0.012914
0.007456
0.000000
0.000000
0.014912
0.000000
0.000000
0.000000
0.005714
0.00000
0.00000
0.00000
Spinelli, S.
Tegoni, M.
Frenken, L.
van Vliet, C.
Cambillau, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
77.435
77.435
175.019
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 H7 N O2
113.115
5-OXO-PYRROLIDINE-2-CARBALDEHYDE
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
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
C19 H16 N8 O10 S3
612.573
5-(4,6-DIAMINO-[1,3,5]TRIAZIN-2-YLAMINO)-4-HYDROXY-3-(2-SULFO-PHENYLAZO)-NAPHTHALENE-2,7-DISULFONIC ACID
REACTIVE RED 1 DYE
non-polymer
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
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
C
N
75
N
C
N
76
N
C
N
77
N
N
N
78
N
O
N
79
N
C
N
80
S
C
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
R
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
S
N
95
N
O
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
N
N
104
S
C
N
105
N
C
N
106
N
O
N
107
N
C
N
108
N
C
N
109
N
C
N
110
N
O
N
111
N
N
N
112
N
O
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
O
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
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
N
N
143
N
C
N
144
N
C
N
145
N
O
N
146
N
O
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
N
N
156
S
C
N
157
N
C
N
158
N
O
N
159
S
C
N
160
N
C
N
161
N
C
N
162
N
C
N
163
N
O
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
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
N
N
178
S
C
N
179
N
C
N
180
N
O
N
181
N
C
N
182
N
C
N
183
N
C
N
184
N
C
N
185
N
O
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
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
N
N
200
S
C
N
201
N
C
N
202
N
O
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
N
N
208
N
O
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
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
N
N
225
S
C
N
226
N
C
N
227
N
O
N
228
N
C
N
229
N
C
N
230
N
S
N
231
N
C
N
232
N
O
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
Y
249
N
C
Y
250
N
C
Y
251
N
C
Y
252
N
C
Y
253
N
C
Y
254
N
C
N
255
N
O
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
O
N
285
N
O
N
286
N
O
N
287
N
S
Y
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
Y
303
N
C
N
304
N
O
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
S
N
309
N
O
N
310
N
O
N
311
N
O
N
312
N
S
N
313
N
N
N
314
N
N
N
315
N
N
Y
316
N
C
Y
317
N
N
Y
318
N
C
Y
319
N
N
Y
320
N
C
Y
321
N
N
N
322
N
N
N
323
N
N
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
N
N
341
S
C
N
342
N
C
N
343
N
O
N
344
N
C
N
345
N
O
N
346
N
O
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
S
N
355
N
O
N
356
N
O
N
357
N
O
N
358
N
O
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
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
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
doub
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
doub
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
doub
N
113
N
sing
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
sing
N
122
N
sing
N
123
N
doub
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
sing
N
141
N
doub
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
sing
N
151
N
sing
N
152
N
doub
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
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
doub
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
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
doub
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
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
doub
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
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
Y
242
N
doub
Y
243
N
sing
Y
244
N
sing
N
245
N
sing
Y
246
N
doub
N
247
N
sing
Y
248
N
doub
N
249
N
sing
Y
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
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
doub
N
274
N
doub
N
275
N
sing
Y
276
N
doub
Y
277
N
sing
Y
278
N
sing
N
279
N
sing
Y
280
N
doub
N
281
N
sing
Y
282
N
sing
N
283
N
sing
Y
284
N
doub
N
285
N
sing
N
286
N
sing
Y
287
N
doub
Y
288
N
sing
N
289
N
sing
Y
290
N
sing
N
291
N
sing
Y
292
N
doub
N
293
N
sing
Y
294
N
sing
N
295
N
sing
Y
296
N
doub
Y
297
N
sing
Y
298
N
sing
Y
299
N
doub
N
300
N
sing
Y
301
N
sing
N
302
N
sing
Y
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
doub
N
310
N
doub
N
311
N
sing
N
312
N
sing
N
313
N
doub
N
314
N
doub
N
315
E
doub
N
316
N
sing
N
317
N
sing
Y
318
N
doub
Y
319
N
sing
Y
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
sing
Y
324
N
doub
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
doub
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
doub
N
344
N
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
doub
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
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
Y
374
N
doub
Y
375
N
sing
Y
376
N
sing
N
377
N
sing
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
385
N
doub
N
386
N
sing
Y
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
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
Y
402
N
doub
Y
403
N
sing
Y
404
N
sing
N
405
N
sing
Y
406
N
doub
N
407
N
sing
Y
408
N
doub
N
409
N
sing
Y
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
sing
N
419
N
sing
N
420
N
sing
N
421
N
doub
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
N
430
N
sing
N
431
N
sing
N
432
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
311
123
129
10.1006/jmbi.2001.4856
11469862
Lateral recognition of a dye hapten by a llama VHH domain.
2001
10.2210/pdb1i3u/pdb
pdb_00001i3u
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
IMAGE PLATE
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.988
1.0
ID2
ESRF
0.988
SYNCHROTRON
ESRF BEAMLINE ID2
13842.268
ANTIBODY VHH LAMA DOMAIN
1
man
polymer
96.063
SULFATE ION
1
syn
non-polymer
612.573
5-(4,6-DIAMINO-[1,3,5]TRIAZIN-2-YLAMINO)-4-HYDROXY-3-(2-SULFO-PHENYLAZO)-NAPHTHALENE-2,7-DISULFONIC ACID
1
syn
non-polymer
18.015
water
164
nat
water
no
yes
(CGN)VQLQESGGGLVQAGDSLKLSCEASGDSIGTYVIGWFRQAPGKERIYLATIGRNLVGPSDFYTRYADSVKGRFAVS
RDNAKNTVNLQMNSLKPEDTAVYYCAAKTTTWGGNDPNNWNYWGQGTQVTV
XVQLQESGGGLVQAGDSLKLSCEASGDSIGTYVIGWFRQAPGKERIYLATIGRNLVGPSDFYTRYADSVKGRFAVSRDNA
KNTVNLQMNSLKPEDTAVYYCAAKTTTWGGNDPNNWNYWGQGTQVTV
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
llama
Lama
Escherichia
sample
9844
Lama glama
562
Escherichia coli
1
3.65
66.27
VAPOR DIFFUSION, HANGING DROP
5.5
MME 5000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
290
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2001-08-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Three-dimensional Structure of
a Lama VHH domain unliganded
SEQUENCE
AN APPROPRIATE SEQUENCE DATABASE MATCH WAS NOT
AVAILABLE AT THE TIME OF PROCESSING.
RCSB
Y
RCSB
2001-02-16
REL
REL
SO4
SULFATE ION
RR1
5-(4,6-DIAMINO-[1,3,5]TRIAZIN-2-YLAMINO)-4-HYDROXY-3-(2-SULFO-PHENYLAZO)-NAPHTHALENE-2,7-DISULFONIC ACID
HOH
water
VHH52 anti-R1 unliganded
Other
experimental model
SO4
1
2
SO4
SO4
402
A
RR1
1
3
RR1
RR1
401
A
WAT
201
4
HOH
HOH
201
A
WAT
202
4
HOH
HOH
202
A
WAT
203
4
HOH
HOH
203
A
WAT
204
4
HOH
HOH
204
A
WAT
205
4
HOH
HOH
205
A
WAT
206
4
HOH
HOH
206
A
WAT
207
4
HOH
HOH
207
A
WAT
208
4
HOH
HOH
208
A
WAT
209
4
HOH
HOH
209
A
WAT
210
4
HOH
HOH
210
A
WAT
211
4
HOH
HOH
211
A
WAT
212
4
HOH
HOH
212
A
WAT
213
4
HOH
HOH
213
A
WAT
214
4
HOH
HOH
214
A
WAT
215
4
HOH
HOH
215
A
WAT
216
4
HOH
HOH
216
A
WAT
217
4
HOH
HOH
217
A
WAT
218
4
HOH
HOH
218
A
WAT
219
4
HOH
HOH
219
A
WAT
220
4
HOH
HOH
220
A
WAT
221
4
HOH
HOH
221
A
WAT
222
4
HOH
HOH
222
A
WAT
223
4
HOH
HOH
223
A
WAT
224
4
HOH
HOH
224
A
WAT
225
4
HOH
HOH
225
A
WAT
226
4
HOH
HOH
226
A
WAT
227
4
HOH
HOH
227
A
WAT
228
4
HOH
HOH
228
A
WAT
229
4
HOH
HOH
229
A
WAT
230
4
HOH
HOH
230
A
WAT
231
4
HOH
HOH
231
A
WAT
232
4
HOH
HOH
232
A
WAT
233
4
HOH
HOH
233
A
WAT
234
4
HOH
HOH
234
A
WAT
235
4
HOH
HOH
235
A
WAT
236
4
HOH
HOH
236
A
WAT
237
4
HOH
HOH
237
A
WAT
238
4
HOH
HOH
238
A
WAT
239
4
HOH
HOH
239
A
WAT
240
4
HOH
HOH
240
A
WAT
241
4
HOH
HOH
241
A
WAT
242
4
HOH
HOH
242
A
WAT
243
4
HOH
HOH
243
A
WAT
244
4
HOH
HOH
244
A
WAT
245
4
HOH
HOH
245
A
WAT
246
4
HOH
HOH
246
A
WAT
247
4
HOH
HOH
247
A
WAT
248
4
HOH
HOH
248
A
WAT
249
4
HOH
HOH
249
A
WAT
250
4
HOH
HOH
250
A
WAT
251
4
HOH
HOH
251
A
WAT
252
4
HOH
HOH
252
A
WAT
253
4
HOH
HOH
253
A
WAT
254
4
HOH
HOH
254
A
WAT
255
4
HOH
HOH
255
A
WAT
256
4
HOH
HOH
256
A
WAT
257
4
HOH
HOH
257
A
WAT
258
4
HOH
HOH
258
A
WAT
259
4
HOH
HOH
259
A
WAT
260
4
HOH
HOH
260
A
WAT
261
4
HOH
HOH
261
A
WAT
262
4
HOH
HOH
262
A
WAT
263
4
HOH
HOH
263
A
WAT
264
4
HOH
HOH
264
A
WAT
265
4
HOH
HOH
265
A
WAT
266
4
HOH
HOH
266
A
WAT
267
4
HOH
HOH
267
A
WAT
268
4
HOH
HOH
268
A
WAT
269
4
HOH
HOH
269
A
WAT
270
4
HOH
HOH
270
A
WAT
271
4
HOH
HOH
271
A
WAT
272
4
HOH
HOH
272
A
WAT
273
4
HOH
HOH
273
A
WAT
274
4
HOH
HOH
274
A
WAT
275
4
HOH
HOH
275
A
WAT
276
4
HOH
HOH
276
A
WAT
277
4
HOH
HOH
277
A
WAT
278
4
HOH
HOH
278
A
WAT
279
4
HOH
HOH
279
A
WAT
280
4
HOH
HOH
280
A
WAT
281
4
HOH
HOH
281
A
WAT
282
4
HOH
HOH
282
A
WAT
283
4
HOH
HOH
283
A
WAT
284
4
HOH
HOH
284
A
WAT
285
4
HOH
HOH
285
A
WAT
286
4
HOH
HOH
286
A
WAT
287
4
HOH
HOH
287
A
WAT
288
4
HOH
HOH
288
A
WAT
289
4
HOH
HOH
289
A
WAT
290
4
HOH
HOH
290
A
WAT
291
4
HOH
HOH
291
A
WAT
292
4
HOH
HOH
292
A
WAT
293
4
HOH
HOH
293
A
WAT
294
4
HOH
HOH
294
A
WAT
295
4
HOH
HOH
295
A
WAT
296
4
HOH
HOH
296
A
WAT
297
4
HOH
HOH
297
A
WAT
298
4
HOH
HOH
298
A
WAT
299
4
HOH
HOH
299
A
WAT
300
4
HOH
HOH
300
A
WAT
301
4
HOH
HOH
301
A
WAT
302
4
HOH
HOH
302
A
WAT
303
4
HOH
HOH
303
A
WAT
304
4
HOH
HOH
304
A
WAT
305
4
HOH
HOH
305
A
WAT
306
4
HOH
HOH
306
A
WAT
307
4
HOH
HOH
307
A
WAT
308
4
HOH
HOH
308
A
WAT
309
4
HOH
HOH
309
A
WAT
310
4
HOH
HOH
310
A
WAT
311
4
HOH
HOH
311
A
WAT
312
4
HOH
HOH
312
A
WAT
313
4
HOH
HOH
313
A
WAT
314
4
HOH
HOH
314
A
WAT
315
4
HOH
HOH
315
A
WAT
316
4
HOH
HOH
316
A
WAT
317
4
HOH
HOH
317
A
WAT
318
4
HOH
HOH
318
A
WAT
319
4
HOH
HOH
319
A
WAT
320
4
HOH
HOH
320
A
WAT
321
4
HOH
HOH
321
A
WAT
322
4
HOH
HOH
322
A
WAT
323
4
HOH
HOH
323
A
WAT
324
4
HOH
HOH
324
A
WAT
325
4
HOH
HOH
325
A
WAT
326
4
HOH
HOH
326
A
WAT
327
4
HOH
HOH
327
A
WAT
328
4
HOH
HOH
328
A
WAT
329
4
HOH
HOH
329
A
WAT
330
4
HOH
HOH
330
A
WAT
331
4
HOH
HOH
331
A
WAT
332
4
HOH
HOH
332
A
WAT
333
4
HOH
HOH
333
A
WAT
334
4
HOH
HOH
334
A
WAT
335
4
HOH
HOH
335
A
WAT
336
4
HOH
HOH
336
A
WAT
337
4
HOH
HOH
337
A
WAT
338
4
HOH
HOH
338
A
WAT
339
4
HOH
HOH
339
A
WAT
340
4
HOH
HOH
340
A
WAT
341
4
HOH
HOH
341
A
WAT
342
4
HOH
HOH
342
A
WAT
343
4
HOH
HOH
343
A
WAT
344
4
HOH
HOH
344
A
WAT
345
4
HOH
HOH
345
A
WAT
346
4
HOH
HOH
346
A
WAT
347
4
HOH
HOH
347
A
WAT
348
4
HOH
HOH
348
A
WAT
349
4
HOH
HOH
349
A
WAT
350
4
HOH
HOH
350
A
WAT
351
4
HOH
HOH
351
A
WAT
352
4
HOH
HOH
352
A
WAT
353
4
HOH
HOH
353
A
WAT
354
4
HOH
HOH
354
A
WAT
355
4
HOH
HOH
355
A
WAT
356
4
HOH
HOH
356
A
WAT
357
4
HOH
HOH
357
A
WAT
358
4
HOH
HOH
358
A
WAT
359
4
HOH
HOH
359
A
WAT
360
4
HOH
HOH
360
A
WAT
361
4
HOH
HOH
361
A
WAT
362
4
HOH
HOH
362
A
WAT
363
4
HOH
HOH
363
A
WAT
364
4
HOH
HOH
364
A
PGL
1
n
1
CGN
1
A
VAL
2
n
2
VAL
2
A
GLN
3
n
3
GLN
3
A
LEU
4
n
4
LEU
4
A
GLN
5
n
5
GLN
5
A
GLU
6
n
6
GLU
6
A
SER
7
n
7
SER
7
A
GLY
8
n
8
GLY
8
A
GLY
9
n
9
GLY
9
A
GLY
10
n
10
GLY
10
A
LEU
11
n
11
LEU
11
A
VAL
12
n
12
VAL
12
A
GLN
13
n
13
GLN
13
A
ALA
14
n
14
ALA
14
A
GLY
15
n
15
GLY
15
A
ASP
16
n
16
ASP
16
A
SER
17
n
17
SER
17
A
LEU
18
n
18
LEU
18
A
LYS
19
n
19
LYS
19
A
LEU
20
n
20
LEU
20
A
SER
21
n
21
SER
21
A
CYS
22
n
22
CYS
22
A
GLU
23
n
23
GLU
23
A
ALA
24
n
24
ALA
24
A
SER
25
n
25
SER
25
A
GLY
26
n
26
GLY
26
A
ASP
27
n
27
ASP
27
A
SER
28
n
28
SER
28
A
ILE
29
n
29
ILE
29
A
GLY
30
n
30
GLY
30
A
THR
31
n
31
THR
31
A
TYR
32
n
32
TYR
32
A
VAL
33
n
33
VAL
33
A
ILE
34
n
34
ILE
34
A
GLY
35
n
35
GLY
35
A
TRP
36
n
36
TRP
36
A
PHE
37
n
37
PHE
37
A
ARG
38
n
38
ARG
38
A
GLN
39
n
39
GLN
39
A
ALA
40
n
40
ALA
40
A
PRO
41
n
41
PRO
41
A
GLY
42
n
42
GLY
42
A
LYS
43
n
43
LYS
43
A
GLU
44
n
44
GLU
44
A
ARG
45
n
45
ARG
45
A
ILE
46
n
46
ILE
46
A
TYR
47
n
47
TYR
47
A
LEU
48
n
48
LEU
48
A
ALA
49
n
49
ALA
49
A
THR
50
n
50
THR
50
A
ILE
51
n
51
ILE
51
A
GLY
52
n
52
GLY
52
A
ARG
53
n
53
ARG
53
A
ASN
54
n
54
ASN
54
A
LEU
55
n
55
LEU
55
A
VAL
56
n
56
VAL
56
A
GLY
57
n
57
GLY
57
A
PRO
58
n
58
PRO
58
A
SER
59
n
59
SER
59
A
ASP
60
n
60
ASP
60
A
PHE
61
n
61
PHE
61
A
TYR
62
n
62
TYR
62
A
THR
63
n
63
THR
63
A
ARG
64
n
64
ARG
64
A
TYR
65
n
65
TYR
65
A
ALA
66
n
66
ALA
66
A
ASP
67
n
67
ASP
67
A
SER
68
n
68
SER
68
A
VAL
69
n
69
VAL
69
A
LYS
70
n
70
LYS
70
A
GLY
71
n
71
GLY
71
A
ARG
72
n
72
ARG
72
A
PHE
73
n
73
PHE
73
A
ALA
74
n
74
ALA
74
A
VAL
75
n
75
VAL
75
A
SER
76
n
76
SER
76
A
ARG
77
n
77
ARG
77
A
ASP
78
n
78
ASP
78
A
ASN
79
n
79
ASN
79
A
ALA
80
n
80
ALA
80
A
LYS
81
n
81
LYS
81
A
ASN
82
n
82
ASN
82
A
THR
83
n
83
THR
83
A
VAL
84
n
84
VAL
84
A
ASN
85
n
85
ASN
85
A
LEU
86
n
86
LEU
86
A
GLN
87
n
87
GLN
87
A
MET
88
n
88
MET
88
A
ASN
89
n
89
ASN
89
A
SER
90
n
90
SER
90
A
LEU
91
n
91
LEU
91
A
LYS
92
n
92
LYS
92
A
PRO
93
n
93
PRO
93
A
GLU
94
n
94
GLU
94
A
ASP
95
n
95
ASP
95
A
THR
96
n
96
THR
96
A
ALA
97
n
97
ALA
97
A
VAL
98
n
98
VAL
98
A
TYR
99
n
99
TYR
99
A
TYR
100
n
100
TYR
100
A
CYS
101
n
101
CYS
101
A
ALA
102
n
102
ALA
102
A
ALA
103
n
103
ALA
103
A
LYS
104
n
104
LYS
104
A
THR
105
n
105
THR
105
A
THR
106
n
106
THR
106
A
THR
107
n
107
THR
107
A
TRP
108
n
108
TRP
108
A
GLY
109
n
109
GLY
109
A
GLY
110
n
110
GLY
110
A
ASN
111
n
111
ASN
111
A
ASP
112
n
112
ASP
112
A
PRO
113
n
113
PRO
113
A
ASN
114
n
114
ASN
114
A
ASN
115
n
115
ASN
115
A
TRP
116
n
116
TRP
116
A
ASN
117
n
117
ASN
117
A
TYR
118
n
118
TYR
118
A
TRP
119
n
119
TRP
119
A
GLY
120
n
120
GLY
120
A
GLN
121
n
121
GLN
121
A
GLY
122
n
122
GLY
122
A
THR
123
n
123
THR
123
A
GLN
124
n
124
GLN
124
A
VAL
125
n
125
VAL
125
A
THR
126
n
126
THR
126
A
VAL
127
n
127
VAL
127
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
SER
7
A
O
SER
7
A
N
SER
21
A
N
SER
21
A
N
CYS
22
A
N
CYS
22
A
O
VAL
84
A
O
VAL
84
A
N
GLN
87
A
N
GLN
87
A
O
ALA
74
A
O
ALA
74
A
O
ARG
64
A
O
ARG
64
A
N
THR
50
A
N
THR
50
A
N
ILE
51
A
N
ILE
51
A
O
ILE
34
A
O
ILE
34
A
N
GLN
39
A
N
GLN
39
A
O
VAL
98
A
O
VAL
98
A
N
ALA
103
A
N
ALA
103
A
O
TYR
118
A
O
TYR
118
A
O
ARG
64
A
O
ARG
64
A
N
THR
50
A
N
THR
50
A
N
ILE
51
A
N
ILE
51
A
O
ILE
34
A
O
ILE
34
A
N
GLN
39
A
N
GLN
39
A
O
VAL
98
A
O
VAL
98
A
N
TYR
99
A
N
TYR
99
A
O
THR
123
A
O
THR
123
A
O
GLN
124
A
O
GLN
124
A
N
GLY
10
A
N
GLY
10
1
A
A
O
O
HOH
HOH
340
340
2.07
1_555
2_655
1
A
ALA
97
171.43
168.98
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
RR1_240399.PARAM
RR1_240399.TOP
SO4.PARAM
SO4.TOP
32.2
5.94
5.75
0.00
5.94
0.00
-11.87
0.266
0.008
0.232
0.232
1.95
18.50
1194
0
15003
8.0
99.3
RANDOM
2310814.65
0.00
1
RESTRAINED
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
VHH52 anti-R1 unliganded
FLAT MODEL
51.87
0.364
0.32
0.27
5.00
0.27
0.23
1.95
18.50
164
1186
45
0
977
0.007
1.5
24.6
0.71
1.24
1.50
2.11
2.00
1.67
2.00
2.38
2.50
0.305
0.026
0.29
2.02
133
1319
0
6
9.2
54.4
20.7
1.95
30
1I3U
189080
15022
0
0
0.057
1
4.7
2.7
99.7
1.95
2.00
4.7
1088
0.144
2.7
99.7
data reduction
DENZO
data scaling
SCALA
phasing
AMoRE
refinement
CNS
1.0
data scaling
CCP4
(SCALA)
THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH THE DYE RR1
1
N
N
2
N
N
3
N
N
4
N
N
A
SER
28
A
SER
28
HELX_P
A
TYR
32
A
TYR
32
5
1
5
A
ASN
79
A
ASN
79
HELX_P
A
LYS
81
A
LYS
81
5
2
3
A
LYS
92
A
LYS
92
HELX_P
A
THR
96
A
THR
96
5
3
5
A
ASP
112
A
ASP
112
HELX_P
A
TRP
116
A
TRP
116
5
4
5
disulf
2.032
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
101
A
SG
CYS
101
1_555
covale
1.324
one
A
CGN
1
A
C
CGN
1
1_555
A
VAL
2
A
N
VAL
2
1_555
IMMUNE SYSTEM
antibody, VHH fragment, Lama glama, IMMUNE SYSTEM
1I3U
PDB
1
1I3U
1
127
1I3U
1
127
1I3U
A
1
1
127
4
5
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
A
GLN
3
A
GLN
3
A
SER
7
A
SER
7
A
LEU
18
A
LEU
18
A
SER
25
A
SER
25
A
THR
83
A
THR
83
A
MET
88
A
MET
88
A
PHE
73
A
PHE
73
A
ASP
78
A
ASP
78
A
PHE
61
A
PHE
61
A
TYR
65
A
TYR
65
A
ILE
46
A
ILE
46
A
LEU
55
A
LEU
55
A
VAL
33
A
VAL
33
A
GLN
39
A
GLN
39
A
ALA
97
A
ALA
97
A
LYS
104
A
LYS
104
A
TYR
118
A
TYR
118
A
TRP
119
A
TRP
119
A
PHE
61
A
PHE
61
A
TYR
65
A
TYR
65
A
ILE
46
A
ILE
46
A
LEU
55
A
LEU
55
A
VAL
33
A
VAL
33
A
GLN
39
A
GLN
39
A
ALA
97
A
ALA
97
A
LYS
104
A
LYS
104
A
THR
123
A
THR
123
A
THR
126
A
THR
126
A
GLY
10
A
GLY
10
A
LEU
11
A
LEU
11
BINDING SITE FOR RESIDUE SO4 A 402
A
SO4
402
Software
2
BINDING SITE FOR RESIDUE RR1 A 401
A
RR1
401
Software
17
A
GLN
39
A
GLN
39
2
1_555
A
ARG
45
A
ARG
45
2
1_555
A
THR
50
A
THR
50
17
1_555
A
GLY
52
A
GLY
52
17
1_555
A
ARG
53
A
ARG
53
17
1_555
A
ASN
54
A
ASN
54
17
1_555
A
LEU
55
A
LEU
55
17
1_555
A
LEU
55
A
LEU
55
17
16_545
A
GLY
57
A
GLY
57
17
16_545
A
PRO
58
A
PRO
58
17
16_545
A
TYR
62
A
TYR
62
17
1_555
A
ARG
64
A
ARG
64
17
1_555
A
LYS
104
A
LYS
104
17
1_555
A
THR
107
A
THR
107
17
1_555
A
TRP
108
A
TRP
108
17
1_555
A
GLY
109
A
GLY
109
17
1_555
A
GLY
110
A
GLY
110
17
1_555
A
HOH
243
D
HOH
17
1_555
A
HOH
267
D
HOH
17
1_555
155
H 3 2