0.014123
0.008154
0.000000
0.000000
0.016308
0.000000
0.000000
0.000000
0.019917
0.00000
0.00000
0.00000
Yoshida, H.
Kamitori, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
70.805
70.805
50.209
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
C6 H12 O6
180.156
beta-D-galactopyranose
beta-D-galactose; D-galactose; galactose
D-saccharide, beta 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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-alpha-D-glucopyranose
N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
D-saccharide, alpha linking
Ni 2
58.693
NICKEL (II) ION
non-polymer
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
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
R
C
N
89
R
C
N
90
S
C
N
91
R
C
N
92
R
C
N
93
N
C
N
94
N
O
N
95
N
O
N
96
N
O
N
97
N
O
N
98
N
O
N
99
N
O
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
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
N
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
H
N
132
N
N
N
133
S
C
N
134
N
C
N
135
N
O
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
O
N
140
N
O
N
141
N
O
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
N
N
152
N
C
N
153
N
C
N
154
N
O
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
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
N
C
Y
166
N
C
Y
167
N
N
Y
168
N
C
Y
169
N
C
Y
170
N
N
N
171
N
O
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
O
N
183
N
H
N
184
N
H
N
185
N
N
N
186
S
C
N
187
N
C
N
188
N
O
N
189
S
C
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
O
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
H
N
207
N
N
N
208
S
C
N
209
N
C
N
210
N
O
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
C
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
N
N
230
S
C
N
231
N
C
N
232
N
O
N
233
N
C
N
234
N
C
N
235
N
C
N
236
N
C
N
237
N
N
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
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
N
259
N
C
N
260
N
S
N
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
S
C
N
275
R
C
N
276
R
C
N
277
S
C
N
278
R
C
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
O
N
285
N
O
N
286
N
O
N
287
N
N
N
288
N
O
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
NI
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
N
316
N
O
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
N
N
329
S
C
N
330
N
C
N
331
N
O
N
332
N
C
N
333
N
C
N
334
N
C
N
335
N
O
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
H
N
343
N
H
N
344
N
H
N
345
N
N
N
346
S
C
N
347
N
C
N
348
N
O
N
349
N
C
N
350
N
O
N
351
N
O
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
R
C
N
364
N
O
N
365
N
C
N
366
N
O
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
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
N
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
Y
413
N
C
N
414
N
O
N
415
N
O
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
N
N
428
S
C
N
429
N
C
N
430
N
O
N
431
N
C
N
432
N
C
N
433
N
C
N
434
N
O
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
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
sing
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
sing
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
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
sing
N
132
N
doub
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
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
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
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
Y
164
N
sing
Y
165
N
doub
Y
166
N
doub
N
167
N
sing
Y
168
N
sing
N
169
N
sing
Y
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
doub
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
doub
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
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
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
sing
N
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
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
doub
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
doub
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
Y
302
N
doub
Y
303
N
sing
Y
304
N
sing
N
305
N
sing
Y
306
N
doub
N
307
N
sing
Y
308
N
doub
N
309
N
sing
Y
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
sing
N
318
N
sing
N
319
N
sing
N
320
N
doub
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
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
doub
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
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
doub
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
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
doub
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
Y
371
N
doub
Y
372
N
sing
Y
373
N
sing
N
374
N
sing
Y
375
N
doub
Y
376
N
sing
Y
377
N
sing
N
378
N
sing
Y
379
N
sing
Y
380
N
doub
N
381
N
sing
Y
382
N
doub
N
383
N
sing
Y
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
doub
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
Y
399
N
doub
Y
400
N
sing
Y
401
N
sing
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
doub
N
406
N
sing
Y
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
doub
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
285
36969
36976
10.1074/jbc.M110.163402
20861009
X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose
2010
10.2210/pdb3nv2/pdb
pdb_00003nv2
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
2009-11-28
ADSC QUANTUM 210r
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
AR-NW12A
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE AR-NW12A
15729.982
Galectin 9 short isoform variant
C-terminal carbohydrate recognition domain, residues 186-323
1
man
polymer
383.349
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
1
man
branched
58.693
NICKEL (II) ION
1
syn
non-polymer
18.015
water
140
nat
water
Galectin-9
N-acetyl-alpha-lactosamine
no
no
YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK
MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT
YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK
MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT
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
human
sample
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
PLASMID
pGEX-4T-2
1
2.31
46.75
VAPOR DIFFUSION, HANGING DROP
8.5
20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
atom_site
chem_comp
entity
entity_name_com
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_molecule_features
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_struct_conn_angle
pdbx_struct_special_symmetry
struct_asym
struct_conn
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
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2010-09-22
1
1
2011-07-13
2
0
2020-07-29
2
1
2023-11-01
_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.occupancy
_atom_site.type_symbol
_chem_comp.name
_chem_comp.type
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_special_symmetry.label_asym_id
_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.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
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
L
NAG
502
n
B
NDG
1
L
GAL
501
n
B
GAL
2
DGalpb
b-D-galactopyranose
b-D-Galp
Gal
DGlcpNAca
N-acetyl-a-D-glucopyranosamine
a-D-GlcpNAc
GlcNAc
The same protein without ligand
The same protein with biantennary oligosaccharide
The same protein with Sialyllactose
RCSB
Y
PDBJ
2010-07-07
REL
REL
oligosaccharide
DGalpb1-4DGlcpNAca1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1
2
PDB2Glycan
1.1.0
WURCS
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}
2
PDB-CARE
LINUCS
C1
O4
GAL
NDG
2
1
2
O1
HO4
sing
n
n
NI
NICKEL (II) ION
HOH
water
THE LIGANDS GAL AND NDG FORM N-ACETYLLACTOSAMINE.
3KOE
PDB entry 3KOE
PDB
experimental model
Glycan component
oligosaccharide
N-acetyl-alpha-lactosamine
Oligosaccharide
NI2
401
3
NI
NI
401
A
HOH
1
4
HOH
HOH
1
A
HOH
2
4
HOH
HOH
2
A
HOH
3
4
HOH
HOH
3
A
HOH
4
4
HOH
HOH
4
A
HOH
5
4
HOH
HOH
5
A
HOH
6
4
HOH
HOH
6
A
HOH
7
4
HOH
HOH
7
A
HOH
8
4
HOH
HOH
8
A
HOH
9
4
HOH
HOH
9
A
HOH
10
4
HOH
HOH
10
A
HOH
11
4
HOH
HOH
11
A
HOH
12
4
HOH
HOH
12
A
HOH
13
4
HOH
HOH
13
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
16
4
HOH
HOH
16
A
HOH
17
4
HOH
HOH
17
A
HOH
18
4
HOH
HOH
18
A
HOH
19
4
HOH
HOH
19
A
HOH
20
4
HOH
HOH
20
A
HOH
21
4
HOH
HOH
21
A
HOH
22
4
HOH
HOH
22
A
HOH
23
4
HOH
HOH
23
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
32
4
HOH
HOH
32
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
36
4
HOH
HOH
36
A
HOH
37
4
HOH
HOH
37
A
HOH
38
4
HOH
HOH
38
A
HOH
39
4
HOH
HOH
39
A
HOH
40
4
HOH
HOH
40
A
HOH
41
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
44
4
HOH
HOH
44
A
HOH
45
4
HOH
HOH
45
A
HOH
46
4
HOH
HOH
46
A
HOH
47
4
HOH
HOH
47
A
HOH
48
4
HOH
HOH
48
A
HOH
49
4
HOH
HOH
49
A
HOH
50
4
HOH
HOH
50
A
HOH
51
4
HOH
HOH
51
A
HOH
52
4
HOH
HOH
52
A
HOH
53
4
HOH
HOH
53
A
HOH
54
4
HOH
HOH
54
A
HOH
55
4
HOH
HOH
55
A
HOH
56
4
HOH
HOH
56
A
HOH
57
4
HOH
HOH
57
A
HOH
58
4
HOH
HOH
58
A
HOH
59
4
HOH
HOH
59
A
HOH
60
4
HOH
HOH
60
A
HOH
61
4
HOH
HOH
61
A
HOH
62
4
HOH
HOH
62
A
HOH
63
4
HOH
HOH
63
A
HOH
64
4
HOH
HOH
64
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
67
4
HOH
HOH
67
A
HOH
68
4
HOH
HOH
68
A
HOH
69
4
HOH
HOH
69
A
HOH
70
4
HOH
HOH
70
A
HOH
71
4
HOH
HOH
71
A
HOH
72
4
HOH
HOH
72
A
HOH
73
4
HOH
HOH
73
A
HOH
74
4
HOH
HOH
74
A
HOH
75
4
HOH
HOH
75
A
HOH
76
4
HOH
HOH
76
A
HOH
77
4
HOH
HOH
77
A
HOH
78
4
HOH
HOH
78
A
HOH
79
4
HOH
HOH
79
A
HOH
80
4
HOH
HOH
80
A
HOH
81
4
HOH
HOH
81
A
HOH
82
4
HOH
HOH
82
A
HOH
83
4
HOH
HOH
83
A
HOH
84
4
HOH
HOH
84
A
HOH
85
4
HOH
HOH
85
A
HOH
86
4
HOH
HOH
86
A
HOH
87
4
HOH
HOH
87
A
HOH
88
4
HOH
HOH
88
A
HOH
89
4
HOH
HOH
89
A
HOH
90
4
HOH
HOH
90
A
HOH
91
4
HOH
HOH
91
A
HOH
92
4
HOH
HOH
92
A
HOH
93
4
HOH
HOH
93
A
HOH
94
4
HOH
HOH
94
A
HOH
95
4
HOH
HOH
95
A
HOH
96
4
HOH
HOH
96
A
HOH
97
4
HOH
HOH
97
A
HOH
98
4
HOH
HOH
98
A
HOH
99
4
HOH
HOH
99
A
HOH
100
4
HOH
HOH
100
A
HOH
101
4
HOH
HOH
101
A
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
108
4
HOH
HOH
108
A
HOH
109
4
HOH
HOH
109
A
HOH
110
4
HOH
HOH
110
A
HOH
111
4
HOH
HOH
111
A
HOH
112
4
HOH
HOH
112
A
HOH
113
4
HOH
HOH
113
A
HOH
114
4
HOH
HOH
114
A
HOH
115
4
HOH
HOH
115
A
HOH
116
4
HOH
HOH
116
A
HOH
117
4
HOH
HOH
117
A
HOH
118
4
HOH
HOH
118
A
HOH
119
4
HOH
HOH
119
A
HOH
120
4
HOH
HOH
120
A
HOH
121
4
HOH
HOH
121
A
HOH
122
4
HOH
HOH
122
A
HOH
123
4
HOH
HOH
123
A
HOH
124
4
HOH
HOH
124
A
HOH
125
4
HOH
HOH
125
A
HOH
126
4
HOH
HOH
126
A
HOH
127
4
HOH
HOH
127
A
HOH
128
4
HOH
HOH
128
A
HOH
129
4
HOH
HOH
129
A
HOH
130
4
HOH
HOH
130
A
HOH
131
4
HOH
HOH
131
A
HOH
132
4
HOH
HOH
132
A
HOH
133
4
HOH
HOH
133
A
HOH
134
4
HOH
HOH
134
A
HOH
135
4
HOH
HOH
135
A
HOH
136
4
HOH
HOH
136
A
HOH
137
4
HOH
HOH
137
A
HOH
138
4
HOH
HOH
138
A
HOH
139
4
HOH
HOH
139
A
HOH
140
4
HOH
HOH
140
A
n
1
186
A
n
2
187
A
HIS
188
n
3
HIS
188
A
PRO
189
n
4
PRO
189
A
ALA
190
n
5
ALA
190
A
TYR
191
n
6
TYR
191
A
PRO
192
n
7
PRO
192
A
MET
193
n
8
MET
193
A
PRO
194
n
9
PRO
194
A
PHE
195
n
10
PHE
195
A
ILE
196
n
11
ILE
196
A
THR
197
n
12
THR
197
A
THR
198
n
13
THR
198
A
ILE
199
n
14
ILE
199
A
LEU
200
n
15
LEU
200
A
GLY
201
n
16
GLY
201
A
GLY
202
n
17
GLY
202
A
LEU
203
n
18
LEU
203
A
TYR
204
n
19
TYR
204
A
PRO
205
n
20
PRO
205
A
SER
206
n
21
SER
206
A
LYS
207
n
22
LYS
207
A
SER
208
n
23
SER
208
A
ILE
209
n
24
ILE
209
A
LEU
210
n
25
LEU
210
A
LEU
211
n
26
LEU
211
A
SER
212
n
27
SER
212
A
GLY
213
n
28
GLY
213
A
THR
214
n
29
THR
214
A
VAL
215
n
30
VAL
215
A
LEU
216
n
31
LEU
216
A
PRO
217
n
32
PRO
217
A
SER
218
n
33
SER
218
A
ALA
219
n
34
ALA
219
A
GLN
220
n
35
GLN
220
A
ARG
221
n
36
ARG
221
A
PHE
222
n
37
PHE
222
A
HIS
223
n
38
HIS
223
A
ILE
224
n
39
ILE
224
A
ASN
225
n
40
ASN
225
A
LEU
226
n
41
LEU
226
A
CYS
227
n
42
CYS
227
A
SER
228
n
43
SER
228
A
GLY
229
n
44
GLY
229
A
ASN
230
n
45
ASN
230
A
HIS
231
n
46
HIS
231
A
ILE
232
n
47
ILE
232
A
ALA
233
n
48
ALA
233
A
PHE
234
n
49
PHE
234
A
HIS
235
n
50
HIS
235
A
LEU
236
n
51
LEU
236
A
ASN
237
n
52
ASN
237
A
PRO
238
n
53
PRO
238
A
ARG
239
n
54
ARG
239
A
PHE
240
n
55
PHE
240
A
ASP
241
n
56
ASP
241
A
GLU
242
n
57
GLU
242
A
ASN
243
n
58
ASN
243
A
ALA
244
n
59
ALA
244
A
VAL
245
n
60
VAL
245
A
VAL
246
n
61
VAL
246
A
ARG
247
n
62
ARG
247
A
ASN
248
n
63
ASN
248
A
THR
249
n
64
THR
249
A
GLN
250
n
65
GLN
250
A
ILE
251
n
66
ILE
251
A
ASP
252
n
67
ASP
252
A
ASN
253
n
68
ASN
253
A
SER
254
n
69
SER
254
A
TRP
255
n
70
TRP
255
A
GLY
256
n
71
GLY
256
A
SER
257
n
72
SER
257
A
GLU
258
n
73
GLU
258
A
GLU
259
n
74
GLU
259
A
ARG
260
n
75
ARG
260
A
SER
261
n
76
SER
261
A
LEU
262
n
77
LEU
262
A
PRO
263
n
78
PRO
263
A
ARG
264
n
79
ARG
264
A
LYS
265
n
80
LYS
265
A
MET
266
n
81
MET
266
A
PRO
267
n
82
PRO
267
A
PHE
268
n
83
PHE
268
A
VAL
269
n
84
VAL
269
A
ARG
270
n
85
ARG
270
A
GLY
271
n
86
GLY
271
A
GLN
272
n
87
GLN
272
A
SER
273
n
88
SER
273
A
PHE
274
n
89
PHE
274
A
SER
275
n
90
SER
275
A
VAL
276
n
91
VAL
276
A
TRP
277
n
92
TRP
277
A
ILE
278
n
93
ILE
278
A
LEU
279
n
94
LEU
279
A
CYS
280
n
95
CYS
280
A
GLU
281
n
96
GLU
281
A
ALA
282
n
97
ALA
282
A
HIS
283
n
98
HIS
283
A
CYS
284
n
99
CYS
284
A
LEU
285
n
100
LEU
285
A
LYS
286
n
101
LYS
286
A
VAL
287
n
102
VAL
287
A
ALA
288
n
103
ALA
288
A
VAL
289
n
104
VAL
289
A
ASP
290
n
105
ASP
290
A
GLY
291
n
106
GLY
291
A
GLN
292
n
107
GLN
292
A
HIS
293
n
108
HIS
293
A
LEU
294
n
109
LEU
294
A
PHE
295
n
110
PHE
295
A
GLU
296
n
111
GLU
296
A
TYR
297
n
112
TYR
297
A
TYR
298
n
113
TYR
298
A
HIS
299
n
114
HIS
299
A
ARG
300
n
115
ARG
300
A
LEU
301
n
116
LEU
301
A
ARG
302
n
117
ARG
302
A
ASN
303
n
118
ASN
303
A
LEU
304
n
119
LEU
304
A
PRO
305
n
120
PRO
305
A
THR
306
n
121
THR
306
A
ILE
307
n
122
ILE
307
A
ASN
308
n
123
ASN
308
A
ARG
309
n
124
ARG
309
A
LEU
310
n
125
LEU
310
A
GLU
311
n
126
GLU
311
A
VAL
312
n
127
VAL
312
A
GLY
313
n
128
GLY
313
A
GLY
314
n
129
GLY
314
A
ASP
315
n
130
ASP
315
A
ILE
316
n
131
ILE
316
A
GLN
317
n
132
GLN
317
A
LEU
318
n
133
LEU
318
A
THR
319
n
134
THR
319
A
HIS
320
n
135
HIS
320
A
VAL
321
n
136
VAL
321
A
GLN
322
n
137
GLN
322
A
THR
323
n
138
THR
323
A
software_defined_assembly
PISA
3
trimeric
2780
-22
17740
A
HOH
16
D
O
HOH
1_555
A
NI
401
C
NI
NI
1_555
A
HIS
320
A
NE2
HIS
135
1_555
99.4
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_665
-y+1,x-y+1,z
crystal symmetry operation
35.4025000000
61.3189287150
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_565
-x+y,-x+1,z
crystal symmetry operation
-35.4025000000
61.3189287150
0.0000000000
A
N
THR
197
A
N
THR
12
A
O
LEU
310
A
O
LEU
125
A
O
ARG
309
A
O
ARG
124
A
N
CYS
227
A
N
CYS
42
A
N
SER
228
A
N
SER
43
A
O
HIS
231
A
O
HIS
46
A
N
ARG
239
A
N
ARG
54
A
O
ALA
244
A
O
ALA
59
A
N
ILE
251
A
N
ILE
66
A
O
SER
254
A
O
SER
69
A
O
LEU
294
A
O
LEU
109
A
N
VAL
287
A
N
VAL
102
A
O
LYS
286
A
O
LYS
101
A
N
LEU
279
A
N
LEU
94
A
O
VAL
276
A
O
VAL
91
A
N
LEU
211
A
N
LEU
26
A
N
THR
214
A
N
THR
29
A
O
GLN
317
A
O
GLN
132
1
A
NI
401
C
NI
1
A
TYR
186
A
TYR
1
1
Y
1
A
PRO
187
A
PRO
2
1
Y
1
A
A
O
O
ASN
HOH
243
67
2.07
1_555
6_654
1
A
A
O
O
HOH
HOH
16
16
2.17
1_555
3_565
1
A
SER
206
86.32
-6.05
1
A
ASP
252
65.09
-122.27
protein_rep.param
protein.top
carbohydrate.param
carbohydrate.top
ion.param
ion.top
water_rep.param
water.top
1.56
2.79
0.00
1.56
0.00
-3.12
0.231
0.009
0.179
0.185
0.179
2.34
38.85
659
5989
5989
11.0
97.5
RANDOM
40669.38
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB entry 3KOE
Engh & Huber
FLAT MODEL
60.142
0.364624
0.30
0.21
5.00
0.25
0.12
2.34
38.85
140
1257
27
0
1090
0.005
1.5
27.2
0.76
0.256
0.025
0.171
2.49
108
829
829
6
11.5
92.8
24.1
2.34
50
3NV2
6135
0.0
0.0
0.075
1
8.7
68565
11.2
100.0
0.385
2.34
2.38
7.4
11.2
100
data collection
ADSC
Quantum
phasing
MOLREP
refinement
CNS
1.1
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of human galectin-9 C-terminal CRD in complex with N-acetyllactosamine
1
N
N
2
N
N
3
N
N
4
N
N
AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.
A
ASN
303
A
ASN
118
HELX_P
A
ILE
307
A
ILE
122
5
1
5
covale
1.388
both
B
NDG
1
B
O4
NDG
1_555
B
GAL
2
B
C1
GAL
1_555
metalc
2.183
A
HOH
16
D
O
HOH
1_555
A
NI
401
C
NI
NI
1_555
metalc
2.246
A
HIS
320
A
NE2
HIS
135
1_555
A
NI
401
C
NI
NI
1_555
SUGAR BINDING PROTEIN
Sugar binding, Sugar Binding Protein
A
MET
193
A
MET
8
1
A
PRO
194
A
PRO
9
0.08
Q53FQ0_HUMAN
UNP
1
186
Q53FQ0
YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK
MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT
186
323
3NV2
186
323
Q53FQ0
A
1
1
138
6
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
PHE
195
A
PHE
10
A
THR
198
A
THR
13
A
ARG
309
A
ARG
124
A
GLY
314
A
GLY
129
A
PHE
222
A
PHE
37
A
SER
228
A
SER
43
A
HIS
231
A
HIS
46
A
ARG
239
A
ARG
54
A
ALA
244
A
ALA
59
A
ILE
251
A
ILE
66
A
SER
254
A
SER
69
A
TRP
255
A
TRP
70
A
GLN
292
A
GLN
107
A
TYR
298
A
TYR
113
A
CYS
284
A
CYS
99
A
VAL
289
A
VAL
104
A
SER
273
A
SER
88
A
CYS
280
A
CYS
95
A
SER
208
A
SER
23
A
VAL
215
A
VAL
30
A
ILE
316
A
ILE
131
A
GLN
322
A
GLN
137
173
P 63