0.013078
0.000000
0.000000
0.000000
0.011896
0.000000
0.000000
0.000000
0.008890
0.00000
0.00000
0.00000
Muzzolini, L.
Versees, W.
Steyaert, J.
Degano, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
76.466
84.062
112.483
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
Ca 2
40.078
CALCIUM ION
non-polymer
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
C5 H10 O5
150.130
alpha-D-ribofuranose
alpha-D-ribose; D-ribose; ribose
D-saccharide, alpha 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
CA
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
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
C
N
96
N
O
N
97
N
N
N
98
N
O
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
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
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
H
N
128
N
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
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
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
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
H
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
O
N
292
N
C
N
293
R
C
N
294
N
O
N
295
S
C
N
296
N
O
N
297
R
C
N
298
N
O
N
299
S
C
N
300
N
O
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
N
C
N
316
N
O
N
317
N
O
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
R
C
N
330
N
O
N
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
N
Y
351
N
C
Y
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
N
356
N
O
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
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
N
N
370
S
C
N
371
N
C
N
372
N
O
N
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
N
380
N
O
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
N
N
394
S
C
N
395
N
C
N
396
N
O
N
397
N
C
N
398
N
C
N
399
N
C
N
400
N
O
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
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
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
sing
N
303
N
doub
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
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
sing
N
332
N
doub
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
Y
337
N
doub
Y
338
N
sing
Y
339
N
sing
N
340
N
sing
Y
341
N
doub
Y
342
N
sing
Y
343
N
sing
N
344
N
sing
Y
345
N
sing
Y
346
N
doub
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
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
N
370
N
sing
Y
371
N
doub
N
372
N
sing
Y
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
sing
N
384
N
doub
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
N
395
N
sing
To be Published
0353
Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
UK
Structure
STRUE6
2005
0969-2126
12
739
749
10.1016/j.str.2004.03.018
15130467
Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy
2004
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
307
1363
1379
10.1006/jmbi.2001.4548
11292348
Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax
2001
US
Biochemistry
BICHAW
0033
0006-2960
37
6277
6285
10.1021/bi973012e
9572842
Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
1998
10.2210/pdb1yoe/pdb
pdb_00001yoe
RIB A 2001 HAS WRONG CHIRALITY AT ATOM C1
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
ADSC QUANTUM 4
Mirrors
SINGLE WAVELENGTH
M
x-ray
1
0.933
1.0
ID14-2
ESRF
0.933
SYNCHROTRON
ESRF BEAMLINE ID14-2
35128.105
Hypothetical protein ybeK
3.2.2.8
1
man
polymer
150.130
alpha-D-ribofuranose
1
man
non-polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
215
nat
water
no
no
MRGSHHHHHHGSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVK
PLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVI
MGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKD
EKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKF
YA
MRGSHHHHHHGSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVK
PLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVI
MGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKD
EKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKF
YA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Escherichia
Escherichia
sample
ybeK/rihA
562
Escherichia coli
562
Escherichia coli
WK6
plasmid
pQE30
1
2.6
51.9
VAPOR DIFFUSION, HANGING DROP
5
MPD, Sodium Acetate, ribose, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
atom_site
chem_comp
database_PDB_caveat
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
pdbx_struct_conn_angle
pdbx_validate_chiral
struct_conn
struct_ref_seq_dif
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Advisory
Derived calculations
Version format compliance
Advisory
Atomic model
Data collection
Database references
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2006-01-17
1
1
2008-04-30
1
2
2011-07-13
2
0
2020-07-29
2
1
2023-10-25
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_pdbx_validate_chiral.auth_atom_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
DRibfa
a-D-ribofuranose
a-D-Ribf
Rib
RCSB
Y
PDBJ
2005-01-27
REL
REL
RIB
alpha-D-ribofuranose
CA
CALCIUM ION
HOH
water
1Q8F
YeiK PDB code 1Q8F
PDB
experimental model
RIB
1
2
RIB
RIB
2001
A
CA
1
3
CA
CA
1001
A
HOH
1
4
HOH
HOH
2002
A
HOH
2
4
HOH
HOH
2003
A
HOH
3
4
HOH
HOH
2004
A
HOH
4
4
HOH
HOH
2005
A
HOH
5
4
HOH
HOH
2006
A
HOH
6
4
HOH
HOH
2007
A
HOH
7
4
HOH
HOH
2008
A
HOH
8
4
HOH
HOH
2009
A
HOH
9
4
HOH
HOH
2010
A
HOH
10
4
HOH
HOH
2011
A
HOH
11
4
HOH
HOH
2012
A
HOH
12
4
HOH
HOH
2013
A
HOH
13
4
HOH
HOH
2014
A
HOH
14
4
HOH
HOH
2015
A
HOH
15
4
HOH
HOH
2016
A
HOH
16
4
HOH
HOH
2017
A
HOH
17
4
HOH
HOH
2018
A
HOH
18
4
HOH
HOH
2019
A
HOH
19
4
HOH
HOH
2020
A
HOH
20
4
HOH
HOH
2021
A
HOH
21
4
HOH
HOH
2022
A
HOH
22
4
HOH
HOH
2023
A
HOH
23
4
HOH
HOH
2024
A
HOH
24
4
HOH
HOH
2025
A
HOH
25
4
HOH
HOH
2026
A
HOH
26
4
HOH
HOH
2027
A
HOH
27
4
HOH
HOH
2028
A
HOH
28
4
HOH
HOH
2029
A
HOH
29
4
HOH
HOH
2030
A
HOH
30
4
HOH
HOH
2031
A
HOH
31
4
HOH
HOH
2032
A
HOH
32
4
HOH
HOH
2033
A
HOH
33
4
HOH
HOH
2034
A
HOH
34
4
HOH
HOH
2035
A
HOH
35
4
HOH
HOH
2036
A
HOH
36
4
HOH
HOH
2037
A
HOH
37
4
HOH
HOH
2038
A
HOH
38
4
HOH
HOH
2039
A
HOH
39
4
HOH
HOH
2040
A
HOH
40
4
HOH
HOH
2041
A
HOH
41
4
HOH
HOH
2042
A
HOH
42
4
HOH
HOH
2043
A
HOH
43
4
HOH
HOH
2044
A
HOH
44
4
HOH
HOH
2045
A
HOH
45
4
HOH
HOH
2046
A
HOH
46
4
HOH
HOH
2047
A
HOH
47
4
HOH
HOH
2048
A
HOH
48
4
HOH
HOH
2049
A
HOH
49
4
HOH
HOH
2050
A
HOH
50
4
HOH
HOH
2051
A
HOH
51
4
HOH
HOH
2052
A
HOH
52
4
HOH
HOH
2053
A
HOH
53
4
HOH
HOH
2054
A
HOH
54
4
HOH
HOH
2055
A
HOH
55
4
HOH
HOH
2056
A
HOH
56
4
HOH
HOH
2057
A
HOH
57
4
HOH
HOH
2058
A
HOH
58
4
HOH
HOH
2059
A
HOH
59
4
HOH
HOH
2060
A
HOH
60
4
HOH
HOH
2061
A
HOH
61
4
HOH
HOH
2062
A
HOH
62
4
HOH
HOH
2063
A
HOH
63
4
HOH
HOH
2064
A
HOH
64
4
HOH
HOH
2065
A
HOH
65
4
HOH
HOH
2066
A
HOH
66
4
HOH
HOH
2067
A
HOH
67
4
HOH
HOH
2068
A
HOH
68
4
HOH
HOH
2069
A
HOH
69
4
HOH
HOH
2070
A
HOH
70
4
HOH
HOH
2071
A
HOH
71
4
HOH
HOH
2072
A
HOH
72
4
HOH
HOH
2073
A
HOH
73
4
HOH
HOH
2074
A
HOH
74
4
HOH
HOH
2075
A
HOH
75
4
HOH
HOH
2076
A
HOH
76
4
HOH
HOH
2077
A
HOH
77
4
HOH
HOH
2078
A
HOH
78
4
HOH
HOH
2079
A
HOH
79
4
HOH
HOH
2080
A
HOH
80
4
HOH
HOH
2081
A
HOH
81
4
HOH
HOH
2082
A
HOH
82
4
HOH
HOH
2083
A
HOH
83
4
HOH
HOH
2084
A
HOH
84
4
HOH
HOH
2085
A
HOH
85
4
HOH
HOH
2086
A
HOH
86
4
HOH
HOH
2087
A
HOH
87
4
HOH
HOH
2088
A
HOH
88
4
HOH
HOH
2089
A
HOH
89
4
HOH
HOH
2090
A
HOH
90
4
HOH
HOH
2091
A
HOH
91
4
HOH
HOH
2092
A
HOH
92
4
HOH
HOH
2093
A
HOH
93
4
HOH
HOH
2094
A
HOH
94
4
HOH
HOH
2095
A
HOH
95
4
HOH
HOH
2096
A
HOH
96
4
HOH
HOH
2097
A
HOH
98
4
HOH
HOH
2098
A
HOH
99
4
HOH
HOH
2099
A
HOH
100
4
HOH
HOH
2100
A
HOH
101
4
HOH
HOH
2101
A
HOH
102
4
HOH
HOH
2102
A
HOH
103
4
HOH
HOH
2103
A
HOH
104
4
HOH
HOH
2104
A
HOH
105
4
HOH
HOH
2105
A
HOH
106
4
HOH
HOH
2106
A
HOH
107
4
HOH
HOH
2107
A
HOH
108
4
HOH
HOH
2108
A
HOH
109
4
HOH
HOH
2109
A
HOH
110
4
HOH
HOH
2110
A
HOH
111
4
HOH
HOH
2111
A
HOH
112
4
HOH
HOH
2112
A
HOH
113
4
HOH
HOH
2113
A
HOH
114
4
HOH
HOH
2114
A
HOH
115
4
HOH
HOH
2115
A
HOH
116
4
HOH
HOH
2116
A
HOH
117
4
HOH
HOH
2117
A
HOH
118
4
HOH
HOH
2118
A
HOH
119
4
HOH
HOH
2119
A
HOH
120
4
HOH
HOH
2120
A
HOH
121
4
HOH
HOH
2121
A
HOH
122
4
HOH
HOH
2122
A
HOH
123
4
HOH
HOH
2123
A
HOH
124
4
HOH
HOH
2124
A
HOH
125
4
HOH
HOH
2125
A
HOH
126
4
HOH
HOH
2126
A
HOH
128
4
HOH
HOH
2127
A
HOH
129
4
HOH
HOH
2128
A
HOH
130
4
HOH
HOH
2129
A
HOH
131
4
HOH
HOH
2130
A
HOH
132
4
HOH
HOH
2131
A
HOH
133
4
HOH
HOH
2132
A
HOH
134
4
HOH
HOH
2133
A
HOH
135
4
HOH
HOH
2134
A
HOH
136
4
HOH
HOH
2135
A
HOH
137
4
HOH
HOH
2136
A
HOH
138
4
HOH
HOH
2137
A
HOH
140
4
HOH
HOH
2138
A
HOH
141
4
HOH
HOH
2139
A
HOH
142
4
HOH
HOH
2140
A
HOH
143
4
HOH
HOH
2141
A
HOH
144
4
HOH
HOH
2142
A
HOH
145
4
HOH
HOH
2143
A
HOH
146
4
HOH
HOH
2144
A
HOH
147
4
HOH
HOH
2145
A
HOH
148
4
HOH
HOH
2146
A
HOH
149
4
HOH
HOH
2147
A
HOH
150
4
HOH
HOH
2148
A
HOH
151
4
HOH
HOH
2149
A
HOH
153
4
HOH
HOH
2150
A
HOH
154
4
HOH
HOH
2151
A
HOH
155
4
HOH
HOH
2152
A
HOH
156
4
HOH
HOH
2153
A
HOH
157
4
HOH
HOH
2154
A
HOH
158
4
HOH
HOH
2155
A
HOH
159
4
HOH
HOH
2156
A
HOH
160
4
HOH
HOH
2157
A
HOH
161
4
HOH
HOH
2158
A
HOH
162
4
HOH
HOH
2159
A
HOH
163
4
HOH
HOH
2160
A
HOH
164
4
HOH
HOH
2161
A
HOH
166
4
HOH
HOH
2162
A
HOH
167
4
HOH
HOH
2163
A
HOH
168
4
HOH
HOH
2164
A
HOH
169
4
HOH
HOH
2165
A
HOH
170
4
HOH
HOH
2166
A
HOH
171
4
HOH
HOH
2167
A
HOH
172
4
HOH
HOH
2168
A
HOH
173
4
HOH
HOH
2169
A
HOH
174
4
HOH
HOH
2170
A
HOH
175
4
HOH
HOH
2171
A
HOH
176
4
HOH
HOH
2172
A
HOH
177
4
HOH
HOH
2173
A
HOH
178
4
HOH
HOH
2174
A
HOH
179
4
HOH
HOH
2175
A
HOH
180
4
HOH
HOH
2176
A
HOH
181
4
HOH
HOH
2177
A
HOH
182
4
HOH
HOH
2178
A
HOH
183
4
HOH
HOH
2179
A
HOH
186
4
HOH
HOH
2180
A
HOH
188
4
HOH
HOH
2181
A
HOH
189
4
HOH
HOH
2182
A
HOH
191
4
HOH
HOH
2183
A
HOH
192
4
HOH
HOH
2184
A
HOH
196
4
HOH
HOH
2185
A
HOH
198
4
HOH
HOH
2186
A
HOH
199
4
HOH
HOH
2187
A
HOH
202
4
HOH
HOH
2188
A
HOH
204
4
HOH
HOH
2189
A
HOH
205
4
HOH
HOH
2190
A
HOH
206
4
HOH
HOH
2191
A
HOH
207
4
HOH
HOH
2192
A
HOH
208
4
HOH
HOH
2193
A
HOH
210
4
HOH
HOH
2194
A
HOH
213
4
HOH
HOH
2195
A
HOH
219
4
HOH
HOH
2196
A
HOH
220
4
HOH
HOH
2197
A
HOH
221
4
HOH
HOH
2198
A
HOH
222
4
HOH
HOH
2199
A
HOH
224
4
HOH
HOH
2200
A
HOH
226
4
HOH
HOH
2201
A
HOH
227
4
HOH
HOH
2202
A
HOH
228
4
HOH
HOH
2203
A
HOH
229
4
HOH
HOH
2204
A
HOH
230
4
HOH
HOH
2205
A
HOH
231
4
HOH
HOH
2206
A
HOH
236
4
HOH
HOH
2207
A
HOH
237
4
HOH
HOH
2208
A
HOH
238
4
HOH
HOH
2209
A
HOH
242
4
HOH
HOH
2210
A
HOH
243
4
HOH
HOH
2211
A
HOH
245
4
HOH
HOH
2212
A
HOH
248
4
HOH
HOH
2213
A
HOH
252
4
HOH
HOH
2214
A
HOH
264
4
HOH
HOH
2215
A
HOH
269
4
HOH
HOH
2216
A
n
1
-10
A
n
2
-9
A
n
3
-8
A
n
4
-7
A
n
5
-6
A
n
6
-5
A
n
7
-4
A
n
8
-3
A
n
9
-2
A
n
10
-1
A
GLY
0
n
11
GLY
0
A
SER
1
n
12
SER
1
A
ALA
2
n
13
ALA
2
A
LEU
3
n
14
LEU
3
A
PRO
4
n
15
PRO
4
A
ILE
5
n
16
ILE
5
A
LEU
6
n
17
LEU
6
A
LEU
7
n
18
LEU
7
A
ASP
8
n
19
ASP
8
A
CYS
9
n
20
CYS
9
A
ASP
10
n
21
ASP
10
A
PRO
11
n
22
PRO
11
A
GLY
12
n
23
GLY
12
A
HIS
13
n
24
HIS
13
A
ASP
14
n
25
ASP
14
A
ASP
15
n
26
ASP
15
A
ALA
16
n
27
ALA
16
A
ILE
17
n
28
ILE
17
A
ALA
18
n
29
ALA
18
A
ILE
19
n
30
ILE
19
A
VAL
20
n
31
VAL
20
A
LEU
21
n
32
LEU
21
A
ALA
22
n
33
ALA
22
A
LEU
23
n
34
LEU
23
A
ALA
24
n
35
ALA
24
A
SER
25
n
36
SER
25
A
PRO
26
n
37
PRO
26
A
GLU
27
n
38
GLU
27
A
LEU
28
n
39
LEU
28
A
ASP
29
n
40
ASP
29
A
VAL
30
n
41
VAL
30
A
LYS
31
n
42
LYS
31
A
ALA
32
n
43
ALA
32
A
ILE
33
n
44
ILE
33
A
THR
34
n
45
THR
34
A
SER
35
n
46
SER
35
A
SER
36
n
47
SER
36
A
ALA
37
n
48
ALA
37
A
GLY
38
n
49
GLY
38
A
ASN
39
n
50
ASN
39
A
GLN
40
n
51
GLN
40
A
THR
41
n
52
THR
41
A
PRO
42
n
53
PRO
42
A
GLU
43
n
54
GLU
43
A
LYS
44
n
55
LYS
44
A
THR
45
n
56
THR
45
A
LEU
46
n
57
LEU
46
A
ARG
47
n
58
ARG
47
A
ASN
48
n
59
ASN
48
A
VAL
49
n
60
VAL
49
A
LEU
50
n
61
LEU
50
A
ARG
51
n
62
ARG
51
A
MET
52
n
63
MET
52
A
LEU
53
n
64
LEU
53
A
THR
54
n
65
THR
54
A
LEU
55
n
66
LEU
55
A
LEU
56
n
67
LEU
56
A
ASN
57
n
68
ASN
57
A
ARG
58
n
69
ARG
58
A
THR
59
n
70
THR
59
A
ASP
60
n
71
ASP
60
A
ILE
61
n
72
ILE
61
A
PRO
62
n
73
PRO
62
A
VAL
63
n
74
VAL
63
A
ALA
64
n
75
ALA
64
A
GLY
65
n
76
GLY
65
A
GLY
66
n
77
GLY
66
A
ALA
67
n
78
ALA
67
A
VAL
68
n
79
VAL
68
A
LYS
69
n
80
LYS
69
A
PRO
70
n
81
PRO
70
A
LEU
71
n
82
LEU
71
A
MET
72
n
83
MET
72
A
ARG
73
n
84
ARG
73
A
GLU
74
n
85
GLU
74
A
LEU
75
n
86
LEU
75
A
ILE
76
n
87
ILE
76
A
ILE
77
n
88
ILE
77
A
ALA
78
n
89
ALA
78
A
n
90
79
A
n
91
80
A
n
92
81
A
n
93
82
A
n
94
83
A
GLU
84
n
95
GLU
84
A
SER
85
n
96
SER
85
A
GLY
86
n
97
GLY
86
A
LEU
87
n
98
LEU
87
A
ASP
88
n
99
ASP
88
A
GLY
89
n
100
GLY
89
A
PRO
90
n
101
PRO
90
A
ALA
91
n
102
ALA
91
A
LEU
92
n
103
LEU
92
A
PRO
93
n
104
PRO
93
A
GLU
94
n
105
GLU
94
A
PRO
95
n
106
PRO
95
A
THR
96
n
107
THR
96
A
PHE
97
n
108
PHE
97
A
ALA
98
n
109
ALA
98
A
PRO
99
n
110
PRO
99
A
GLN
100
n
111
GLN
100
A
ASN
101
n
112
ASN
101
A
CYS
102
n
113
CYS
102
A
THR
103
n
114
THR
103
A
ALA
104
n
115
ALA
104
A
VAL
105
n
116
VAL
105
A
GLU
106
n
117
GLU
106
A
LEU
107
n
118
LEU
107
A
MET
108
n
119
MET
108
A
ALA
109
n
120
ALA
109
A
LYS
110
n
121
LYS
110
A
THR
111
n
122
THR
111
A
LEU
112
n
123
LEU
112
A
ARG
113
n
124
ARG
113
A
GLU
114
n
125
GLU
114
A
SER
115
n
126
SER
115
A
ALA
116
n
127
ALA
116
A
GLU
117
n
128
GLU
117
A
PRO
118
n
129
PRO
118
A
VAL
119
n
130
VAL
119
A
THR
120
n
131
THR
120
A
ILE
121
n
132
ILE
121
A
VAL
122
n
133
VAL
122
A
SER
123
n
134
SER
123
A
THR
124
n
135
THR
124
A
GLY
125
n
136
GLY
125
A
PRO
126
n
137
PRO
126
A
GLN
127
n
138
GLN
127
A
THR
128
n
139
THR
128
A
ASN
129
n
140
ASN
129
A
VAL
130
n
141
VAL
130
A
ALA
131
n
142
ALA
131
A
LEU
132
n
143
LEU
132
A
LEU
133
n
144
LEU
133
A
LEU
134
n
145
LEU
134
A
ASN
135
n
146
ASN
135
A
SER
136
n
147
SER
136
A
HIS
137
n
148
HIS
137
A
PRO
138
n
149
PRO
138
A
GLU
139
n
150
GLU
139
A
LEU
140
n
151
LEU
140
A
HIS
141
n
152
HIS
141
A
SER
142
n
153
SER
142
A
LYS
143
n
154
LYS
143
A
ILE
144
n
155
ILE
144
A
ALA
145
n
156
ALA
145
A
ARG
146
n
157
ARG
146
A
ILE
147
n
158
ILE
147
A
VAL
148
n
159
VAL
148
A
ILE
149
n
160
ILE
149
A
MET
150
n
161
MET
150
A
GLY
151
n
162
GLY
151
A
GLY
152
n
163
GLY
152
A
ALA
153
n
164
ALA
153
A
MET
154
n
165
MET
154
A
GLY
155
n
166
GLY
155
A
LEU
156
n
167
LEU
156
A
GLY
157
n
168
GLY
157
A
ASN
158
n
169
ASN
158
A
TRP
159
n
170
TRP
159
A
THR
160
n
171
THR
160
A
PRO
161
n
172
PRO
161
A
ALA
162
n
173
ALA
162
A
ALA
163
n
174
ALA
163
A
GLU
164
n
175
GLU
164
A
PHE
165
n
176
PHE
165
A
ASN
166
n
177
ASN
166
A
ILE
167
n
178
ILE
167
A
TYR
168
n
179
TYR
168
A
VAL
169
n
180
VAL
169
A
ASP
170
n
181
ASP
170
A
PRO
171
n
182
PRO
171
A
GLU
172
n
183
GLU
172
A
ALA
173
n
184
ALA
173
A
ALA
174
n
185
ALA
174
A
GLU
175
n
186
GLU
175
A
ILE
176
n
187
ILE
176
A
VAL
177
n
188
VAL
177
A
PHE
178
n
189
PHE
178
A
GLN
179
n
190
GLN
179
A
SER
180
n
191
SER
180
A
GLY
181
n
192
GLY
181
A
ILE
182
n
193
ILE
182
A
PRO
183
n
194
PRO
183
A
VAL
184
n
195
VAL
184
A
VAL
185
n
196
VAL
185
A
MET
186
n
197
MET
186
A
ALA
187
n
198
ALA
187
A
GLY
188
n
199
GLY
188
A
LEU
189
n
200
LEU
189
A
ASP
190
n
201
ASP
190
A
VAL
191
n
202
VAL
191
A
THR
192
n
203
THR
192
A
HIS
193
n
204
HIS
193
A
LYS
194
n
205
LYS
194
A
ALA
195
n
206
ALA
195
A
GLN
196
n
207
GLN
196
A
ILE
197
n
208
ILE
197
A
HIS
198
n
209
HIS
198
A
VAL
199
n
210
VAL
199
A
GLU
200
n
211
GLU
200
A
ASP
201
n
212
ASP
201
A
THR
202
n
213
THR
202
A
GLU
203
n
214
GLU
203
A
ARG
204
n
215
ARG
204
A
PHE
205
n
216
PHE
205
A
ARG
206
n
217
ARG
206
A
ALA
207
n
218
ALA
207
A
ILE
208
n
219
ILE
208
A
GLY
209
n
220
GLY
209
A
ASN
210
n
221
ASN
210
A
PRO
211
n
222
PRO
211
A
VAL
212
n
223
VAL
212
A
SER
213
n
224
SER
213
A
THR
214
n
225
THR
214
A
ILE
215
n
226
ILE
215
A
VAL
216
n
227
VAL
216
A
ALA
217
n
228
ALA
217
A
GLU
218
n
229
GLU
218
A
LEU
219
n
230
LEU
219
A
LEU
220
n
231
LEU
220
A
ASP
221
n
232
ASP
221
A
PHE
222
n
233
PHE
222
A
PHE
223
n
234
PHE
223
A
LEU
224
n
235
LEU
224
A
GLU
225
n
236
GLU
225
A
n
237
226
A
n
238
227
A
n
239
228
A
n
240
229
A
n
241
230
A
LYS
231
n
242
LYS
231
A
TRP
232
n
243
TRP
232
A
GLY
233
n
244
GLY
233
A
PHE
234
n
245
PHE
234
A
VAL
235
n
246
VAL
235
A
GLY
236
n
247
GLY
236
A
ALA
237
n
248
ALA
237
A
PRO
238
n
249
PRO
238
A
LEU
239
n
250
LEU
239
A
HIS
240
n
251
HIS
240
A
ASP
241
n
252
ASP
241
A
PRO
242
n
253
PRO
242
A
CYS
243
n
254
CYS
243
A
THR
244
n
255
THR
244
A
ILE
245
n
256
ILE
245
A
ALA
246
n
257
ALA
246
A
TRP
247
n
258
TRP
247
A
LEU
248
n
259
LEU
248
A
LEU
249
n
260
LEU
249
A
LYS
250
n
261
LYS
250
A
PRO
251
n
262
PRO
251
A
GLU
252
n
263
GLU
252
A
LEU
253
n
264
LEU
253
A
PHE
254
n
265
PHE
254
A
THR
255
n
266
THR
255
A
SER
256
n
267
SER
256
A
VAL
257
n
268
VAL
257
A
GLU
258
n
269
GLU
258
A
ARG
259
n
270
ARG
259
A
TRP
260
n
271
TRP
260
A
VAL
261
n
272
VAL
261
A
GLY
262
n
273
GLY
262
A
VAL
263
n
274
VAL
263
A
GLU
264
n
275
GLU
264
A
THR
265
n
276
THR
265
A
GLN
266
n
277
GLN
266
A
GLY
267
n
278
GLY
267
A
LYS
268
n
279
LYS
268
A
TYR
269
n
280
TYR
269
A
THR
270
n
281
THR
270
A
GLN
271
n
282
GLN
271
A
GLY
272
n
283
GLY
272
A
MET
273
n
284
MET
273
A
THR
274
n
285
THR
274
A
VAL
275
n
286
VAL
275
A
VAL
276
n
287
VAL
276
A
ASP
277
n
288
ASP
277
A
TYR
278
n
289
TYR
278
A
TYR
279
n
290
TYR
279
A
TYR
280
n
291
TYR
280
A
LEU
281
n
292
LEU
281
A
THR
282
n
293
THR
282
A
GLY
283
n
294
GLY
283
A
ASN
284
n
295
ASN
284
A
LYS
285
n
296
LYS
285
A
PRO
286
n
297
PRO
286
A
ASN
287
n
298
ASN
287
A
ALA
288
n
299
ALA
288
A
THR
289
n
300
THR
289
A
VAL
290
n
301
VAL
290
A
MET
291
n
302
MET
291
A
VAL
292
n
303
VAL
292
A
ASP
293
n
304
ASP
293
A
VAL
294
n
305
VAL
294
A
ASP
295
n
306
ASP
295
A
ARG
296
n
307
ARG
296
A
GLN
297
n
308
GLN
297
A
GLY
298
n
309
GLY
298
A
PHE
299
n
310
PHE
299
A
VAL
300
n
311
VAL
300
A
ASP
301
n
312
ASP
301
A
LEU
302
n
313
LEU
302
A
LEU
303
n
314
LEU
303
A
ALA
304
n
315
ALA
304
A
ASP
305
n
316
ASP
305
A
ARG
306
n
317
ARG
306
A
LEU
307
n
318
LEU
307
A
LYS
308
n
319
LYS
308
A
PHE
309
n
320
PHE
309
A
TYR
310
n
321
TYR
310
A
ALA
311
n
322
ALA
311
A
0.1453
0.0651
0.0439
0.3512
0.0581
0.1442
-0.0032
0.0185
0.0038
-0.0295
0.0249
0.0211
-0.0068
0.0061
-0.0217
0.0052
-0.0005
-0.0056
0.0178
0.0012
0.0061
refined
-4.4330
20.7639
36.7434
X-RAY DIFFRACTION
A
1
A
12
A
311
A
322
X-RAY DIFFRACTION
1
author_defined_assembly
4
tetrameric
software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PQS
4
tetrameric
10290
-118
41620
2640
-38
23320
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
15
A
OD1
ASP
26
1_555
82.0
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
15
A
OD2
ASP
26
1_555
71.2
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
15
A
OD2
ASP
26
1_555
51.9
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
THR
124
A
O
THR
135
1_555
91.9
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
THR
124
A
O
THR
135
1_555
137.6
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
THR
124
A
O
THR
135
1_555
86.3
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
241
A
OD2
ASP
252
1_555
141.7
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
241
A
OD2
ASP
252
1_555
74.3
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
241
A
OD2
ASP
252
1_555
70.5
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
ASP
241
A
OD2
ASP
252
1_555
86.1
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O2
RIB
1_555
120.8
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O2
RIB
1_555
82.4
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O2
RIB
1_555
132.2
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O2
RIB
1_555
134.0
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O2
RIB
1_555
85.7
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
123.2
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
75.6
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
124.3
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
137.8
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
79.5
A
RIB
2001
A
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O2
RIB
1_555
8.2
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
136.6
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
133.7
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
146.6
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
76.3
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
79.9
A
RIB
2001
A
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
57.6
A
RIB
2001
B
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
A
B
O3
RIB
1_555
62.2
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
140.0
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
133.2
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
141.7
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
73.8
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
75.7
A
RIB
2001
A
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
60.3
A
RIB
2001
B
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
64.3
A
RIB
2001
A
B
O3
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
B
O3
RIB
1_555
4.9
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
70.6
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
124.2
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
141.7
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
92.0
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
147.6
A
RIB
2001
A
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
72.5
A
RIB
2001
B
B
O2
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
80.4
A
RIB
2001
A
B
O3
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
68.3
A
RIB
2001
B
B
O3
RIB
1_555
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
72.7
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_556
-x,y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
112.4830000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_556
x,-y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
112.4830000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_565
-x,-y+1,z
crystal symmetry operation
0.0000000000
84.0620000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_566
x,-y+1,-z+1
crystal symmetry operation
0.0000000000
84.0620000000
112.4830000000
A
O
ALA
64
A
O
ALA
75
A
N
SER
35
A
N
SER
46
A
O
LYS
31
A
O
LYS
42
A
N
ILE
5
A
N
ILE
16
A
N
LEU
6
A
N
LEU
17
A
O
VAL
122
A
O
VAL
133
A
N
ILE
121
A
N
ILE
132
A
O
VAL
148
A
O
VAL
159
A
N
ILE
149
A
N
ILE
160
A
O
VAL
185
A
O
VAL
196
A
N
MET
186
A
N
MET
197
A
O
THR
289
A
O
THR
300
A
O
VAL
290
A
O
VAL
301
A
N
VAL
257
A
N
VAL
268
A
N
ILE
197
A
N
ILE
208
A
O
ALA
237
A
O
ALA
248
A
N
GLY
262
A
N
GLY
273
A
O
VAL
275
A
O
VAL
286
1
A
MET
-10
A
MET
1
1
Y
1
A
ARG
-9
A
ARG
2
1
Y
1
A
GLY
-8
A
GLY
3
1
Y
1
A
SER
-7
A
SER
4
1
Y
1
A
HIS
-6
A
HIS
5
1
Y
1
A
HIS
-5
A
HIS
6
1
Y
1
A
HIS
-4
A
HIS
7
1
Y
1
A
HIS
-3
A
HIS
8
1
Y
1
A
HIS
-2
A
HIS
9
1
Y
1
A
HIS
-1
A
HIS
10
1
Y
1
A
ASP
79
A
ASP
90
1
Y
1
A
ASN
80
A
ASN
91
1
Y
1
A
VAL
81
A
VAL
92
1
Y
1
A
HIS
82
A
HIS
93
1
Y
1
A
GLY
83
A
GLY
94
1
Y
1
A
TYR
226
A
TYR
237
1
Y
1
A
HIS
227
A
HIS
238
1
Y
1
A
LYS
228
A
LYS
239
1
Y
1
A
ASP
229
A
ASP
240
1
Y
1
A
GLU
230
A
GLU
241
1
Y
1
A
C1
RIB
2001
WRONG HAND
B
17.623
0.62
0.00
0.00
-0.79
0.00
0.17
0.954
0.947
0.19276
0.16733
0.1681
0.16811
1.78
25.0
1086
34056
34056
3.2
97.8
1.818
0.058
RANDOM
LIKELY RESIDUAL
1
Individual + TLS
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.102
0.098
0.80
0.80
1.40
YeiK PDB code 1Q8F
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
0.098
0.102
1.78
25.0
215
2521
11
0
2295
0.009
0.022
2399
1.305
1.975
3278
5.275
5.000
301
0.072
0.200
388
0.004
0.020
1780
0.191
0.200
1123
0.093
0.200
165
0.060
0.200
1
0.180
0.200
60
0.131
0.200
38
1.000
3.000
1516
1.743
5.000
2467
2.862
7.000
883
4.618
10.000
811
0.242
0.192
1.831
64
1826
1826
20
75.8
18
1.78
25
1YOE
34056
34056
-3
-3
0.116
1
26.2
12.5
97.8
1.78
1.86
2.9
2669
0.475
1
77.4
refinement
REFMAC
5.1.19
data reduction
DENZO
data scaling
SCALEPACK
phasing
MOLREP
Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
1
N
N
2
N
N
3
N
N
4
N
N
A
GLY
12
A
GLY
23
HELX_P
A
ALA
24
A
ALA
35
1
1
13
A
THR
41
A
THR
52
HELX_P
A
LEU
56
A
LEU
67
1
2
16
A
THR
103
A
THR
114
HELX_P
A
SER
115
A
SER
126
1
3
13
A
GLN
127
A
GLN
138
HELX_P
A
HIS
137
A
HIS
148
1
4
11
A
PRO
138
A
PRO
149
HELX_P
A
SER
142
A
SER
153
5
5
5
A
GLU
164
A
GLU
175
HELX_P
A
ASP
170
A
ASP
181
1
6
7
A
ASP
170
A
ASP
181
HELX_P
A
GLN
179
A
GLN
190
1
7
10
A
GLY
188
A
GLY
199
HELX_P
A
HIS
193
A
HIS
204
1
8
6
A
HIS
198
A
HIS
209
HELX_P
A
GLY
209
A
GLY
220
1
9
12
A
ASN
210
A
ASN
221
HELX_P
A
GLU
225
A
GLU
236
1
10
16
A
ASP
241
A
ASP
252
HELX_P
A
LYS
250
A
LYS
261
1
11
10
A
ASP
295
A
ASP
306
HELX_P
A
LYS
308
A
LYS
319
1
12
14
A
PHE
309
A
PHE
320
HELX_P
A
ALA
311
A
ALA
322
5
13
3
metalc
2.460
A
ASP
10
A
OD1
ASP
21
1_555
A
CA
1001
C
CA
CA
1_555
metalc
2.478
A
ASP
15
A
OD1
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
metalc
2.487
A
ASP
15
A
OD2
ASP
26
1_555
A
CA
1001
C
CA
CA
1_555
metalc
2.360
A
THR
124
A
O
THR
135
1_555
A
CA
1001
C
CA
CA
1_555
metalc
2.423
A
ASP
241
A
OD2
ASP
252
1_555
A
CA
1001
C
CA
CA
1_555
metalc
2.727
A
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
O2
RIB
1_555
metalc
2.437
B
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
O2
RIB
1_555
metalc
2.700
A
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
O3
RIB
1_555
metalc
2.606
B
A
CA
1001
C
CA
CA
1_555
A
RIB
2001
B
O3
RIB
1_555
metalc
2.521
A
CA
1001
C
CA
CA
1_555
A
HOH
2002
D
O
HOH
1_555
HYDROLASE
Pyrimidine nucleoside hydrolase, bacterial nucleosidase, ribose, enzyme-product complex, Hydrolase
A
PRO
11
A
PRO
22
1
A
GLY
12
A
GLY
23
-10.94
YBEK_ECOLI
UNP
1
2
P41409
ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNV
HGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTP
AAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHD
PCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA
2
311
1YOE
2
311
P41409
A
1
13
322
1
expression tag
MET
-10
1YOE
A
P41409
UNP
1
1
expression tag
ARG
-9
1YOE
A
P41409
UNP
2
1
expression tag
GLY
-8
1YOE
A
P41409
UNP
3
1
expression tag
SER
-7
1YOE
A
P41409
UNP
4
1
expression tag
HIS
-6
1YOE
A
P41409
UNP
5
1
expression tag
HIS
-5
1YOE
A
P41409
UNP
6
1
expression tag
HIS
-4
1YOE
A
P41409
UNP
7
1
expression tag
HIS
-3
1YOE
A
P41409
UNP
8
1
expression tag
HIS
-2
1YOE
A
P41409
UNP
9
1
expression tag
HIS
-1
1YOE
A
P41409
UNP
10
1
expression tag
GLY
0
1YOE
A
P41409
UNP
11
1
expression tag
SER
1
1YOE
A
P41409
UNP
12
8
2
2
parallel
parallel
parallel
parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
63
A
VAL
74
A
GLY
65
A
GLY
76
A
LEU
28
A
LEU
39
A
SER
35
A
SER
46
A
LEU
3
A
LEU
14
A
CYS
9
A
CYS
20
A
VAL
119
A
VAL
130
A
SER
123
A
SER
134
A
ILE
144
A
ILE
155
A
MET
150
A
MET
161
A
VAL
184
A
VAL
195
A
ALA
187
A
ALA
198
A
ALA
288
A
ALA
299
A
VAL
294
A
VAL
305
A
PHE
254
A
PHE
265
A
ARG
259
A
ARG
270
A
GLN
196
A
GLN
207
A
ILE
197
A
ILE
208
A
ALA
237
A
ALA
248
A
PRO
238
A
PRO
249
A
VAL
261
A
VAL
272
A
VAL
263
A
VAL
274
A
THR
274
A
THR
285
A
VAL
276
A
VAL
287
23
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