0.031427
0.000000
0.000000
0.000000
0.025253
0.000000
0.000000
0.000000
0.015713
0.00000
0.00000
0.00000
Saul, F.A.
Rovira, P.
Boulot, G.
Van Damme, E.J.M.
Peumans, W.J.
Truffa-Bachi, P.
Bentley, G.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
31.820
39.600
63.640
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta linking
C5 H7 N O3
129.114
n
PYROGLUTAMIC ACID
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
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
R
C
N
231
R
C
N
232
R
C
N
233
S
C
N
234
R
C
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
N
N
239
N
O
N
240
N
O
N
241
N
O
N
242
N
O
N
243
N
O
N
244
N
O
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
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
O
N
266
N
C
N
267
N
O
N
268
N
O
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
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
C
N
282
N
C
N
283
N
O
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
H
N
292
N
H
N
293
N
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
O
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
R
C
N
312
N
O
N
313
N
C
N
314
N
O
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
N
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
N
338
N
O
N
339
N
H
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
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
N
362
N
O
N
363
N
O
N
364
N
H
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
N
N
376
S
C
N
377
N
C
N
378
N
O
N
379
N
C
N
380
N
C
N
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
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
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
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
doub
N
261
N
doub
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
doub
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
doub
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
doub
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
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
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
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
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
sing
N
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
doub
N
369
N
sing
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
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
8
593
603
10.1016/S0969-2126(00)00142-8
10873861
Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
2000
NE
Plant Mol.Biol.
PMBIDB
2006
0167-4412
39
335
347
10.1023/A:1006134932290
Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family
1999
10.2210/pdb1en2/pdb
pdb_00001en2
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
298.0
1
IMAGE PLATE
1999-07-06
MARRESEARCH
IMAGE PLATE
1999-07-16
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.375
1.0
0.966
1.0
D41A
LURE
1.375
SYNCHROTRON
LURE BEAMLINE D41A
DW32
LURE
0.966
SYNCHROTRON
LURE BEAMLINE DW32
THREE ISOFORMS ARE PRESENT IN THE CRYSTAL: ISOLECTIN I, V, AND VI
9350.269
AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI
1
nat
polymer
830.786
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
18.015
water
76
nat
water
UDA
no
yes
(PCA)RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDY
CSGGNCQYRCSSS
QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG
NCQYRCSSS
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
y
y
n
n
n
y
y
n
y
y
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
y
y
y
y
n
n
n
n
n
n
n
n
great nettle
PURIFIED FROM THE RHIZOMES
Urtica
sample
3501
Urtica dioica
1
2.13
42.25
VAPOR DIFFUSION, SITTING DROP
6.0
PEG 6000, sodium acetate, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
290.0
entity_poly
pdbx_struct_mod_residue
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_ref_seq_dif
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
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_close_contact
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_unobs_or_zero_occ_atoms
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Other
Advisory
Database references
Derived calculations
Polymer sequence
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
Advisory
Data collection
Database references
Refinement description
Structure summary
1
0
2000-06-21
1
1
2008-04-27
1
2
2011-07-13
1
3
2014-02-05
2
0
2019-12-25
3
0
2020-07-29
3
1
2023-08-09
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_struct_mod_residue.parent_comp_id
_struct_conn.pdbx_leaving_atom_flag
_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_seq_id
_atom_site.label_asym_id
_atom_site.occupancy
_chem_comp.name
_chem_comp.type
_entity.formula_weight
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.type
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_unobs_or_zero_occ_atoms.auth_asym_id
_pdbx_unobs_or_zero_occ_atoms.auth_seq_id
_pdbx_unobs_or_zero_occ_atoms.label_seq_id
_pdbx_validate_close_contact.auth_asym_id_1
_pdbx_validate_close_contact.auth_seq_id_1
_struct_conn.pdbx_dist_value
_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
E
NAG
4
n
B
NAG
1
D
NAG
3
n
B
NAG
2
C
NAG
2
n
B
NAG
3
B
NAG
1
n
B
NAG
4
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
UDA uncomplexed form
UDA trisaccharide complex
RCSB
Y
RCSB
2000-03-20
REL
REL
oligosaccharide
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1
2
PDB2Glycan
1.1.0
WURCS
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}
2
PDB-CARE
LINUCS
C1
O4
NAG
NAG
2
1
2
O1
HO4
sing
C1
O4
NAG
NAG
3
2
2
O1
HO4
sing
C1
O4
NAG
NAG
4
3
2
O1
HO4
sing
n
n
n
n
HOH
water
The structure comprises two hevein-like domains,
each containing a distinct saccharide-binding site.
The two binding sites are located at opposite
extremities of the molecule.
THE N-TERMINAL RESIDUE IS PYRROLIDONE CARBOXYLIC
ACID (PCA). A DUAL CONFORMATION IS SEEN for all or
part of the residue at LEU15, GLU28, SER45, ASN74.
NO INTERPRETABLE DENSITY IS SEEN FOR C-TERMINAL
RESIDUES SER87, SER88, AND SER89.
The principal binding-site residues are SER 19,
TRP 21, TRP 23, and TYR 30 on the first domain,
and the homologous residues SER 65, HIS 67,
TRP 69, and TYR 76 on the second domain.
The crystallographic asymmetric unit contains one
molecule of UDA and a single tetrasaccharide ligand.
The ligand interacts simultaneously with the
binding site on the N-terminal domain of one
molecule and that of the C-terminal domain of
a symmetry-related molecule.
1EIS
PDB
experimental model
WAT
1
3
HOH
HOH
94
A
WAT
2
3
HOH
HOH
95
A
WAT
3
3
HOH
HOH
96
A
WAT
4
3
HOH
HOH
97
A
WAT
5
3
HOH
HOH
98
A
WAT
6
3
HOH
HOH
99
A
WAT
7
3
HOH
HOH
100
A
WAT
8
3
HOH
HOH
101
A
WAT
9
3
HOH
HOH
102
A
WAT
10
3
HOH
HOH
103
A
WAT
11
3
HOH
HOH
104
A
WAT
12
3
HOH
HOH
105
A
WAT
13
3
HOH
HOH
106
A
WAT
14
3
HOH
HOH
107
A
WAT
15
3
HOH
HOH
108
A
WAT
16
3
HOH
HOH
109
A
WAT
17
3
HOH
HOH
110
A
WAT
18
3
HOH
HOH
111
A
WAT
19
3
HOH
HOH
112
A
WAT
20
3
HOH
HOH
113
A
WAT
21
3
HOH
HOH
114
A
WAT
22
3
HOH
HOH
115
A
WAT
23
3
HOH
HOH
116
A
WAT
24
3
HOH
HOH
117
A
WAT
25
3
HOH
HOH
118
A
WAT
26
3
HOH
HOH
119
A
WAT
27
3
HOH
HOH
120
A
WAT
28
3
HOH
HOH
121
A
WAT
29
3
HOH
HOH
122
A
WAT
30
3
HOH
HOH
123
A
WAT
31
3
HOH
HOH
124
A
WAT
32
3
HOH
HOH
125
A
WAT
33
3
HOH
HOH
126
A
WAT
34
3
HOH
HOH
127
A
WAT
35
3
HOH
HOH
128
A
WAT
36
3
HOH
HOH
129
A
WAT
37
3
HOH
HOH
130
A
WAT
38
3
HOH
HOH
131
A
WAT
39
3
HOH
HOH
132
A
WAT
40
3
HOH
HOH
133
A
WAT
41
3
HOH
HOH
134
A
WAT
42
3
HOH
HOH
135
A
WAT
43
3
HOH
HOH
136
A
WAT
44
3
HOH
HOH
137
A
WAT
45
3
HOH
HOH
138
A
WAT
46
3
HOH
HOH
139
A
WAT
47
3
HOH
HOH
140
A
WAT
48
3
HOH
HOH
141
A
WAT
49
3
HOH
HOH
142
A
WAT
50
3
HOH
HOH
143
A
WAT
51
3
HOH
HOH
144
A
WAT
52
3
HOH
HOH
145
A
WAT
53
3
HOH
HOH
146
A
WAT
54
3
HOH
HOH
147
A
WAT
55
3
HOH
HOH
148
A
WAT
56
3
HOH
HOH
149
A
WAT
57
3
HOH
HOH
150
A
WAT
58
3
HOH
HOH
151
A
WAT
59
3
HOH
HOH
152
A
WAT
60
3
HOH
HOH
153
A
WAT
61
3
HOH
HOH
154
A
WAT
62
3
HOH
HOH
155
A
WAT
63
3
HOH
HOH
156
A
WAT
64
3
HOH
HOH
157
A
WAT
65
3
HOH
HOH
158
A
WAT
66
3
HOH
HOH
159
A
WAT
67
3
HOH
HOH
160
A
WAT
68
3
HOH
HOH
161
A
WAT
69
3
HOH
HOH
162
A
WAT
70
3
HOH
HOH
163
A
WAT
71
3
HOH
HOH
164
A
WAT
72
3
HOH
HOH
165
A
WAT
73
3
HOH
HOH
166
A
WAT
74
3
HOH
HOH
167
A
WAT
76
3
HOH
HOH
168
A
WAT
77
3
HOH
HOH
169
A
PCA
1
n
1
PCA
1
A
ARG
2
n
2
ARG
2
A
CYS
3
n
3
CYS
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
GLN
6
n
6
GLN
6
A
GLY
7
n
7
GLY
7
A
GLY
8
n
8
GLY
8
A
GLY
9
n
9
GLY
9
A
SER
10
y
10
SER
10
A
GLY
10
y
10
GLY
10
A
THR
11
n
11
THR
11
A
CYS
12
n
12
CYS
12
A
PRO
13
n
13
PRO
13
A
GLY
14
y
14
GLY
14
A
ALA
14
y
14
ALA
14
A
LEU
15
n
15
LEU
15
A
ARG
16
y
16
ARG
16
A
TRP
16
y
16
TRP
16
A
CYS
17
n
17
CYS
17
A
CYS
18
n
18
CYS
18
A
SER
19
n
19
SER
19
A
ILE
20
n
20
ILE
20
A
TRP
21
n
21
TRP
21
A
GLY
22
n
22
GLY
22
A
TRP
23
n
23
TRP
23
A
CYS
24
n
24
CYS
24
A
GLY
25
n
25
GLY
25
A
ASP
26
n
26
ASP
26
A
SER
27
n
27
SER
27
A
GLU
28
n
28
GLU
28
A
PRO
29
n
29
PRO
29
A
TYR
30
n
30
TYR
30
A
CYS
31
n
31
CYS
31
A
GLY
32
n
32
GLY
32
A
ARG
33
n
33
ARG
33
A
THR
34
n
34
THR
34
A
CYS
35
n
35
CYS
35
A
GLU
36
n
36
GLU
36
A
ASN
37
n
37
ASN
37
A
LYS
38
n
38
LYS
38
A
CYS
39
n
39
CYS
39
A
TRP
40
n
40
TRP
40
A
SER
41
n
41
SER
41
A
GLY
42
n
42
GLY
42
A
GLU
43
n
43
GLU
43
A
ARG
44
n
44
ARG
44
A
SER
45
n
45
SER
45
A
ASP
46
n
46
ASP
46
A
HIS
47
n
47
HIS
47
A
ARG
48
n
48
ARG
48
A
CYS
49
n
49
CYS
49
A
GLY
50
n
50
GLY
50
A
ALA
51
n
51
ALA
51
A
ALA
52
n
52
ALA
52
A
VAL
53
n
53
VAL
53
A
GLY
54
n
54
GLY
54
A
ASN
55
n
55
ASN
55
A
PRO
56
n
56
PRO
56
A
PRO
57
n
57
PRO
57
A
CYS
58
n
58
CYS
58
A
GLY
59
n
59
GLY
59
A
GLN
60
n
60
GLN
60
A
ASP
61
n
61
ASP
61
A
ARG
62
n
62
ARG
62
A
CYS
63
n
63
CYS
63
A
CYS
64
n
64
CYS
64
A
SER
65
n
65
SER
65
A
VAL
66
n
66
VAL
66
A
HIS
67
n
67
HIS
67
A
GLY
68
n
68
GLY
68
A
TRP
69
n
69
TRP
69
A
CYS
70
n
70
CYS
70
A
GLY
71
n
71
GLY
71
A
GLY
72
n
72
GLY
72
A
GLY
73
n
73
GLY
73
A
ASN
74
n
74
ASN
74
A
ASP
75
n
75
ASP
75
A
TYR
76
n
76
TYR
76
A
CYS
77
n
77
CYS
77
A
SER
78
n
78
SER
78
A
GLY
79
n
79
GLY
79
A
GLY
80
y
80
GLY
80
A
SER
80
y
80
SER
80
A
ASN
81
y
81
ASN
81
A
LYS
81
y
81
LYS
81
A
CYS
82
n
82
CYS
82
A
GLN
83
n
83
GLN
83
A
TYR
84
n
84
TYR
84
A
ARG
85
n
85
ARG
85
A
CYS
86
n
86
CYS
86
A
n
87
87
A
n
88
88
A
n
89
89
A
author_defined_assembly
1
monomeric
A
PCA
1
PYROGLUTAMIC ACID
A
PCA
1
GLN
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
GLY
25
A
N
GLY
25
A
O
CYS
17
A
O
CYS
17
A
O
CYS
18
A
O
CYS
18
A
N
GLU
36
A
N
GLU
36
A
O
GLY
71
A
O
GLY
71
A
N
CYS
63
A
N
CYS
63
A
O
CYS
64
A
O
CYS
64
A
N
GLN
83
A
N
GLN
83
1
A
CG
ARG
33
A
CG
ARG
33
0
Y
1
A
CD
ARG
33
A
CD
ARG
33
0
Y
1
A
NE
ARG
33
A
NE
ARG
33
0
Y
1
A
CZ
ARG
33
A
CZ
ARG
33
0
Y
1
A
NH1
ARG
33
A
NH1
ARG
33
0
Y
1
A
NH2
ARG
33
A
NH2
ARG
33
0
Y
1
B
O1
NAG
1
B
O1
NAG
1
1
N
1
B
C7
NAG
1
B
C7
NAG
0
N
1
B
C8
NAG
1
B
C8
NAG
0
N
1
B
O7
NAG
1
B
O7
NAG
0
N
1
A
SER
87
A
SER
87
1
Y
1
A
SER
88
A
SER
88
1
Y
1
A
SER
89
A
SER
89
1
Y
1
A
A
O
O
HOH
HOH
167
168
2.16
1
B
A
O7
O
NAG
HOH
1
166
2.18
1
A
GLY
79
16.01
A
1
A
LYS
81
-11.33
B
1
A
A
GLY
GLY
79
80
A
A
148.64
1
A
A
C
N
GLY
GLY
79
80
1.13
A
A
1
A
A
C
N
GLY
SER
79
80
0.84
B
B
1
3.63
0.50
120.30
123.93
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
33
33
33
N
1
22.90
2.00
116.20
139.10
A
A
A
CA
C
N
GLY
GLY
GLY
79
79
80
A
A
A
Y
1
-26.25
1.70
123.20
96.95
A
A
A
O
C
N
GLY
GLY
GLY
79
79
80
A
A
A
Y
1
31.73
2.10
122.30
154.03
A
A
A
C
N
CA
GLY
GLY
GLY
79
80
80
A
A
A
Y
1
20.43
2.20
117.20
137.63
A
A
A
CA
C
N
GLY
GLY
SER
79
79
80
B
B
B
Y
1
-22.50
1.60
122.70
100.20
A
A
A
O
C
N
GLY
GLY
SER
79
79
80
B
B
B
Y
1
37.08
2.50
121.70
158.78
A
A
A
C
N
CA
GLY
SER
SER
79
80
80
B
B
B
Y
1
-4.53
0.50
120.30
115.77
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
85
85
85
N
1
A
A
C
N
GLY
GLY
79
80
-0.204
0.023
1.336
1.132
A
A
Y
1
A
A
C
N
GLY
SER
79
80
-0.493
0.023
1.336
0.843
B
B
Y
1
A
SER
80
B
47.98
-0.68
The structure was determined by molecular replacement methods based on the uncomplexed UDA structure (1EIS). A bulk solvent correction was applied.
0.203
0.189
0.198
0.198
1.4
25.0
766
15499
15499
96.2
RANDOM
1
0.0
0.0
MOLECULAR REPLACEMENT
1EIS
Engh & Huber
1.4
25.0
76
792
56
0
660
0.014
0.020
0.015
0.020
0.017
0.030
0.020
0.132
0.150
0.152
0.300
0.210
0.300
0.000
15.000
4.900
7.000
16.700
15.000
27.800
20.000
1.466
2.000
2.291
3.000
2.387
3.000
3.555
4.000
22.3
1.4
25.0
1EN2
15524
15524
0.0
0.049
1
25.5
9.4
96.5
0.328
1.40
1.45
1473
1
7.3
94.2
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
REFMAC
UDA TETRASACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II
1
N
N
2
N
N
3
N
N
A
CYS
12
A
CYS
12
HELX_P
A
ARG
16
A
ARG
16
5
1
5
A
SER
27
A
SER
27
HELX_P
A
GLY
32
A
GLY
32
1
2
6
A
CYS
39
A
CYS
39
HELX_P
A
GLU
43
A
GLU
43
5
3
5
A
GLY
50
A
GLY
50
HELX_P
A
GLY
54
A
GLY
54
5
4
5
A
GLY
73
A
GLY
73
HELX_P
A
SER
78
A
SER
78
1
5
6
disulf
2.051
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
18
A
SG
CYS
18
1_555
disulf
2.029
A
CYS
12
A
SG
CYS
12
1_555
A
CYS
24
A
SG
CYS
24
1_555
disulf
2.063
A
CYS
17
A
SG
CYS
17
1_555
A
CYS
31
A
SG
CYS
31
1_555
disulf
2.031
A
CYS
35
A
SG
CYS
35
1_555
A
CYS
39
A
SG
CYS
39
1_555
disulf
2.020
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
64
A
SG
CYS
64
1_555
disulf
2.042
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
70
A
SG
CYS
70
1_555
disulf
2.039
A
CYS
63
A
SG
CYS
63
1_555
A
CYS
77
A
SG
CYS
77
1_555
disulf
2.020
A
CYS
82
A
SG
CYS
82
1_555
A
CYS
86
A
SG
CYS
86
1_555
covale
1.314
both
A
PCA
1
A
C
PCA
1
1_555
A
ARG
2
A
N
ARG
2
1_555
covale
1.437
both
B
NAG
1
B
O4
NAG
1_555
B
NAG
2
B
C1
NAG
1_555
covale
1.444
both
B
NAG
2
B
O4
NAG
1_555
B
NAG
3
B
C1
NAG
1_555
covale
1.386
both
B
NAG
3
B
O4
NAG
1_555
B
NAG
4
B
C1
NAG
1_555
SUGAR BINDING PROTEIN
LECTIN, HEVEIN DOMAIN, UDA, SUPERANTIGEN, SACCHARIDE BINDING, SUGAR BINDING PROTEIN
AAD03614
GB
1
24
4138900
QRCGSQGGGGTCPALWCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGS
KCQYRCSSS
24
112
1EN2
1
89
4138900
A
1
1
89
1
GLY
microheterogeneity
SER
10
1EN2
A
4138900
GB
33
10
1
ALA
microheterogeneity
GLY
14
1EN2
A
4138900
GB
37
14
1
TRP
microheterogeneity
ARG
16
1EN2
A
4138900
GB
39
16
1
SER
microheterogeneity
GLY
80
1EN2
A
4138900
GB
103
80
1
LYS
microheterogeneity
ASN
81
1EN2
A
4138900
GB
104
81
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
CYS
24
A
CYS
24
A
GLY
25
A
GLY
25
A
CYS
17
A
CYS
17
A
SER
19
A
SER
19
A
CYS
35
A
CYS
35
A
ASN
37
A
ASN
37
A
CYS
70
A
CYS
70
A
GLY
71
A
GLY
71
A
CYS
63
A
CYS
63
A
SER
65
A
SER
65
A
CYS
82
A
CYS
82
A
TYR
84
A
TYR
84
19
P 21 21 21