0.022815
0.000000
0.000000
0.000000
0.018961
0.000000
0.000000
0.000000
0.012690
0.00000
0.00000
0.00000
Joshi, M.D.
Sidhu, G.
Pot, I.
Brayer, G.D.
Withers, S.G.
Mcintosh, L.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
43.830
52.740
78.800
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 H9 F O3
136.122
1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
D-saccharide
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
C5 H10 O5
150.130
beta-D-xylopyranose
beta-D-xylose; D-xylose; xylose
D-saccharide, beta 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
C
N
75
S
C
N
76
S
C
N
77
R
C
N
78
N
C
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
F
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
H
N
90
N
H
N
91
N
H
N
92
N
N
N
93
S
C
N
94
N
C
N
95
N
O
N
96
N
C
N
97
N
C
N
98
N
C
N
99
N
O
N
100
N
N
N
101
N
O
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
H
N
110
N
H
N
111
N
H
N
112
N
N
N
113
S
C
N
114
N
C
N
115
N
O
N
116
N
C
N
117
N
C
N
118
N
C
N
119
N
O
N
120
N
O
N
121
N
O
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
H
N
129
N
H
N
130
N
H
N
131
N
N
N
132
N
C
N
133
N
C
N
134
N
O
N
135
N
O
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
N
C
Y
146
N
C
Y
147
N
N
Y
148
N
C
Y
149
N
C
Y
150
N
N
N
151
N
O
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
H
N
160
N
H
N
161
N
H
N
162
N
O
N
163
N
H
N
164
N
H
N
165
N
N
N
166
S
C
N
167
N
C
N
168
N
O
N
169
S
C
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
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
H
N
185
N
H
N
186
N
H
N
187
N
N
N
188
S
C
N
189
N
C
N
190
N
O
N
191
N
C
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
O
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
H
N
207
N
H
N
208
N
H
N
209
N
N
N
210
S
C
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
C
N
216
N
C
N
217
N
N
N
218
N
O
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
H
N
232
N
H
N
233
N
H
N
234
N
N
N
235
S
C
N
236
N
C
N
237
N
O
N
238
N
C
N
239
N
C
N
240
N
S
N
241
N
C
N
242
N
O
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
H
N
252
N
H
N
253
N
H
N
254
N
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
Y
262
N
C
Y
263
N
C
Y
264
N
C
N
265
N
O
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
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
C
N
283
N
C
N
284
N
O
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
H
N
292
N
H
N
293
N
H
N
294
N
N
N
295
S
C
N
296
N
C
N
297
N
O
N
298
N
C
N
299
N
O
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
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
R
C
N
313
N
O
N
314
N
C
N
315
N
O
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
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
N
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
N
339
N
O
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
N
N
353
S
C
N
354
N
C
N
355
N
O
N
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
O
N
364
N
O
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
N
381
N
C
N
382
N
C
N
383
N
O
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
O
N
396
R
C
N
397
R
C
N
398
S
C
N
399
R
C
N
400
N
C
N
401
N
O
N
402
N
O
N
403
N
O
N
404
N
O
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
412
N
H
N
413
N
H
N
414
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
sing
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
doub
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
doub
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
Y
145
N
sing
Y
146
N
doub
Y
147
N
doub
N
148
N
sing
Y
149
N
sing
N
150
N
sing
Y
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
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
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
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
doub
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
doub
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
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
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
doub
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
Y
253
N
doub
Y
254
N
sing
Y
255
N
sing
N
256
N
sing
Y
257
N
doub
N
258
N
sing
Y
259
N
doub
N
260
N
sing
Y
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
doub
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
doub
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
doub
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
doub
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
Y
322
N
doub
Y
323
N
sing
Y
324
N
sing
N
325
N
sing
Y
326
N
doub
Y
327
N
sing
Y
328
N
sing
N
329
N
sing
Y
330
N
sing
Y
331
N
doub
N
332
N
sing
Y
333
N
doub
N
334
N
sing
Y
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
sing
N
345
N
doub
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
Y
350
N
doub
Y
351
N
sing
Y
352
N
sing
N
353
N
sing
Y
354
N
doub
N
355
N
sing
Y
356
N
doub
N
357
N
sing
Y
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
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
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
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
299
255
279
10.1006/jmbi.2000.3722
10860737
Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
2000
10.2210/pdb1c5i/pdb
pdb_00001c5i
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
IMAGE PLATE
RIGAKU RAXIS IIC
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
2-DEOXY-2-FLUORO-XYLOBIOSE COVALENTLY BONDED TO GLU 78 OE2
20409.988
ENDO-1,4-BETA-XYLANASE
3.2.1.8
CATALYTIC DOMAIN
N35D
1
man
polymer
268.237
beta-D-xylopyranose-(1-4)-1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
1
man
branched
18.015
water
129
nat
water
BCX
no
no
ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGDFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYY
VVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNL
GSNWAYQVMATEGYQSSGSSNVTVW
ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGDFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYY
VVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNL
GSNWAYQVMATEGYQSSGSSNVTVW
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
Bacillus
Escherichia
Escherichia coli
sample
1397
Bacillus circulans
511693
Escherichia coli BL21
BL21
PLASMID
PCW
1
2.23
44.86
7.5
pH 7.5
atom_site
chem_comp
entity
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
database_2
struct_conn
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Atomic model
Data collection
Derived calculations
Structure summary
Database references
Derived calculations
Structure summary
Data collection
1
0
2000-05-12
1
1
2007-10-16
1
2
2011-07-13
2
0
2020-07-29
2
1
2021-11-03
2
2
2023-12-27
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.type_symbol
_chem_comp.name
_chem_comp.type
_pdbx_struct_assembly_gen.asym_id_list
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_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_asym_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
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
DFX
501
n
B
DFX
1
DFX
501
n
B
XYP
2
D-1-deoxy-Xylp2fluoro
DXylpb
b-D-xylopyranose
b-D-Xylp
Xyl
RCSB
Y
RCSB
1999-11-24
REL
REL
oligosaccharide
WURCS=2.0/2,2,1/[h212h_1-5_2*F][a212h-1b_1-5]/1-2/a4-b1
2
PDB2Glycan
1.1.0
WURCS
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{}}
2
PDB-CARE
LINUCS
C1
O4
XYP
DFX
2
1
2
O1
HO4
sing
n
n
HOH
water
HOH
1
3
HOH
HOH
503
A
HOH
2
3
HOH
HOH
504
A
HOH
3
3
HOH
HOH
505
A
HOH
4
3
HOH
HOH
506
A
HOH
5
3
HOH
HOH
507
A
HOH
7
3
HOH
HOH
508
A
HOH
8
3
HOH
HOH
509
A
HOH
9
3
HOH
HOH
510
A
HOH
10
3
HOH
HOH
511
A
HOH
11
3
HOH
HOH
512
A
HOH
12
3
HOH
HOH
513
A
HOH
13
3
HOH
HOH
514
A
HOH
14
3
HOH
HOH
515
A
HOH
15
3
HOH
HOH
516
A
HOH
16
3
HOH
HOH
517
A
HOH
17
3
HOH
HOH
518
A
HOH
18
3
HOH
HOH
519
A
HOH
19
3
HOH
HOH
520
A
HOH
20
3
HOH
HOH
521
A
HOH
21
3
HOH
HOH
522
A
HOH
22
3
HOH
HOH
523
A
HOH
24
3
HOH
HOH
524
A
HOH
25
3
HOH
HOH
525
A
HOH
26
3
HOH
HOH
526
A
HOH
27
3
HOH
HOH
527
A
HOH
28
3
HOH
HOH
528
A
HOH
29
3
HOH
HOH
529
A
HOH
30
3
HOH
HOH
530
A
HOH
31
3
HOH
HOH
531
A
HOH
32
3
HOH
HOH
532
A
HOH
33
3
HOH
HOH
533
A
HOH
34
3
HOH
HOH
534
A
HOH
35
3
HOH
HOH
535
A
HOH
36
3
HOH
HOH
536
A
HOH
37
3
HOH
HOH
537
A
HOH
38
3
HOH
HOH
538
A
HOH
39
3
HOH
HOH
539
A
HOH
40
3
HOH
HOH
540
A
HOH
41
3
HOH
HOH
541
A
HOH
42
3
HOH
HOH
542
A
HOH
43
3
HOH
HOH
543
A
HOH
44
3
HOH
HOH
544
A
HOH
45
3
HOH
HOH
545
A
HOH
46
3
HOH
HOH
546
A
HOH
47
3
HOH
HOH
547
A
HOH
48
3
HOH
HOH
548
A
HOH
49
3
HOH
HOH
549
A
HOH
50
3
HOH
HOH
550
A
HOH
52
3
HOH
HOH
551
A
HOH
53
3
HOH
HOH
552
A
HOH
54
3
HOH
HOH
553
A
HOH
55
3
HOH
HOH
554
A
HOH
56
3
HOH
HOH
555
A
HOH
58
3
HOH
HOH
556
A
HOH
59
3
HOH
HOH
557
A
HOH
60
3
HOH
HOH
558
A
HOH
61
3
HOH
HOH
559
A
HOH
62
3
HOH
HOH
560
A
HOH
63
3
HOH
HOH
561
A
HOH
64
3
HOH
HOH
562
A
HOH
66
3
HOH
HOH
563
A
HOH
67
3
HOH
HOH
564
A
HOH
68
3
HOH
HOH
565
A
HOH
69
3
HOH
HOH
566
A
HOH
70
3
HOH
HOH
567
A
HOH
72
3
HOH
HOH
568
A
HOH
73
3
HOH
HOH
569
A
HOH
75
3
HOH
HOH
570
A
HOH
76
3
HOH
HOH
571
A
HOH
77
3
HOH
HOH
572
A
HOH
78
3
HOH
HOH
573
A
HOH
79
3
HOH
HOH
574
A
HOH
80
3
HOH
HOH
575
A
HOH
81
3
HOH
HOH
576
A
HOH
82
3
HOH
HOH
577
A
HOH
83
3
HOH
HOH
578
A
HOH
85
3
HOH
HOH
579
A
HOH
86
3
HOH
HOH
580
A
HOH
87
3
HOH
HOH
581
A
HOH
89
3
HOH
HOH
582
A
HOH
90
3
HOH
HOH
583
A
HOH
91
3
HOH
HOH
584
A
HOH
92
3
HOH
HOH
585
A
HOH
93
3
HOH
HOH
586
A
HOH
94
3
HOH
HOH
587
A
HOH
100
3
HOH
HOH
588
A
HOH
101
3
HOH
HOH
589
A
HOH
103
3
HOH
HOH
590
A
HOH
104
3
HOH
HOH
591
A
HOH
105
3
HOH
HOH
592
A
HOH
107
3
HOH
HOH
593
A
HOH
108
3
HOH
HOH
594
A
HOH
109
3
HOH
HOH
595
A
HOH
110
3
HOH
HOH
596
A
HOH
111
3
HOH
HOH
597
A
HOH
112
3
HOH
HOH
598
A
HOH
113
3
HOH
HOH
599
A
HOH
117
3
HOH
HOH
600
A
HOH
118
3
HOH
HOH
601
A
HOH
119
3
HOH
HOH
602
A
HOH
120
3
HOH
HOH
603
A
HOH
122
3
HOH
HOH
604
A
HOH
123
3
HOH
HOH
605
A
HOH
125
3
HOH
HOH
606
A
HOH
127
3
HOH
HOH
607
A
HOH
128
3
HOH
HOH
608
A
HOH
129
3
HOH
HOH
609
A
HOH
131
3
HOH
HOH
610
A
HOH
132
3
HOH
HOH
611
A
HOH
134
3
HOH
HOH
612
A
HOH
137
3
HOH
HOH
613
A
HOH
139
3
HOH
HOH
614
A
HOH
141
3
HOH
HOH
615
A
HOH
142
3
HOH
HOH
616
A
HOH
143
3
HOH
HOH
617
A
HOH
144
3
HOH
HOH
618
A
HOH
145
3
HOH
HOH
619
A
HOH
146
3
HOH
HOH
620
A
HOH
151
3
HOH
HOH
621
A
HOH
153
3
HOH
HOH
622
A
HOH
154
3
HOH
HOH
623
A
HOH
155
3
HOH
HOH
624
A
HOH
156
3
HOH
HOH
625
A
HOH
157
3
HOH
HOH
626
A
HOH
159
3
HOH
HOH
627
A
HOH
161
3
HOH
HOH
628
A
HOH
170
3
HOH
HOH
629
A
HOH
171
3
HOH
HOH
630
A
HOH
176
3
HOH
HOH
631
A
ALA
1
n
1
ALA
1
A
SER
2
n
2
SER
2
A
THR
3
n
3
THR
3
A
ASP
4
n
4
ASP
4
A
TYR
5
n
5
TYR
5
A
TRP
6
n
6
TRP
6
A
GLN
7
n
7
GLN
7
A
ASN
8
n
8
ASN
8
A
TRP
9
n
9
TRP
9
A
THR
10
n
10
THR
10
A
ASP
11
n
11
ASP
11
A
GLY
12
n
12
GLY
12
A
GLY
13
n
13
GLY
13
A
GLY
14
n
14
GLY
14
A
ILE
15
n
15
ILE
15
A
VAL
16
n
16
VAL
16
A
ASN
17
n
17
ASN
17
A
ALA
18
n
18
ALA
18
A
VAL
19
n
19
VAL
19
A
ASN
20
n
20
ASN
20
A
GLY
21
n
21
GLY
21
A
SER
22
n
22
SER
22
A
GLY
23
n
23
GLY
23
A
GLY
24
n
24
GLY
24
A
ASN
25
n
25
ASN
25
A
TYR
26
n
26
TYR
26
A
SER
27
n
27
SER
27
A
VAL
28
n
28
VAL
28
A
ASN
29
n
29
ASN
29
A
TRP
30
n
30
TRP
30
A
SER
31
n
31
SER
31
A
ASN
32
n
32
ASN
32
A
THR
33
n
33
THR
33
A
GLY
34
n
34
GLY
34
A
ASP
35
n
35
ASP
35
A
PHE
36
n
36
PHE
36
A
VAL
37
n
37
VAL
37
A
VAL
38
n
38
VAL
38
A
GLY
39
n
39
GLY
39
A
LYS
40
n
40
LYS
40
A
GLY
41
n
41
GLY
41
A
TRP
42
n
42
TRP
42
A
THR
43
n
43
THR
43
A
THR
44
n
44
THR
44
A
GLY
45
n
45
GLY
45
A
SER
46
n
46
SER
46
A
PRO
47
n
47
PRO
47
A
PHE
48
n
48
PHE
48
A
ARG
49
n
49
ARG
49
A
THR
50
n
50
THR
50
A
ILE
51
n
51
ILE
51
A
ASN
52
n
52
ASN
52
A
TYR
53
n
53
TYR
53
A
ASN
54
n
54
ASN
54
A
ALA
55
n
55
ALA
55
A
GLY
56
n
56
GLY
56
A
VAL
57
n
57
VAL
57
A
TRP
58
n
58
TRP
58
A
ALA
59
n
59
ALA
59
A
PRO
60
n
60
PRO
60
A
ASN
61
n
61
ASN
61
A
GLY
62
n
62
GLY
62
A
ASN
63
n
63
ASN
63
A
GLY
64
n
64
GLY
64
A
TYR
65
n
65
TYR
65
A
LEU
66
n
66
LEU
66
A
THR
67
n
67
THR
67
A
LEU
68
n
68
LEU
68
A
TYR
69
n
69
TYR
69
A
GLY
70
n
70
GLY
70
A
TRP
71
n
71
TRP
71
A
THR
72
n
72
THR
72
A
ARG
73
n
73
ARG
73
A
SER
74
n
74
SER
74
A
PRO
75
n
75
PRO
75
A
LEU
76
n
76
LEU
76
A
ILE
77
n
77
ILE
77
A
GLU
78
n
78
GLU
78
A
TYR
79
n
79
TYR
79
A
TYR
80
n
80
TYR
80
A
VAL
81
n
81
VAL
81
A
VAL
82
n
82
VAL
82
A
ASP
83
n
83
ASP
83
A
SER
84
n
84
SER
84
A
TRP
85
n
85
TRP
85
A
GLY
86
n
86
GLY
86
A
THR
87
n
87
THR
87
A
TYR
88
n
88
TYR
88
A
ARG
89
n
89
ARG
89
A
PRO
90
n
90
PRO
90
A
THR
91
n
91
THR
91
A
GLY
92
n
92
GLY
92
A
THR
93
n
93
THR
93
A
TYR
94
n
94
TYR
94
A
LYS
95
n
95
LYS
95
A
GLY
96
n
96
GLY
96
A
THR
97
n
97
THR
97
A
VAL
98
n
98
VAL
98
A
LYS
99
n
99
LYS
99
A
SER
100
n
100
SER
100
A
ASP
101
n
101
ASP
101
A
GLY
102
n
102
GLY
102
A
GLY
103
n
103
GLY
103
A
THR
104
n
104
THR
104
A
TYR
105
n
105
TYR
105
A
ASP
106
n
106
ASP
106
A
ILE
107
n
107
ILE
107
A
TYR
108
n
108
TYR
108
A
THR
109
n
109
THR
109
A
THR
110
n
110
THR
110
A
THR
111
n
111
THR
111
A
ARG
112
n
112
ARG
112
A
TYR
113
n
113
TYR
113
A
ASN
114
n
114
ASN
114
A
ALA
115
n
115
ALA
115
A
PRO
116
n
116
PRO
116
A
SER
117
n
117
SER
117
A
ILE
118
n
118
ILE
118
A
ASP
119
n
119
ASP
119
A
GLY
120
n
120
GLY
120
A
ASP
121
n
121
ASP
121
A
ARG
122
n
122
ARG
122
A
THR
123
n
123
THR
123
A
THR
124
n
124
THR
124
A
PHE
125
n
125
PHE
125
A
THR
126
n
126
THR
126
A
GLN
127
n
127
GLN
127
A
TYR
128
n
128
TYR
128
A
TRP
129
n
129
TRP
129
A
SER
130
n
130
SER
130
A
VAL
131
n
131
VAL
131
A
ARG
132
n
132
ARG
132
A
GLN
133
n
133
GLN
133
A
SER
134
n
134
SER
134
A
LYS
135
n
135
LYS
135
A
ARG
136
n
136
ARG
136
A
PRO
137
n
137
PRO
137
A
THR
138
n
138
THR
138
A
GLY
139
n
139
GLY
139
A
SER
140
n
140
SER
140
A
ASN
141
n
141
ASN
141
A
ALA
142
n
142
ALA
142
A
THR
143
n
143
THR
143
A
ILE
144
n
144
ILE
144
A
THR
145
n
145
THR
145
A
PHE
146
n
146
PHE
146
A
THR
147
n
147
THR
147
A
ASN
148
n
148
ASN
148
A
HIS
149
n
149
HIS
149
A
VAL
150
n
150
VAL
150
A
ASN
151
n
151
ASN
151
A
ALA
152
n
152
ALA
152
A
TRP
153
n
153
TRP
153
A
LYS
154
n
154
LYS
154
A
SER
155
n
155
SER
155
A
HIS
156
n
156
HIS
156
A
GLY
157
n
157
GLY
157
A
MET
158
n
158
MET
158
A
ASN
159
n
159
ASN
159
A
LEU
160
n
160
LEU
160
A
GLY
161
n
161
GLY
161
A
SER
162
n
162
SER
162
A
ASN
163
n
163
ASN
163
A
TRP
164
n
164
TRP
164
A
ALA
165
n
165
ALA
165
A
TYR
166
n
166
TYR
166
A
GLN
167
n
167
GLN
167
A
VAL
168
n
168
VAL
168
A
MET
169
n
169
MET
169
A
ALA
170
n
170
ALA
170
A
THR
171
n
171
THR
171
A
GLU
172
n
172
GLU
172
A
GLY
173
n
173
GLY
173
A
TYR
174
n
174
TYR
174
A
GLN
175
n
175
GLN
175
A
SER
176
n
176
SER
176
A
SER
177
n
177
SER
177
A
GLY
178
n
178
GLY
178
A
SER
179
n
179
SER
179
A
SER
180
n
180
SER
180
A
ASN
181
n
181
ASN
181
A
VAL
182
n
182
VAL
182
A
THR
183
n
183
THR
183
A
VAL
184
n
184
VAL
184
A
TRP
185
n
185
TRP
185
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
O
TYR
5
A
O
TYR
5
A
N
GLY
41
A
N
GLY
41
A
O
PHE
36
A
O
PHE
36
A
N
GLY
173
A
N
GLY
173
A
O
VAL
168
A
O
VAL
168
A
N
TYR
69
A
N
TYR
69
A
O
LEU
66
A
O
LEU
66
A
N
SER
84
A
N
SER
84
A
O
GLU
78
A
O
GLU
78
A
N
THR
126
A
N
THR
126
A
O
PHE
125
A
O
PHE
125
A
N
ARG
112
A
N
ARG
112
A
O
GLY
103
A
O
GLY
103
A
N
SER
100
A
N
SER
100
A
O
ILE
15
A
O
ILE
15
A
N
SER
31
A
N
SER
31
A
O
TYR
26
A
O
TYR
26
A
N
VAL
182
A
N
VAL
182
A
O
SER
177
A
O
SER
177
A
N
ASN
61
A
N
ASN
61
A
O
ILE
51
A
O
ILE
51
A
N
ILE
144
A
N
ILE
144
1
-15.46
2.50
113.10
97.64
A
A
A
N
CA
C
GLY
GLY
GLY
34
34
34
N
1
A
ASN
61
-111.26
61.86
1
A
ASP
121
52.50
-150.46
1
A
ALA
165
-100.59
-158.26
0.193
0.193
1.8
10
16559
94
1
0.0
OTHER
1.8
10
129
1595
18
0
1448
0.007
1.136
1.8
50
1C5I
17579
0
0.073
1
25.8
5.6
99.9
model building
X-PLOR
refinement
X-PLOR
3.851
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE
1
N
N
2
N
N
3
N
N
A
PHE
146
A
PHE
146
HELX_P
A
HIS
156
A
HIS
156
1
1
11
covale
1.448
none
A
GLU
78
A
OE2
GLU
78
1_555
B
DFX
1
B
C1
DFX
1_555
covale
1.428
one
B
DFX
1
B
O4
DFX
1_555
B
XYP
2
B
C1
XYP
1_555
HYDROLASE
GLYCOSIDASE, PH-DEPENDENT ENZYME MECHANISM, GENERAL ACID/ BASE CATALYSIS, ISOTOPE SHIFT, SHORT HYDROGEN BONDS, XYLAN, HYDROLASE
A
SER
74
A
SER
74
1
A
PRO
75
A
PRO
75
-0.09
XYNA_BACCI
UNP
1
P09850
29
213
1C5I
1
185
P09850
A
1
1
185
1
ASN
engineered mutation
ASP
35
1C5I
A
P09850
UNP
63
35
8
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
5
A
TYR
5
A
THR
10
A
THR
10
A
ASP
35
A
ASP
35
A
TRP
42
A
TRP
42
A
GLN
167
A
GLN
167
A
TYR
174
A
TYR
174
A
GLY
64
A
GLY
64
A
THR
72
A
THR
72
A
ILE
77
A
ILE
77
A
TRP
85
A
TRP
85
A
PHE
125
A
PHE
125
A
ARG
132
A
ARG
132
A
GLY
103
A
GLY
103
A
ARG
112
A
ARG
112
A
THR
93
A
THR
93
A
SER
100
A
SER
100
A
ILE
15
A
ILE
15
A
ASN
20
A
ASN
20
A
ASN
25
A
ASN
25
A
SER
31
A
SER
31
A
SER
177
A
SER
177
A
TRP
185
A
TRP
185
A
THR
50
A
THR
50
A
ASN
61
A
ASN
61
A
ALA
142
A
ALA
142
A
THR
145
A
THR
145
THE NUCLEOPHILE TO WHICH THE INHIBITOR IS COVALENTLY ATTACHED IS GLU 78.
Author
1
THE ACID BASE CATALYST IS RESIDUE GLU 172.
Author
1
A
GLU
78
A
GLU
78
1
1_555
A
GLU
172
A
GLU
172
1
1_555
19
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