0.028415
0.000000
0.000000
0.000000
0.028415
0.000000
0.000000
0.000000
0.004870
0.000000
0.000000
0.000000
Kumar, P.R.
Bonanno, J.
Ahmed, M.
Banu, R.
Bhosle, R.
Calarese, D.
Celikigil, A.
Chamala, S.
Chan, M.K.
Chowdhury, S.
Fiser, A.
Garforth, S.
Glenn, A.S.
Hillerich, B.
Khafizov, K.
Love, J.
Patel, H.
Seidel, R.
Stead, M.
Toro, R.
Nathenson, S.G.
Almo, S.C.
New York Structural Genomics Research Consortium (NYSGRC)
Atoms-to-Animals: The Immune Function Network (IFN)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
35.193
35.193
205.331
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
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
C
N
89
N
O
N
90
N
C
N
91
N
O
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
N
N
99
S
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
O
N
127
N
O
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
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
N
C
N
139
N
C
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
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
N
C
Y
152
N
C
Y
153
N
N
Y
154
N
C
Y
155
N
C
Y
156
N
N
N
157
N
O
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
O
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
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
N
N
194
S
C
N
195
N
C
N
196
N
O
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
N
N
202
N
O
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
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
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
Y
223
N
C
Y
224
N
C
Y
225
N
C
Y
226
N
C
Y
227
N
C
Y
228
N
C
N
229
N
O
N
230
N
H
N
231
N
H
N
232
N
H
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
N
N
242
S
C
N
243
N
C
N
244
N
O
N
245
N
C
N
246
N
C
N
247
N
C
N
248
N
O
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
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
O
N
264
N
O
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
N
N
273
S
C
N
274
N
C
N
275
N
O
N
276
R
C
N
277
N
O
N
278
N
C
N
279
N
O
N
280
N
H
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
N
N
290
S
C
N
291
N
C
N
292
N
O
N
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
N
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
N
303
N
O
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
N
N
317
S
C
N
318
N
C
N
319
N
O
N
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
N
327
N
O
N
328
N
O
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
C
N
346
N
C
N
347
N
O
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
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
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
doub
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
doub
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
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
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
doub
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
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
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
Y
149
N
sing
Y
150
N
doub
Y
151
N
doub
N
152
N
sing
Y
153
N
sing
N
154
N
sing
Y
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
doub
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
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
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
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
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
Y
217
N
doub
Y
218
N
sing
Y
219
N
sing
N
220
N
sing
Y
221
N
doub
N
222
N
sing
Y
223
N
doub
N
224
N
sing
Y
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
doub
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
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
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
doub
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
Y
286
N
doub
Y
287
N
sing
Y
288
N
sing
N
289
N
sing
Y
290
N
doub
Y
291
N
sing
Y
292
N
sing
N
293
N
sing
Y
294
N
sing
Y
295
N
doub
N
296
N
sing
Y
297
N
doub
N
298
N
sing
Y
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
doub
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
Y
314
N
doub
Y
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
doub
N
319
N
sing
Y
320
N
doub
N
321
N
sing
Y
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
doub
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
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
to be published
0353
Crystal structure of the D1 domain of human Nectin-4 extracellular fragment [NYSGRC-005624]
10.2210/pdb4jjh/pdb
pdb_00004jjh
100
1
MIRRORS
CCD
2013-02-07
ADSC QUANTUM 315
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.0750
1.0
X29A
NSLS
1.0750
SYNCHROTRON
NSLS BEAMLINE X29A
14439.062
Poliovirus receptor-related protein 4
D1 domain (UNP residues 32-153)
2
man
polymer
62.068
1,2-ETHANEDIOL
1
syn
non-polymer
18.015
water
1
nat
water
Ig superfamily receptor LNIR, Nectin-4, Processed poliovirus receptor-related protein 4
no
no
QDYGGGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRN
PLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLAENLYF
QDYGGGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRN
PLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLAENLYF
A,B
NYSGRC-005624
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
human
sample
LNIR, Nectin-4, PRR4, PVRL4
9606
Homo sapiens
7111
Trichoplusia ni
Hi5
Plasmid
pIEX
1
2.20
44.13
VAPOR DIFFUSION, SITTING DROP
7.0
Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K
298
New York Structural Genomics Research Consortium
NYSGRC
PSI:Biology
Atoms-to-Animals: The Immune Function Network
IFN
PSI:Biology
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Structure summary
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-03-27
1
1
2013-11-27
1
2
2017-11-15
1
3
2023-09-20
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.language
_software.location
_software.name
_software.type
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2013-03-07
REL
REL
EDO
1,2-ETHANEDIOL
HOH
water
4FRW
PDB
experimental model
EDO
1
2
EDO
EDO
201
A
HOH
1
3
HOH
HOH
201
B
n
1
27
A
n
2
28
A
n
3
29
A
n
4
30
A
n
5
31
A
n
6
32
A
n
7
33
A
n
8
34
A
n
9
35
A
THR
36
n
10
THR
36
A
SER
37
n
11
SER
37
A
ASP
38
n
12
ASP
38
A
VAL
39
n
13
VAL
39
A
VAL
40
n
14
VAL
40
A
THR
41
n
15
THR
41
A
VAL
42
n
16
VAL
42
A
VAL
43
n
17
VAL
43
A
LEU
44
n
18
LEU
44
A
GLY
45
n
19
GLY
45
A
GLN
46
n
20
GLN
46
A
ASP
47
n
21
ASP
47
A
ALA
48
n
22
ALA
48
A
LYS
49
n
23
LYS
49
A
LEU
50
n
24
LEU
50
A
PRO
51
n
25
PRO
51
A
CYS
52
n
26
CYS
52
A
PHE
53
n
27
PHE
53
A
TYR
54
n
28
TYR
54
A
ARG
55
n
29
ARG
55
A
GLY
56
n
30
GLY
56
A
ASP
57
n
31
ASP
57
A
n
32
58
A
n
33
59
A
GLU
60
n
34
GLU
60
A
GLN
61
n
35
GLN
61
A
VAL
62
n
36
VAL
62
A
GLY
63
n
37
GLY
63
A
GLN
64
n
38
GLN
64
A
VAL
65
n
39
VAL
65
A
ALA
66
n
40
ALA
66
A
TRP
67
n
41
TRP
67
A
ALA
68
n
42
ALA
68
A
ARG
69
n
43
ARG
69
A
VAL
70
n
44
VAL
70
A
n
45
71
A
n
46
72
A
n
47
73
A
n
48
74
A
n
49
75
A
ALA
76
n
50
ALA
76
A
GLN
77
n
51
GLN
77
A
GLU
78
n
52
GLU
78
A
LEU
79
n
53
LEU
79
A
ALA
80
n
54
ALA
80
A
LEU
81
n
55
LEU
81
A
LEU
82
n
56
LEU
82
A
HIS
83
n
57
HIS
83
A
SER
84
n
58
SER
84
A
LYS
85
n
59
LYS
85
A
TYR
86
n
60
TYR
86
A
GLY
87
n
61
GLY
87
A
LEU
88
n
62
LEU
88
A
HIS
89
n
63
HIS
89
A
VAL
90
n
64
VAL
90
A
SER
91
n
65
SER
91
A
PRO
92
n
66
PRO
92
A
ALA
93
n
67
ALA
93
A
TYR
94
n
68
TYR
94
A
GLU
95
n
69
GLU
95
A
GLY
96
n
70
GLY
96
A
ARG
97
n
71
ARG
97
A
VAL
98
n
72
VAL
98
A
GLU
99
n
73
GLU
99
A
GLN
100
n
74
GLN
100
A
PRO
101
n
75
PRO
101
A
PRO
102
n
76
PRO
102
A
PRO
103
n
77
PRO
103
A
PRO
104
n
78
PRO
104
A
ARG
105
n
79
ARG
105
A
ASN
106
n
80
ASN
106
A
PRO
107
n
81
PRO
107
A
LEU
108
n
82
LEU
108
A
ASP
109
n
83
ASP
109
A
GLY
110
n
84
GLY
110
A
SER
111
n
85
SER
111
A
VAL
112
n
86
VAL
112
A
LEU
113
n
87
LEU
113
A
LEU
114
n
88
LEU
114
A
ARG
115
n
89
ARG
115
A
ASN
116
n
90
ASN
116
A
ALA
117
n
91
ALA
117
A
VAL
118
n
92
VAL
118
A
GLN
119
n
93
GLN
119
A
ALA
120
n
94
ALA
120
A
ASP
121
n
95
ASP
121
A
GLU
122
n
96
GLU
122
A
GLY
123
n
97
GLY
123
A
GLU
124
n
98
GLU
124
A
TYR
125
n
99
TYR
125
A
GLU
126
n
100
GLU
126
A
CYS
127
n
101
CYS
127
A
ARG
128
n
102
ARG
128
A
VAL
129
n
103
VAL
129
A
SER
130
n
104
SER
130
A
THR
131
n
105
THR
131
A
PHE
132
n
106
PHE
132
A
PRO
133
n
107
PRO
133
A
ALA
134
n
108
ALA
134
A
GLY
135
n
109
GLY
135
A
SER
136
n
110
SER
136
A
PHE
137
n
111
PHE
137
A
GLN
138
n
112
GLN
138
A
ALA
139
n
113
ALA
139
A
ARG
140
n
114
ARG
140
A
LEU
141
n
115
LEU
141
A
ARG
142
n
116
ARG
142
A
LEU
143
n
117
LEU
143
A
ARG
144
n
118
ARG
144
A
VAL
145
n
119
VAL
145
A
LEU
146
n
120
LEU
146
A
VAL
147
n
121
VAL
147
A
PRO
148
n
122
PRO
148
A
PRO
149
n
123
PRO
149
A
LEU
150
n
124
LEU
150
A
PRO
151
n
125
PRO
151
A
SER
152
n
126
SER
152
A
LEU
153
n
127
LEU
153
A
n
128
154
A
n
129
155
A
n
130
156
A
n
131
157
A
n
132
158
A
n
133
159
A
n
1
27
B
n
2
28
B
n
3
29
B
n
4
30
B
n
5
31
B
n
6
32
B
n
7
33
B
n
8
34
B
n
9
35
B
THR
36
n
10
THR
36
B
SER
37
n
11
SER
37
B
ASP
38
n
12
ASP
38
B
VAL
39
n
13
VAL
39
B
VAL
40
n
14
VAL
40
B
THR
41
n
15
THR
41
B
VAL
42
n
16
VAL
42
B
VAL
43
n
17
VAL
43
B
LEU
44
n
18
LEU
44
B
GLY
45
n
19
GLY
45
B
GLN
46
n
20
GLN
46
B
ASP
47
n
21
ASP
47
B
ALA
48
n
22
ALA
48
B
LYS
49
n
23
LYS
49
B
LEU
50
n
24
LEU
50
B
PRO
51
n
25
PRO
51
B
CYS
52
n
26
CYS
52
B
PHE
53
n
27
PHE
53
B
TYR
54
n
28
TYR
54
B
ARG
55
n
29
ARG
55
B
n
30
56
B
ASP
57
n
31
ASP
57
B
SER
58
n
32
SER
58
B
GLY
59
n
33
GLY
59
B
GLU
60
n
34
GLU
60
B
GLN
61
n
35
GLN
61
B
VAL
62
n
36
VAL
62
B
GLY
63
n
37
GLY
63
B
GLN
64
n
38
GLN
64
B
VAL
65
n
39
VAL
65
B
ALA
66
n
40
ALA
66
B
TRP
67
n
41
TRP
67
B
ALA
68
n
42
ALA
68
B
ARG
69
n
43
ARG
69
B
VAL
70
n
44
VAL
70
B
n
45
71
B
n
46
72
B
n
47
73
B
n
48
74
B
n
49
75
B
ALA
76
n
50
ALA
76
B
GLN
77
n
51
GLN
77
B
GLU
78
n
52
GLU
78
B
LEU
79
n
53
LEU
79
B
ALA
80
n
54
ALA
80
B
LEU
81
n
55
LEU
81
B
LEU
82
n
56
LEU
82
B
HIS
83
n
57
HIS
83
B
SER
84
n
58
SER
84
B
LYS
85
n
59
LYS
85
B
TYR
86
n
60
TYR
86
B
GLY
87
n
61
GLY
87
B
LEU
88
n
62
LEU
88
B
HIS
89
n
63
HIS
89
B
VAL
90
n
64
VAL
90
B
SER
91
n
65
SER
91
B
PRO
92
n
66
PRO
92
B
ALA
93
n
67
ALA
93
B
TYR
94
n
68
TYR
94
B
GLU
95
n
69
GLU
95
B
GLY
96
n
70
GLY
96
B
ARG
97
n
71
ARG
97
B
VAL
98
n
72
VAL
98
B
GLU
99
n
73
GLU
99
B
GLN
100
n
74
GLN
100
B
PRO
101
n
75
PRO
101
B
PRO
102
n
76
PRO
102
B
PRO
103
n
77
PRO
103
B
PRO
104
n
78
PRO
104
B
ARG
105
n
79
ARG
105
B
ASN
106
n
80
ASN
106
B
PRO
107
n
81
PRO
107
B
LEU
108
n
82
LEU
108
B
ASP
109
n
83
ASP
109
B
GLY
110
n
84
GLY
110
B
SER
111
n
85
SER
111
B
VAL
112
n
86
VAL
112
B
LEU
113
n
87
LEU
113
B
LEU
114
n
88
LEU
114
B
ARG
115
n
89
ARG
115
B
ASN
116
n
90
ASN
116
B
ALA
117
n
91
ALA
117
B
VAL
118
n
92
VAL
118
B
GLN
119
n
93
GLN
119
B
ALA
120
n
94
ALA
120
B
ASP
121
n
95
ASP
121
B
GLU
122
n
96
GLU
122
B
GLY
123
n
97
GLY
123
B
GLU
124
n
98
GLU
124
B
TYR
125
n
99
TYR
125
B
GLU
126
n
100
GLU
126
B
CYS
127
n
101
CYS
127
B
ARG
128
n
102
ARG
128
B
VAL
129
n
103
VAL
129
B
SER
130
n
104
SER
130
B
THR
131
n
105
THR
131
B
PHE
132
n
106
PHE
132
B
PRO
133
n
107
PRO
133
B
ALA
134
n
108
ALA
134
B
GLY
135
n
109
GLY
135
B
SER
136
n
110
SER
136
B
PHE
137
n
111
PHE
137
B
GLN
138
n
112
GLN
138
B
ALA
139
n
113
ALA
139
B
ARG
140
n
114
ARG
140
B
LEU
141
n
115
LEU
141
B
ARG
142
n
116
ARG
142
B
LEU
143
n
117
LEU
143
B
ARG
144
n
118
ARG
144
B
VAL
145
n
119
VAL
145
B
LEU
146
n
120
LEU
146
B
VAL
147
n
121
VAL
147
B
PRO
148
n
122
PRO
148
B
PRO
149
n
123
PRO
149
B
LEU
150
n
124
LEU
150
B
PRO
151
n
125
PRO
151
B
SER
152
n
126
SER
152
B
LEU
153
n
127
LEU
153
B
n
128
154
B
n
129
155
B
n
130
156
B
n
131
157
B
n
132
158
B
n
133
159
B
1.6044
0.6878
-0.6024
0.3371
-0.4122
1.9620
0.1437
-0.0385
0.0170
-0.3051
-0.1328
-0.0295
0.1291
0.3278
-0.0947
0.3675
0.0593
0.0403
0.1034
-0.0093
0.1464
refined
10.8380
16.8543
8.8493
X-RAY DIFFRACTION
0.9495
0.3743
0.2047
2.4122
-0.4364
1.6564
0.1556
0.2011
0.3479
-0.4060
-0.0390
0.2041
-0.2627
-0.0859
-0.0956
0.2871
-0.0291
0.0608
0.1693
-0.0180
0.1382
refined
4.4242
30.1113
8.3973
X-RAY DIFFRACTION
2.0956
-0.3116
-0.5076
1.1282
-0.0857
2.2514
0.3350
-0.3084
0.2572
0.0141
-0.1546
-0.0131
-0.2177
0.3006
-0.0958
0.2018
-0.0395
0.0148
0.1120
-0.0127
0.1532
refined
9.1193
24.0951
15.6561
X-RAY DIFFRACTION
0.7936
-0.2934
0.0892
1.5272
-0.8917
1.5600
0.1292
0.0041
-0.0649
-0.5916
-0.0161
0.2213
0.0600
0.0442
0.3348
0.3315
0.0301
-0.0795
0.2189
0.0063
0.0338
refined
3.2954
15.8873
9.3497
X-RAY DIFFRACTION
0.9405
0.8592
1.3006
1.2080
0.8145
2.1200
-0.0312
-0.5123
0.0182
0.1830
0.1530
-0.1276
-0.3007
-0.0872
-0.0500
0.2751
0.0298
-0.0106
0.3067
-0.0786
0.1396
refined
16.7874
10.9231
34.0479
X-RAY DIFFRACTION
2.5470
-0.8312
-0.2359
0.8658
-0.3603
2.1579
0.0018
-0.2065
-0.5370
0.2632
0.1527
-0.1516
-0.1648
0.2274
-0.0915
0.1355
0.0218
0.0057
0.3006
-0.0070
0.1169
refined
29.7509
4.7662
33.9077
X-RAY DIFFRACTION
1.9353
0.3840
0.3894
1.3198
0.0855
1.5667
-0.4456
0.0550
0.0486
0.0358
0.4062
0.0562
-0.1809
0.4411
0.0672
0.1889
0.0298
-0.0055
0.2030
-0.0455
0.1351
refined
23.0507
9.6830
26.7705
X-RAY DIFFRACTION
0.9003
0.8132
0.6197
1.1678
0.5358
1.5080
-0.0081
-0.4351
-0.2405
0.0799
-0.1070
-0.0985
0.0228
-0.0946
0.1908
0.1961
-0.0193
0.0871
0.3584
0.0598
0.0975
refined
15.6869
3.7562
32.7558
X-RAY DIFFRACTION
A
0
A
0
X-RAY DIFFRACTION
1
chain 'A' and (resid 36 through 60 )
A
0
A
0
X-RAY DIFFRACTION
2
chain 'A' and (resid 61 through 93)
A
0
A
0
X-RAY DIFFRACTION
3
chain 'A' and (resid 94 through 120 )
A
0
A
0
X-RAY DIFFRACTION
4
chain 'A' and (resid 121 through 153 )
B
0
B
0
X-RAY DIFFRACTION
5
chain 'B' and (resid 36 through 60 )
B
0
B
0
X-RAY DIFFRACTION
6
chain 'B' and (resid 61 through 93 )
B
0
B
0
X-RAY DIFFRACTION
7
chain 'B' and (resid 94 through 120 )
B
0
B
0
X-RAY DIFFRACTION
8
chain 'B' and (resid 121 through 153 )
1
0.500
author_defined_assembly
2
dimeric
software_defined_assembly
PISA
1
monomeric
software_defined_assembly
PISA
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
VAL
40
A
N
VAL
14
A
O
ARG
144
A
O
ARG
118
A
O
PHE
137
A
O
PHE
111
A
N
VAL
129
A
N
VAL
103
A
O
ARG
128
A
O
ARG
102
A
N
ALA
66
A
N
ALA
40
A
N
TRP
67
A
N
TRP
41
A
O
LEU
79
A
O
LEU
53
A
N
LEU
81
A
N
LEU
55
A
O
HIS
89
A
O
HIS
63
A
N
LEU
50
A
N
LEU
24
A
O
VAL
112
A
O
VAL
86
A
O
LEU
113
A
O
LEU
87
A
N
GLU
99
A
N
GLU
73
B
N
VAL
40
B
N
VAL
14
B
O
ARG
142
B
O
ARG
116
B
O
LEU
143
B
O
LEU
117
B
N
GLY
123
B
N
GLY
97
B
O
PHE
132
B
O
PHE
106
B
N
GLN
61
B
N
GLN
35
B
N
ARG
69
B
N
ARG
43
B
O
GLN
77
B
O
GLN
51
B
N
LEU
81
B
N
LEU
55
B
O
HIS
89
B
O
HIS
63
B
N
LEU
50
B
N
LEU
24
B
O
VAL
112
B
O
VAL
86
B
O
LEU
113
B
O
LEU
87
B
N
GLU
99
B
N
GLU
73
1
A
GLN
27
A
GLN
1
1
Y
1
A
ASP
28
A
ASP
2
1
Y
1
A
TYR
29
A
TYR
3
1
Y
1
A
GLY
30
A
GLY
4
1
Y
1
A
GLY
31
A
GLY
5
1
Y
1
A
GLY
32
A
GLY
6
1
Y
1
A
GLU
33
A
GLU
7
1
Y
1
A
LEU
34
A
LEU
8
1
Y
1
A
GLU
35
A
GLU
9
1
Y
1
A
SER
58
A
SER
32
1
Y
1
A
GLY
59
A
GLY
33
1
Y
1
A
ASP
71
A
ASP
45
1
Y
1
A
ALA
72
A
ALA
46
1
Y
1
A
GLY
73
A
GLY
47
1
Y
1
A
GLU
74
A
GLU
48
1
Y
1
A
GLY
75
A
GLY
49
1
Y
1
A
ALA
154
A
ALA
128
1
Y
1
A
GLU
155
A
GLU
129
1
Y
1
A
ASN
156
A
ASN
130
1
Y
1
A
LEU
157
A
LEU
131
1
Y
1
A
TYR
158
A
TYR
132
1
Y
1
A
PHE
159
A
PHE
133
1
Y
1
B
GLN
27
B
GLN
1
1
Y
1
B
ASP
28
B
ASP
2
1
Y
1
B
TYR
29
B
TYR
3
1
Y
1
B
GLY
30
B
GLY
4
1
Y
1
B
GLY
31
B
GLY
5
1
Y
1
B
GLY
32
B
GLY
6
1
Y
1
B
GLU
33
B
GLU
7
1
Y
1
B
LEU
34
B
LEU
8
1
Y
1
B
GLU
35
B
GLU
9
1
Y
1
B
GLY
56
B
GLY
30
1
Y
1
B
ASP
71
B
ASP
45
1
Y
1
B
ALA
72
B
ALA
46
1
Y
1
B
GLY
73
B
GLY
47
1
Y
1
B
GLU
74
B
GLU
48
1
Y
1
B
GLY
75
B
GLY
49
1
Y
1
B
ALA
154
B
ALA
128
1
Y
1
B
GLU
155
B
GLU
129
1
Y
1
B
ASN
156
B
ASN
130
1
Y
1
B
LEU
157
B
LEU
131
1
Y
1
B
TYR
158
B
TYR
132
1
Y
1
B
PHE
159
B
PHE
133
1
Y
1
A
CYS
52
-151.49
79.43
1
A
ASN
116
54.30
73.46
1
A
ALA
134
-144.13
-2.69
1
B
SER
58
69.33
-106.37
1
B
ASN
116
59.22
74.65
1
B
ALA
134
-145.55
-4.42
72.530
31.2146
9.260
0.2921
0.2222
0.2257
2.2500
35.1930
541
11454
4.7200
97.2400
1.000
1.000
0.7540
RANDOM
1
1.420
MOLECULAR REPLACEMENT
31.5600
0.9000
1.1100
4FRW
TWIN_LSQ_F
FLAT BULK SOLVENT MODEL
2.2500
35.1930
1
1727
4
0
1722
0.011
1765
1.488
2400
0.055
269
0.008
319
15.216
659
0.3010
0.2551
2.4788
125
2805
2930
4
96.0000
0.2878
0.2463
2.8356
147
2740
2887
4
95.0000
0.3208
0.2336
3.5657
140
2800
2940
4
94.0000
0.2766
0.1907
15.6931
128
2520
2648
4
86.0000
2.250
50.000
4JJH
11848
11529
0.069
1.038
1
8.3
9.000
97.300
0.262
2.250
2.290
585
0.842
1
9.500
100.000
0.273
2.290
2.330
600
0.854
1
10.000
100.000
0.262
2.330
2.380
594
0.833
1
9.900
100.000
0.241
2.380
2.420
554
0.905
1
10.000
100.000
0.203
2.420
2.480
625
0.912
1
10.000
100.000
0.182
2.480
2.530
600
0.997
1
9.900
100.000
0.166
2.530
2.600
561
1.033
1
9.900
100.000
0.154
2.600
2.670
581
1.019
1
9.900
100.000
0.130
2.670
2.750
609
1.133
1
9.700
100.000
0.109
2.750
2.830
556
1.172
1
9.400
100.000
0.098
2.830
2.940
642
1.200
1
9.400
100.000
0.082
2.940
3.050
547
1.205
1
9.100
99.800
0.079
3.050
3.190
617
1.238
1
9.000
100.000
0.067
3.190
3.360
574
1.231
1
8.400
99.800
0.061
3.360
3.570
579
1.158
1
7.900
96.300
0.058
3.570
3.850
560
1.114
1
7.800
94.800
0.054
3.850
4.230
514
1.071
1
6.800
88.000
0.053
4.230
4.850
471
1.011
1
6.400
78.100
0.051
4.850
6.100
566
0.950
1
7.700
94.300
0.053
6.100
50.000
594
0.984
1
8.300
96.300
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.8.2_1309
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data collection
CBASS
data reduction
HKL-2000
phasing
PHENIX
1.8.2_1309
Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]
1
N
N
1
N
N
2
N
N
3
N
N
A
PRO
92
A
PRO
66
HELX_P
A
GLU
95
A
GLU
69
5
1
4
A
VAL
118
A
VAL
92
HELX_P
A
GLU
122
A
GLU
96
5
2
5
B
PRO
92
B
PRO
66
HELX_P
B
GLU
95
B
GLU
69
5
3
4
B
VAL
118
B
VAL
92
HELX_P
B
GLU
122
B
GLU
96
5
4
5
disulf
2.027
A
CYS
52
A
SG
CYS
26
1_555
A
CYS
127
A
SG
CYS
101
1_555
disulf
2.015
B
CYS
52
B
SG
CYS
26
1_555
B
CYS
127
B
SG
CYS
101
1_555
CELL ADHESION
Nectin-4, Ig-like D1 domain, Ig superfamily, IMMUNE SYSTEM, Cell adhesion, Structural genomics, PSI-Biology, New York Structural Genomics Research Consortium, NYSGRC, Atoms-to-Animals: The Immune Function Network, IFN
A
PRO
103
A
PRO
77
1
A
PRO
104
A
PRO
78
3.04
A
PHE
132
A
PHE
106
1
A
PRO
133
A
PRO
107
-6.27
B
PRO
103
B
PRO
77
1
B
PRO
104
B
PRO
78
-0.78
B
PHE
132
B
PHE
106
1
B
PRO
133
B
PRO
107
-8.61
PVRL4_HUMAN
UNP
1
32
Q96NY8
GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGS
VLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSL
32
153
4JJH
32
153
Q96NY8
A
1
6
127
32
153
4JJH
32
153
Q96NY8
B
1
6
127
1
expression tag
GLN
27
4JJH
A
Q96NY8
UNP
1
1
expression tag
ASP
28
4JJH
A
Q96NY8
UNP
2
1
expression tag
TYR
29
4JJH
A
Q96NY8
UNP
3
1
expression tag
GLY
30
4JJH
A
Q96NY8
UNP
4
1
expression tag
GLY
31
4JJH
A
Q96NY8
UNP
5
1
expression tag
ALA
154
4JJH
A
Q96NY8
UNP
128
1
expression tag
GLU
155
4JJH
A
Q96NY8
UNP
129
1
expression tag
ASN
156
4JJH
A
Q96NY8
UNP
130
1
expression tag
LEU
157
4JJH
A
Q96NY8
UNP
131
1
expression tag
TYR
158
4JJH
A
Q96NY8
UNP
132
1
expression tag
PHE
159
4JJH
A
Q96NY8
UNP
133
2
expression tag
GLN
27
4JJH
B
Q96NY8
UNP
1
2
expression tag
ASP
28
4JJH
B
Q96NY8
UNP
2
2
expression tag
TYR
29
4JJH
B
Q96NY8
UNP
3
2
expression tag
GLY
30
4JJH
B
Q96NY8
UNP
4
2
expression tag
GLY
31
4JJH
B
Q96NY8
UNP
5
2
expression tag
ALA
154
4JJH
B
Q96NY8
UNP
128
2
expression tag
GLU
155
4JJH
B
Q96NY8
UNP
129
2
expression tag
ASN
156
4JJH
B
Q96NY8
UNP
130
2
expression tag
LEU
157
4JJH
B
Q96NY8
UNP
131
2
expression tag
TYR
158
4JJH
B
Q96NY8
UNP
132
2
expression tag
PHE
159
4JJH
B
Q96NY8
UNP
133
6
3
6
3
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
39
A
VAL
13
A
VAL
43
A
VAL
17
A
SER
136
A
SER
110
A
LEU
146
A
LEU
120
A
GLY
123
A
GLY
97
A
THR
131
A
THR
105
A
VAL
62
A
VAL
36
A
ARG
69
A
ARG
43
A
GLN
77
A
GLN
51
A
HIS
83
A
HIS
57
A
GLY
87
A
GLY
61
A
VAL
90
A
VAL
64
A
ALA
48
A
ALA
22
A
LEU
50
A
LEU
24
A
VAL
112
A
VAL
86
A
LEU
114
A
LEU
88
A
VAL
98
A
VAL
72
A
GLU
99
A
GLU
73
B
VAL
39
B
VAL
13
B
VAL
43
B
VAL
17
B
SER
136
B
SER
110
B
LEU
146
B
LEU
120
B
GLY
123
B
GLY
97
B
PHE
132
B
PHE
106
B
GLN
61
B
GLN
35
B
ARG
69
B
ARG
43
B
GLN
77
B
GLN
51
B
HIS
83
B
HIS
57
B
GLY
87
B
GLY
61
B
VAL
90
B
VAL
64
B
ALA
48
B
ALA
22
B
LEU
50
B
LEU
24
B
VAL
112
B
VAL
86
B
LEU
114
B
LEU
88
B
VAL
98
B
VAL
72
B
GLU
99
B
GLU
73
BINDING SITE FOR RESIDUE EDO A 201
A
EDO
201
Software
4
A
VAL
90
A
VAL
64
4
1_555
A
GLU
95
A
GLU
69
4
1_555
A
GLY
96
A
GLY
70
4
1_555
B
VAL
147
B
VAL
121
4
1_565
76
P 41