0.012063
0.000000
0.000000
0.000000
0.016945
0.000000
0.000000
0.000000
0.015666
0.00000
0.00000
0.00000
Schubert, H.L.
Phillips, J.D.
Hill, C.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
82.897
59.013
63.832
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
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
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
C
N
294
N
S
N
295
N
C
N
296
N
O
N
297
N
O
N
298
N
C
N
299
S
C
N
300
N
O
N
301
S
C
N
302
N
O
N
303
R
C
N
304
N
O
N
305
R
C
Y
306
N
N
Y
307
N
C
Y
308
N
N
Y
309
N
C
Y
310
N
C
N
311
N
N
Y
312
N
N
Y
313
N
C
Y
314
N
N
Y
315
N
C
N
316
N
H
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
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
O
N
342
N
O
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
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
R
C
N
355
N
O
N
356
N
C
N
357
N
O
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
H
N
366
N
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
N
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
N
381
N
O
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
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
N
405
N
O
N
406
N
O
N
407
N
H
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
N
N
419
S
C
N
420
N
C
N
421
N
O
N
422
N
C
N
423
N
C
N
424
N
C
N
425
N
O
N
426
N
H
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
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
Biochemistry
BICHAW
0033
0006-2960
42
5592
5599
10.1021/bi034026p
12741815
Structures along the Catalytic Pathway of PrmC/HemK, an N(5)-Glutamine
AdoMet-Dependent Methyltransferase
2003
10.2210/pdb1nv9/pdb
pdb_00001nv9
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
2002-03-30
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
0.97
1.0
BL9-2
SSRL
0.97
SYNCHROTRON
SSRL BEAMLINE BL9-2
31781.535
hemK protein
2.1.1.-
HemK
1
man
polymer
384.411
S-ADENOSYL-L-HOMOCYSTEINE
1
syn
non-polymer
18.015
water
20
nat
water
no
no
GAMDTRKNVSGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYP
LHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVE
IARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDT
SGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS
GAMDTRKNVSGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYP
LHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVE
IARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDT
SGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS
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
Thermotoga
Escherichia
sample
HemK
2336
Thermotoga maritima
562
Escherichia coli
BL21(DE3)codon+
plasmid
pET14b
1
2.46
49.91
VAPOR DIFFUSION, HANGING DROP
5.5
PEG3000, Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K
292.0
exptl_crystal_grow
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Experimental preparation
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-05-27
1
1
2008-04-29
1
2
2011-07-13
1
3
2018-01-31
1
4
2023-08-16
_exptl_crystal_grow.temp
_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
N5-glutamine methyltransferase, HemK
RCSB
Y
RCSB
2003-02-02
REL
REL
SAH
S-ADENOSYL-L-HOMOCYSTEINE
HOH
water
1NV8
PDB ENTRY 1NV8
PDB
experimental model
SAH
300
2
SAH
SAH
300
A
HOH
1
3
HOH
HOH
301
A
HOH
3
3
HOH
HOH
302
A
HOH
4
3
HOH
HOH
303
A
HOH
5
3
HOH
HOH
304
A
HOH
6
3
HOH
HOH
305
A
HOH
7
3
HOH
HOH
306
A
HOH
8
3
HOH
HOH
307
A
HOH
9
3
HOH
HOH
308
A
HOH
10
3
HOH
HOH
309
A
HOH
11
3
HOH
HOH
310
A
HOH
12
3
HOH
HOH
311
A
HOH
13
3
HOH
HOH
312
A
HOH
14
3
HOH
HOH
313
A
HOH
15
3
HOH
HOH
314
A
HOH
18
3
HOH
HOH
315
A
HOH
19
3
HOH
HOH
316
A
HOH
21
3
HOH
HOH
317
A
HOH
22
3
HOH
HOH
318
A
HOH
23
3
HOH
HOH
319
A
HOH
24
3
HOH
HOH
320
A
n
1
-1
A
n
2
-2
A
n
3
1
A
n
4
2
A
n
5
3
A
n
6
4
A
n
7
5
A
n
8
6
A
n
9
7
A
n
10
8
A
n
11
9
A
n
12
10
A
n
13
11
A
n
14
12
A
LYS
13
n
15
LYS
13
A
ILE
14
n
16
ILE
14
A
TRP
15
n
17
TRP
15
A
SER
16
n
18
SER
16
A
LEU
17
n
19
LEU
17
A
ILE
18
n
20
ILE
18
A
ARG
19
n
21
ARG
19
A
ASP
20
n
22
ASP
20
A
CYS
21
n
23
CYS
21
A
SER
22
n
24
SER
22
A
GLY
23
n
25
GLY
23
A
LYS
24
n
26
LYS
24
A
LEU
25
n
27
LEU
25
A
GLU
26
n
28
GLU
26
A
GLY
27
n
29
GLY
27
A
VAL
28
n
30
VAL
28
A
THR
29
n
31
THR
29
A
GLU
30
n
32
GLU
30
A
THR
31
n
33
THR
31
A
SER
32
n
34
SER
32
A
VAL
33
n
35
VAL
33
A
LEU
34
n
36
LEU
34
A
GLU
35
n
37
GLU
35
A
VAL
36
n
38
VAL
36
A
LEU
37
n
39
LEU
37
A
LEU
38
n
40
LEU
38
A
ILE
39
n
41
ILE
39
A
VAL
40
n
42
VAL
40
A
SER
41
n
43
SER
41
A
ARG
42
n
44
ARG
42
A
VAL
43
n
45
VAL
43
A
LEU
44
n
46
LEU
44
A
GLY
45
n
47
GLY
45
A
ILE
46
n
48
ILE
46
A
ARG
47
n
49
ARG
47
A
LYS
48
n
50
LYS
48
A
GLU
49
n
51
GLU
49
A
ASP
50
n
52
ASP
50
A
LEU
51
n
53
LEU
51
A
PHE
52
n
54
PHE
52
A
LEU
53
n
55
LEU
53
A
LYS
54
n
56
LYS
54
A
ASP
55
n
57
ASP
55
A
LEU
56
n
58
LEU
56
A
GLY
57
n
59
GLY
57
A
VAL
58
n
60
VAL
58
A
SER
59
n
61
SER
59
A
PRO
60
n
62
PRO
60
A
THR
61
n
63
THR
61
A
GLU
62
n
64
GLU
62
A
GLU
63
n
65
GLU
63
A
LYS
64
n
66
LYS
64
A
ARG
65
n
67
ARG
65
A
ILE
66
n
68
ILE
66
A
LEU
67
n
69
LEU
67
A
GLU
68
n
70
GLU
68
A
LEU
69
n
71
LEU
69
A
VAL
70
n
72
VAL
70
A
GLU
71
n
73
GLU
71
A
LYS
72
n
74
LYS
72
A
ARG
73
n
75
ARG
73
A
ALA
74
n
76
ALA
74
A
SER
75
n
77
SER
75
A
GLY
76
n
78
GLY
76
A
TYR
77
n
79
TYR
77
A
PRO
78
n
80
PRO
78
A
LEU
79
n
81
LEU
79
A
HIS
80
n
82
HIS
80
A
TYR
81
n
83
TYR
81
A
ILE
82
n
84
ILE
82
A
LEU
83
n
85
LEU
83
A
GLY
84
n
86
GLY
84
A
GLU
85
n
87
GLU
85
A
LYS
86
n
88
LYS
86
A
GLU
87
n
89
GLU
87
A
PHE
88
n
90
PHE
88
A
MET
89
n
91
MET
89
A
GLY
90
n
92
GLY
90
A
LEU
91
n
93
LEU
91
A
SER
92
n
94
SER
92
A
PHE
93
n
95
PHE
93
A
LEU
94
n
96
LEU
94
A
VAL
95
n
97
VAL
95
A
GLU
96
n
98
GLU
96
A
GLU
97
n
99
GLU
97
A
GLY
98
n
100
GLY
98
A
VAL
99
n
101
VAL
99
A
PHE
100
n
102
PHE
100
A
VAL
101
n
103
VAL
101
A
PRO
102
n
104
PRO
102
A
ARG
103
n
105
ARG
103
A
PRO
104
n
106
PRO
104
A
GLU
105
n
107
GLU
105
A
THR
106
n
108
THR
106
A
GLU
107
n
109
GLU
107
A
GLU
108
n
110
GLU
108
A
LEU
109
n
111
LEU
109
A
VAL
110
n
112
VAL
110
A
GLU
111
n
113
GLU
111
A
LEU
112
n
114
LEU
112
A
ALA
113
n
115
ALA
113
A
LEU
114
n
116
LEU
114
A
GLU
115
n
117
GLU
115
A
LEU
116
n
118
LEU
116
A
ILE
117
n
119
ILE
117
A
ARG
118
n
120
ARG
118
A
LYS
119
n
121
LYS
119
A
TYR
120
n
122
TYR
120
A
GLY
121
n
123
GLY
121
A
ILE
122
n
124
ILE
122
A
LYS
123
n
125
LYS
123
A
THR
124
n
126
THR
124
A
VAL
125
n
127
VAL
125
A
ALA
126
n
128
ALA
126
A
ASP
127
n
129
ASP
127
A
ILE
128
n
130
ILE
128
A
GLY
129
n
131
GLY
129
A
THR
130
n
132
THR
130
A
GLY
131
n
133
GLY
131
A
SER
132
n
134
SER
132
A
GLY
133
n
135
GLY
133
A
ALA
134
n
136
ALA
134
A
ILE
135
n
137
ILE
135
A
GLY
136
n
138
GLY
136
A
VAL
137
n
139
VAL
137
A
SER
138
n
140
SER
138
A
VAL
139
n
141
VAL
139
A
ALA
140
n
142
ALA
140
A
LYS
141
n
143
LYS
141
A
PHE
142
n
144
PHE
142
A
SER
143
n
145
SER
143
A
ASP
144
n
146
ASP
144
A
ALA
145
n
147
ALA
145
A
ILE
146
n
148
ILE
146
A
VAL
147
n
149
VAL
147
A
PHE
148
n
150
PHE
148
A
ALA
149
n
151
ALA
149
A
THR
150
n
152
THR
150
A
ASP
151
n
153
ASP
151
A
VAL
152
n
154
VAL
152
A
SER
153
n
155
SER
153
A
SER
154
n
156
SER
154
A
LYS
155
n
157
LYS
155
A
ALA
156
n
158
ALA
156
A
VAL
157
n
159
VAL
157
A
GLU
158
n
160
GLU
158
A
ILE
159
n
161
ILE
159
A
ALA
160
n
162
ALA
160
A
ARG
161
n
163
ARG
161
A
LYS
162
n
164
LYS
162
A
ASN
163
n
165
ASN
163
A
ALA
164
n
166
ALA
164
A
GLU
165
n
167
GLU
165
A
ARG
166
n
168
ARG
166
A
HIS
167
n
169
HIS
167
A
GLY
168
n
170
GLY
168
A
VAL
169
n
171
VAL
169
A
SER
170
n
172
SER
170
A
ASP
171
n
173
ASP
171
A
ARG
172
n
174
ARG
172
A
PHE
173
n
175
PHE
173
A
PHE
174
n
176
PHE
174
A
VAL
175
n
177
VAL
175
A
ARG
176
n
178
ARG
176
A
LYS
177
n
179
LYS
177
A
GLY
178
n
180
GLY
178
A
GLU
179
n
181
GLU
179
A
PHE
180
n
182
PHE
180
A
LEU
181
n
183
LEU
181
A
GLU
182
n
184
GLU
182
A
PRO
183
n
185
PRO
183
A
PHE
184
n
186
PHE
184
A
LYS
185
n
187
LYS
185
A
GLU
186
n
188
GLU
186
A
LYS
187
n
189
LYS
187
A
PHE
188
n
190
PHE
188
A
ALA
189
n
191
ALA
189
A
SER
190
n
192
SER
190
A
ILE
191
n
193
ILE
191
A
GLU
192
n
194
GLU
192
A
MET
193
n
195
MET
193
A
ILE
194
n
196
ILE
194
A
LEU
195
n
197
LEU
195
A
SER
196
n
198
SER
196
A
ASN
197
n
199
ASN
197
A
PRO
198
n
200
PRO
198
A
PRO
199
n
201
PRO
199
A
TYR
200
n
202
TYR
200
A
VAL
201
n
203
VAL
201
A
LYS
202
n
204
LYS
202
A
SER
203
n
205
SER
203
A
SER
204
n
206
SER
204
A
ALA
205
n
207
ALA
205
A
n
208
206
A
n
209
207
A
n
210
208
A
n
211
209
A
n
212
210
A
n
213
211
A
LEU
212
n
214
LEU
212
A
PHE
213
n
215
PHE
213
A
GLU
214
n
216
GLU
214
A
PRO
215
n
217
PRO
215
A
PRO
216
n
218
PRO
216
A
GLU
217
n
219
GLU
217
A
ALA
218
n
220
ALA
218
A
LEU
219
n
221
LEU
219
A
PHE
220
n
222
PHE
220
A
GLY
221
n
223
GLY
221
A
GLY
222
n
224
GLY
222
A
GLU
223
n
225
GLU
223
A
ASP
224
n
226
ASP
224
A
GLY
225
n
227
GLY
225
A
LEU
226
n
228
LEU
226
A
ASP
227
n
229
ASP
227
A
PHE
228
n
230
PHE
228
A
TYR
229
n
231
TYR
229
A
ARG
230
n
232
ARG
230
A
GLU
231
n
233
GLU
231
A
PHE
232
n
234
PHE
232
A
PHE
233
n
235
PHE
233
A
GLY
234
n
236
GLY
234
A
ARG
235
n
237
ARG
235
A
TYR
236
n
238
TYR
236
A
ASP
237
n
239
ASP
237
A
THR
238
n
240
THR
238
A
SER
239
n
241
SER
239
A
GLY
240
n
242
GLY
240
A
LYS
241
n
243
LYS
241
A
ILE
242
n
244
ILE
242
A
VAL
243
n
245
VAL
243
A
LEU
244
n
246
LEU
244
A
MET
245
n
247
MET
245
A
GLU
246
n
248
GLU
246
A
ILE
247
n
249
ILE
247
A
GLY
248
n
250
GLY
248
A
GLU
249
n
251
GLU
249
A
ASP
250
n
252
ASP
250
A
GLN
251
n
253
GLN
251
A
VAL
252
n
254
VAL
252
A
GLU
253
n
255
GLU
253
A
GLU
254
n
256
GLU
254
A
LEU
255
n
257
LEU
255
A
LYS
256
n
258
LYS
256
A
LYS
257
n
259
LYS
257
A
ILE
258
n
260
ILE
258
A
VAL
259
n
261
VAL
259
A
SER
260
n
262
SER
260
A
ASP
261
n
263
ASP
261
A
THR
262
n
264
THR
262
A
VAL
263
n
265
VAL
263
A
PHE
264
n
266
PHE
264
A
LEU
265
n
267
LEU
265
A
LYS
266
n
268
LYS
266
A
ASP
267
n
269
ASP
267
A
SER
268
n
270
SER
268
A
ALA
269
n
271
ALA
269
A
GLY
270
n
272
GLY
270
A
LYS
271
n
273
LYS
271
A
TYR
272
n
274
TYR
272
A
ARG
273
n
275
ARG
273
A
PHE
274
n
276
PHE
274
A
LEU
275
n
277
LEU
275
A
LEU
276
n
278
LEU
276
A
LEU
277
n
279
LEU
277
A
ASN
278
n
280
ASN
278
A
ARG
279
n
281
ARG
279
A
ARG
280
n
282
ARG
280
A
SER
281
n
283
SER
281
A
SER
282
n
284
SER
282
A
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
PHE
88
A
N
PHE
90
A
O
LEU
91
A
O
LEU
93
A
O
ARG
176
A
O
ARG
178
A
N
ALA
149
A
N
ALA
151
A
O
PHE
148
A
O
PHE
150
A
N
VAL
125
A
N
VAL
127
A
N
ALA
126
A
N
ALA
128
A
O
LEU
195
A
O
LEU
197
A
N
ILE
194
A
N
ILE
196
A
O
ILE
242
A
O
ILE
244
A
N
VAL
243
A
N
VAL
245
A
O
LEU
277
A
O
LEU
279
A
O
ARG
273
A
O
ARG
275
A
N
LEU
265
A
N
LEU
267
1
A
GLY
-1
A
GLY
1
1
Y
1
A
ALA
-2
A
ALA
2
1
Y
1
A
MET
1
A
MET
3
1
Y
1
A
ASP
2
A
ASP
4
1
Y
1
A
THR
3
A
THR
5
1
Y
1
A
ARG
4
A
ARG
6
1
Y
1
A
LYS
5
A
LYS
7
1
Y
1
A
ASN
6
A
ASN
8
1
Y
1
A
VAL
7
A
VAL
9
1
Y
1
A
SER
8
A
SER
10
1
Y
1
A
GLY
9
A
GLY
11
1
Y
1
A
ALA
10
A
ALA
12
1
Y
1
A
GLU
11
A
GLU
13
1
Y
1
A
ARG
12
A
ARG
14
1
Y
1
A
HIS
206
A
HIS
208
1
Y
1
A
LEU
207
A
LEU
209
1
Y
1
A
PRO
208
A
PRO
210
1
Y
1
A
LYS
209
A
LYS
211
1
Y
1
A
ASP
210
A
ASP
212
1
Y
1
A
VAL
211
A
VAL
213
1
Y
1
A
A
O
N
GLY
THR
27
29
2.04
1
A
A
NH2
O
ARG
HOH
279
308
2.12
1
A
A
SER
SER
281
282
149.49
1
-17.08
2.50
113.10
96.02
A
A
A
N
CA
C
GLY
GLY
GLY
27
27
27
N
1
5.98
0.90
118.30
124.28
A
A
A
CB
CG
OD2
ASP
ASP
ASP
50
50
50
N
1
-15.35
2.50
113.10
97.75
A
A
A
N
CA
C
GLY
GLY
GLY
57
57
57
N
1
5.90
0.90
118.30
124.20
A
A
A
CB
CG
OD2
ASP
ASP
ASP
127
127
127
N
1
20.96
2.30
115.30
136.26
A
A
A
CA
CB
CG
LEU
LEU
LEU
275
275
275
N
1
-13.50
1.70
111.00
97.50
A
A
A
CB
CG
CD1
LEU
LEU
LEU
275
275
275
N
1
A
A
SD
CE
MET
MET
245
245
-0.382
0.056
1.774
1.392
N
1
A
A
OE2
OE1
GLU
GLU
30
223
2.12
1_555
3_555
1
A
GLU
26
-74.07
29.07
1
A
VAL
28
10.26
-43.52
1
A
THR
31
-119.79
59.78
1
A
ASP
55
60.88
81.42
1
A
PRO
60
1.73
-91.89
1
A
THR
61
-24.96
-57.21
1
A
GLU
62
-43.36
-79.83
1
A
PHE
180
45.09
-123.37
1
A
SER
204
-55.55
76.49
1
A
VAL
252
-48.04
-83.16
1
A
ARG
273
-140.33
-18.60
41.043
0.00
0.00
0.00
-3.61
0.00
3.62
0.922
0.892
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.30034
0.23869
0.24166
0.24166
2.356
50.00
657
12707
12707
4.9
99.01
13.479
0.326
RANDOM
1
THROUGHOUT
0
MAD
0.410
0.296
0.80
0.80
1.40
PDB ENTRY 1NV8
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.356
50.00
20
2133
26
0
2087
0.026
0.022
2151
0.001
0.020
2030
2.611
2.003
2892
1.088
3.000
4723
6.582
3.000
262
22.235
15.000
410
0.151
0.200
327
0.010
0.020
2334
0.003
0.020
444
0.297
0.300
528
0.255
0.300
2174
0.029
0.500
1
0.212
0.500
144
0.152
0.500
9
0.408
0.300
11
0.348
0.300
19
0.282
0.500
7
1.175
1.500
1310
2.154
2.000
2109
2.939
3.000
841
5.042
4.500
783
0.339
0.306
2.417
56
787
20
2.35
50
1NV9
13364
13340
0
0
0.039
1
20
97.7
0.404
2.35
2.43
2.3
79.4
refinement
REFMAC
5.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
MOLREP
HemK, apo structure
1
N
N
2
N
N
3
N
N
A
ILE
14
A
ILE
16
HELX_P
A
LYS
24
A
LYS
26
1
1
11
A
THR
31
A
THR
33
HELX_P
A
GLY
45
A
GLY
47
1
2
15
A
ARG
47
A
ARG
49
HELX_P
A
LEU
53
A
LEU
55
5
3
7
A
PRO
60
A
PRO
62
HELX_P
A
SER
75
A
SER
77
1
4
16
A
PRO
78
A
PRO
80
HELX_P
A
GLY
84
A
GLY
86
1
5
7
A
GLU
105
A
GLU
107
HELX_P
A
GLY
121
A
GLY
123
1
6
17
A
GLY
133
A
GLY
135
HELX_P
A
SER
143
A
SER
145
1
7
11
A
SER
153
A
SER
155
HELX_P
A
HIS
167
A
HIS
169
1
8
15
A
LEU
181
A
LEU
183
HELX_P
A
PHE
188
A
PHE
190
5
9
8
A
PRO
215
A
PRO
217
HELX_P
A
PHE
220
A
PHE
222
1
10
6
A
LEU
226
A
LEU
228
HELX_P
A
TYR
236
A
TYR
238
1
11
11
A
GLN
251
A
GLN
253
HELX_P
A
LYS
256
A
LYS
258
1
12
6
TRANSFERASE
Class I methyltransferase fold, TRANSFERASE
Q9WYV8_THEMA
UNP
1
1
Q9WYV8
MDTRKNVSGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLH
YILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIA
RKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSG
KIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS
1
282
1NV9
1
282
Q9WYV8
A
1
3
284
1
expression tag
GLY
-1
1NV9
A
Q9WYV8
UNP
1
1
expression tag
ALA
-2
1NV9
A
Q9WYV8
UNP
2
2
7
anti-parallel
parallel
parallel
parallel
parallel
anti-parallel
anti-parallel
A
GLU
85
A
GLU
87
A
PHE
88
A
PHE
90
A
LEU
91
A
LEU
93
A
LEU
94
A
LEU
96
A
PHE
173
A
PHE
175
A
LYS
177
A
LYS
179
A
ILE
146
A
ILE
148
A
ASP
151
A
ASP
153
A
THR
124
A
THR
126
A
ILE
128
A
ILE
130
A
MET
193
A
MET
195
A
SER
196
A
SER
198
A
ILE
242
A
ILE
244
A
GLU
246
A
GLU
248
A
TYR
272
A
TYR
274
A
ASN
278
A
ASN
280
A
VAL
263
A
VAL
265
A
LYS
266
A
LYS
268
BINDING SITE FOR RESIDUE SAH A 300
A
SAH
300
Software
14
A
PHE
100
A
PHE
102
14
1_555
A
PRO
102
A
PRO
104
14
1_555
A
GLY
129
A
GLY
131
14
1_555
A
THR
130
A
THR
132
14
1_555
A
GLY
131
A
GLY
133
14
1_555
A
ASP
151
A
ASP
153
14
1_555
A
GLU
179
A
GLU
181
14
1_555
A
PHE
180
A
PHE
182
14
1_555
A
ASN
197
A
ASN
199
14
1_555
A
PRO
199
A
PRO
201
14
1_555
A
GLU
217
A
GLU
219
14
1_555
A
ALA
218
A
ALA
220
14
1_555
A
HOH
304
C
HOH
14
1_555
A
HOH
319
C
HOH
14
1_555
18
P 21 21 2