P
A
LEU
148
A
LEU
148
1
9
17
TRANSFERASE
methyltransferase, S-adenosylhomocysteine, spoU family, Structure 2 Function Project, S2F, Structural Genomics, TRANSFERASE
A
GLU
33
A
GLU
33
1
A
PRO
34
A
PRO
34
0.35
Y766_HAEIN
UNP
1
1
P44868
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT
KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK
1
160
1MXI
1
160
P44868
A
1
1
160
6
parallel
parallel
parallel
parallel
parallel
A
LYS
58
A
LYS
58
A
HIS
60
A
HIS
60
A
ARG
28
A
ARG
28
A
ILE
32
A
ILE
32
A
ASP
3
A
ASP
3
A
TYR
7
A
TYR
7
A
ASP
95
A
ASP
95
A
PHE
99
A
PHE
99
A
ARG
74
A
ARG
74
A
LEU
78
A
LEU
78
A
LYS
119
A
LYS
119
A
ILE
120
A
ILE
120
BINDING SITE FOR RESIDUE IOD A 2001
A
IOD
2001
Software
1
BINDING SITE FOR RESIDUE SAH A 302
A
SAH
302
Software
16
A
MET
131
A
MET
131
1
1_555
A
LEU
78
A
LEU
78
16
1_555
A
THR
79
A
THR
79
16
1_555
A
THR
80
A
THR
80
16
1_555
A
PHE
99
A
PHE
99
16
1_555
A
GLY
100
A
GLY
100
16
1_555
A
PRO
101
A
PRO
101
16
1_555
A
GLU
102
A
GLU
102
16
1_555
A
ARG
104
A
ARG
104
16
1_555
A
GLY
105
A
GLY
105
16
1_555
A
ARG
121
A
ARG
121
16
1_555
A
ILE
122
A
ILE
122
16
1_555
A
MET
124
A
MET
124
16
1_555
A
SER
130
A
SER
130
16
1_555
A
MET
131
A
MET
131
16
1_555
A
SER
136
A
SER
136
16
1_555
A
HOH
1002
D
HOH
16
1_555
92
P 41 21 2