0.041728
0.000000
0.000000
0.000000
0.019684
0.000000
0.000000
0.000000
0.013284
0.00000
0.00000
0.00000
Zhang, X.
Schwartz, J.-C.D.
Guo, X.
Cao, E.
Chen, L.
Zhang, Z.-Y.
Nathenson, S.G.
Almo, S.C.
0000-0002-2487-9713
Burley, S.K.
New York SGX Research Center for Structural Genomics (NYSGXRC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
23.965
50.802
75.278
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
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
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
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
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
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
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
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
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
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
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
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
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
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
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
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
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
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
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
US
Immunity
IUNIEH
2048
1074-7613
20
337
347
10.1016/S1074-7613(04)00051-2
15030777
Structural and functional analysis of the costimulatory receptor programmed death-1.
2004
10.2210/pdb1npu/pdb
pdb_00001npu
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
2002-05-01
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
0.9746
1.0
X9B
NSLS
0.9746
SYNCHROTRON
NSLS BEAMLINE X9B
13176.714
Programmed cell death protein 1
Ig V-type domain
C50S
1
man
polymer
18.015
water
73
nat
water
Protein PD-1, mPD-1
no
no
SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDT
RRNDSGIYLCGAISLHPKAKIEESPGAELVVTERILE
SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDT
RRNDSGIYLCGAISLHPKAKIEESPGAELVVTERILE
A
NYSGXRC-T749
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
house mouse
Mus
Escherichia
Escherichia coli
sample
PDCD1 OR PD1
10090
Mus musculus
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pET3a
1
1.67
25.8
VAPOR DIFFUSION, HANGING DROP
6.5
PEG8000, NaAc, NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
New York SGX Research Center for Structural Genomics
NYSGXRC
PSI, Protein Structure Initiative
audit_author
database_2
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Structure summary
Database references
Data collection
Refinement description
1
0
2004-03-23
1
1
2008-04-29
1
2
2011-07-13
1
3
2021-02-03
1
4
2021-10-27
1
5
2023-08-16
_audit_author.identifier_ORCID
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2003-01-20
REL
REL
HOH
water
1B88
PDB ENTRY 1B88
PDB
experimental model
HOH
1
2
HOH
HOH
118
A
HOH
2
2
HOH
HOH
119
A
HOH
3
2
HOH
HOH
120
A
HOH
4
2
HOH
HOH
121
A
HOH
5
2
HOH
HOH
122
A
HOH
6
2
HOH
HOH
123
A
HOH
7
2
HOH
HOH
124
A
HOH
8
2
HOH
HOH
125
A
HOH
9
2
HOH
HOH
126
A
HOH
10
2
HOH
HOH
127
A
HOH
11
2
HOH
HOH
128
A
HOH
12
2
HOH
HOH
129
A
HOH
13
2
HOH
HOH
130
A
HOH
14
2
HOH
HOH
131
A
HOH
15
2
HOH
HOH
132
A
HOH
16
2
HOH
HOH
133
A
HOH
17
2
HOH
HOH
134
A
HOH
18
2
HOH
HOH
135
A
HOH
19
2
HOH
HOH
136
A
HOH
20
2
HOH
HOH
137
A
HOH
21
2
HOH
HOH
138
A
HOH
22
2
HOH
HOH
139
A
HOH
23
2
HOH
HOH
140
A
HOH
24
2
HOH
HOH
141
A
HOH
25
2
HOH
HOH
142
A
HOH
26
2
HOH
HOH
143
A
HOH
27
2
HOH
HOH
144
A
HOH
28
2
HOH
HOH
145
A
HOH
29
2
HOH
HOH
146
A
HOH
30
2
HOH
HOH
147
A
HOH
31
2
HOH
HOH
148
A
HOH
32
2
HOH
HOH
149
A
HOH
33
2
HOH
HOH
150
A
HOH
34
2
HOH
HOH
151
A
HOH
35
2
HOH
HOH
152
A
HOH
36
2
HOH
HOH
153
A
HOH
37
2
HOH
HOH
154
A
HOH
38
2
HOH
HOH
155
A
HOH
39
2
HOH
HOH
156
A
HOH
40
2
HOH
HOH
157
A
HOH
41
2
HOH
HOH
158
A
HOH
42
2
HOH
HOH
159
A
HOH
43
2
HOH
HOH
160
A
HOH
44
2
HOH
HOH
161
A
HOH
45
2
HOH
HOH
162
A
HOH
46
2
HOH
HOH
163
A
HOH
47
2
HOH
HOH
164
A
HOH
48
2
HOH
HOH
165
A
HOH
49
2
HOH
HOH
166
A
HOH
50
2
HOH
HOH
167
A
HOH
51
2
HOH
HOH
168
A
HOH
52
2
HOH
HOH
169
A
HOH
53
2
HOH
HOH
170
A
HOH
54
2
HOH
HOH
171
A
HOH
55
2
HOH
HOH
172
A
HOH
56
2
HOH
HOH
173
A
HOH
57
2
HOH
HOH
174
A
HOH
58
2
HOH
HOH
175
A
HOH
59
2
HOH
HOH
176
A
HOH
60
2
HOH
HOH
177
A
HOH
61
2
HOH
HOH
178
A
HOH
62
2
HOH
HOH
179
A
HOH
63
2
HOH
HOH
180
A
HOH
64
2
HOH
HOH
181
A
HOH
65
2
HOH
HOH
182
A
HOH
66
2
HOH
HOH
183
A
HOH
67
2
HOH
HOH
184
A
HOH
68
2
HOH
HOH
185
A
HOH
69
2
HOH
HOH
186
A
HOH
70
2
HOH
HOH
187
A
HOH
71
2
HOH
HOH
188
A
HOH
72
2
HOH
HOH
189
A
HOH
73
2
HOH
HOH
190
A
SER
1
n
1
SER
1
A
LEU
2
n
2
LEU
2
A
THR
3
n
3
THR
3
A
PHE
4
n
4
PHE
4
A
TYR
5
n
5
TYR
5
A
PRO
6
n
6
PRO
6
A
ALA
7
n
7
ALA
7
A
TRP
8
n
8
TRP
8
A
LEU
9
n
9
LEU
9
A
THR
10
n
10
THR
10
A
VAL
11
n
11
VAL
11
A
SER
12
n
12
SER
12
A
GLU
13
n
13
GLU
13
A
GLY
14
n
14
GLY
14
A
ALA
15
n
15
ALA
15
A
ASN
16
n
16
ASN
16
A
ALA
17
n
17
ALA
17
A
THR
18
n
18
THR
18
A
PHE
19
n
19
PHE
19
A
THR
20
n
20
THR
20
A
CYS
21
n
21
CYS
21
A
SER
22
n
22
SER
22
A
LEU
23
n
23
LEU
23
A
SER
24
n
24
SER
24
A
ASN
25
n
25
ASN
25
A
TRP
26
n
26
TRP
26
A
SER
27
n
27
SER
27
A
GLU
28
n
28
GLU
28
A
ASP
29
n
29
ASP
29
A
LEU
30
n
30
LEU
30
A
MET
31
n
31
MET
31
A
LEU
32
n
32
LEU
32
A
ASN
33
n
33
ASN
33
A
TRP
34
n
34
TRP
34
A
ASN
35
n
35
ASN
35
A
ARG
36
n
36
ARG
36
A
LEU
37
n
37
LEU
37
A
SER
38
n
38
SER
38
A
PRO
39
n
39
PRO
39
A
SER
40
n
40
SER
40
A
ASN
41
n
41
ASN
41
A
GLN
42
n
42
GLN
42
A
THR
43
n
43
THR
43
A
GLU
44
n
44
GLU
44
A
LYS
45
n
45
LYS
45
A
GLN
46
n
46
GLN
46
A
ALA
47
n
47
ALA
47
A
ALA
48
n
48
ALA
48
A
PHE
49
n
49
PHE
49
A
SER
50
n
50
SER
50
A
ASN
51
n
51
ASN
51
A
GLY
52
n
52
GLY
52
A
LEU
53
n
53
LEU
53
A
SER
54
n
54
SER
54
A
GLN
55
n
55
GLN
55
A
PRO
56
n
56
PRO
56
A
VAL
57
n
57
VAL
57
A
GLN
58
n
58
GLN
58
A
ASP
59
n
59
ASP
59
A
ALA
60
n
60
ALA
60
A
ARG
61
n
61
ARG
61
A
PHE
62
n
62
PHE
62
A
GLN
63
n
63
GLN
63
A
ILE
64
n
64
ILE
64
A
ILE
65
n
65
ILE
65
A
GLN
66
n
66
GLN
66
A
LEU
67
n
67
LEU
67
A
PRO
68
n
68
PRO
68
A
ASN
69
n
69
ASN
69
A
ARG
70
n
70
ARG
70
A
HIS
71
n
71
HIS
71
A
ASP
72
n
72
ASP
72
A
PHE
73
n
73
PHE
73
A
HIS
74
n
74
HIS
74
A
MET
75
n
75
MET
75
A
ASN
76
n
76
ASN
76
A
ILE
77
n
77
ILE
77
A
LEU
78
n
78
LEU
78
A
ASP
79
n
79
ASP
79
A
THR
80
n
80
THR
80
A
ARG
81
n
81
ARG
81
A
ARG
82
n
82
ARG
82
A
ASN
83
n
83
ASN
83
A
ASP
84
n
84
ASP
84
A
SER
85
n
85
SER
85
A
GLY
86
n
86
GLY
86
A
ILE
87
n
87
ILE
87
A
TYR
88
n
88
TYR
88
A
LEU
89
n
89
LEU
89
A
CYS
90
n
90
CYS
90
A
GLY
91
n
91
GLY
91
A
ALA
92
n
92
ALA
92
A
ILE
93
n
93
ILE
93
A
SER
94
n
94
SER
94
A
LEU
95
n
95
LEU
95
A
ALA
96
n
96
HIS
96
A
ALA
97
n
97
PRO
97
A
LYS
98
n
98
LYS
98
A
ALA
99
n
99
ALA
99
A
ALA
100
n
100
LYS
100
A
ILE
101
n
101
ILE
101
A
GLU
102
n
102
GLU
102
A
GLU
103
n
103
GLU
103
A
SER
104
n
104
SER
104
A
PRO
105
n
105
PRO
105
A
GLY
106
n
106
GLY
106
A
ALA
107
n
107
ALA
107
A
GLU
108
n
108
GLU
108
A
LEU
109
n
109
LEU
109
A
VAL
110
n
110
VAL
110
A
VAL
111
n
111
VAL
111
A
THR
112
n
112
THR
112
A
GLU
113
n
113
GLU
113
A
ARG
114
n
114
ARG
114
A
ILE
115
n
115
ILE
115
A
LEU
116
n
116
LEU
116
A
n
117
117
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
N
TYR
5
A
N
TYR
5
A
O
THR
20
A
O
THR
20
A
N
ALA
17
A
N
ALA
17
A
O
ILE
77
A
O
ILE
77
A
O
HIS
74
A
O
HIS
74
A
N
ILE
65
A
N
ILE
65
A
O
GLN
55
A
O
GLN
55
A
N
ALA
48
A
N
ALA
48
A
O
GLN
46
A
O
GLN
46
A
N
TRP
34
A
N
TRP
34
A
N
MET
31
A
N
MET
31
A
O
ILE
93
A
O
ILE
93
A
N
SER
94
A
N
SER
94
A
O
LYS
100
A
O
LYS
100
A
O
GLN
55
A
O
GLN
55
A
N
ALA
48
A
N
ALA
48
A
O
GLN
46
A
O
GLN
46
A
N
TRP
34
A
N
TRP
34
A
N
MET
31
A
N
MET
31
A
O
ILE
93
A
O
ILE
93
A
N
TYR
88
A
N
TYR
88
A
O
ALA
107
A
O
ALA
107
A
O
THR
112
A
O
THR
112
A
N
VAL
11
A
N
VAL
11
1
A
CG
HIS
96
A
CG
HIS
96
1
Y
1
A
ND1
HIS
96
A
ND1
HIS
96
1
Y
1
A
CD2
HIS
96
A
CD2
HIS
96
1
Y
1
A
CE1
HIS
96
A
CE1
HIS
96
1
Y
1
A
NE2
HIS
96
A
NE2
HIS
96
1
Y
1
A
CG
PRO
97
A
CG
PRO
97
1
Y
1
A
CD
PRO
97
A
CD
PRO
97
1
Y
1
A
CG
LYS
100
A
CG
LYS
100
1
Y
1
A
CD
LYS
100
A
CD
LYS
100
1
Y
1
A
CE
LYS
100
A
CE
LYS
100
1
Y
1
A
NZ
LYS
100
A
NZ
LYS
100
1
Y
1
A
GLU
117
A
GLU
117
1
Y
1
A
GLN
58
-146.74
-18.16
1
A
ARG
70
69.25
-25.27
1
A
LEU
95
-104.56
47.01
1
A
HIS
96
-118.42
-137.42
1
A
PRO
97
-22.87
-68.86
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
18.6
-1.63
0.00
0.00
-3.29
0.00
4.92
0.228
0.009
0.198
0.213
0.198
2.00
18.78
672
6626
6425
10.5
97.1
RANDOM
178575.39
0.000000
1
RESTRAINED
THROUGHOUT
0
MOLECULAR REPLACEMENT
PDB ENTRY 1B88
Engh & Huber
FLAT MODEL
41.0753
0.38404
0.27
0.21
5.00
0.19
0.14
2.00
18.78
73
979
0
0
906
0.005
1.3
27.2
0.78
1.33
1.50
2.02
2.00
1.96
2.00
2.73
2.50
0.228
0.030
0.202
2.07
57
503
10
10.2
92.0
8.7
2.00
20.00
1NPU
6677
6677
0
0
1
99.7
0.276
2.00
2.07
97
refinement
CNS
1.0
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
EPMR
CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1
1
N
N
2
N
N
A
ARG
81
A
ARG
81
HELX_P
A
SER
85
A
SER
85
5
1
5
disulf
2.036
A
CYS
21
A
SG
CYS
21
1_555
A
CYS
90
A
SG
CYS
90
1_555
IMMUNE SYSTEM
Ig V-type domain, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, IMMUNE SYSTEM
A
TYR
5
A
TYR
5
1
A
PRO
6
A
PRO
6
0.00
PDCD1_MOUSE
UNP
1
34
Q02242
SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFCNGLSQPVQDARFQIIQLPNRHDFHMNILDT
RRNDSGIYLCGAISLHPKAKIEESPGAELVVTERILE
34
150
1NPU
1
117
Q02242
A
1
1
117
1
CYS
engineered mutation
SER
50
1NPU
A
Q02242
UNP
83
50
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
LEU
2
A
LEU
2
A
TYR
5
A
TYR
5
A
ALA
17
A
ALA
17
A
LEU
23
A
LEU
23
A
ASP
72
A
ASP
72
A
ILE
77
A
ILE
77
A
PHE
62
A
PHE
62
A
GLN
66
A
GLN
66
A
LEU
53
A
LEU
53
A
PRO
56
A
PRO
56
A
THR
43
A
THR
43
A
SER
50
A
SER
50
A
MET
31
A
MET
31
A
LEU
37
A
LEU
37
A
GLY
86
A
GLY
86
A
SER
94
A
SER
94
A
LYS
100
A
LYS
100
A
GLU
103
A
GLU
103
A
LEU
53
A
LEU
53
A
PRO
56
A
PRO
56
A
THR
43
A
THR
43
A
SER
50
A
SER
50
A
MET
31
A
MET
31
A
LEU
37
A
LEU
37
A
GLY
86
A
GLY
86
A
SER
94
A
SER
94
A
ALA
107
A
ALA
107
A
THR
112
A
THR
112
A
TRP
8
A
TRP
8
A
SER
12
A
SER
12
19
P 21 21 21