0.019482
0.000000
0.000000
0.000000
0.010947
0.000000
0.000000
0.000000
0.009242
0.00000
0.00000
0.00000
Li, H.
Margulies, D.H.
Mariuzza, R.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
51.330
91.350
108.200
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
283
179
191
10.1006/jmbi.1998.2091
9761682
Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120.
1998
US
J.Exp.Med.
JEMEAV
0774
0022-1007
178
1877
H-2Dd Exploits a Four Residue Peptide Binding Motif
1993
10.2210/pdb1ddh/pdb
pdb_00001ddh
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
IMAGE PLATE
1997-07
MAR scanner 300 mm plate
M
x-ray
1
0.773
1.0
BL9-1
SSRL
0.773
SYNCHROTRON
SSRL BEAMLINE BL9-1
31862.404
MHC CLASS I H-2DD HEAVY CHAIN
EXTRACELLULAR DOMAINS
G1M
1
man
polymer
11678.388
BETA-2 MICROGLOBULIN
EXTRACELLULAR DOMAIN
I1M
1
man
polymer
1075.265
HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120
RESIDUES 308-322
1
man
polymer
18.015
water
4
nat
water
no
no
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRANGNEQSFRVDLRT
ALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYL
EGECVEWLRRYLKNGNATLLATDPPKAHVTHHRRPEGDVTLRCWALGFYPAEITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKQQKYTCHVEHEGLPEPLTLRW
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRANGNEQSFRVDLRT
ALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYL
EGECVEWLRRYLKNGNATLLATDPPKAHVTHHRRPEGDVTLRCWALGFYPAEITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKQQKYTCHVEHEGLPEPLTLRW
A
polypeptide(L)
no
no
MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHASMAEPKTVYWDRDM
MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHASMAEPKTVYWDRDM
B
polypeptide(L)
no
no
RGPGRAFVTI
RGPGRAFVTI
P
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
BL21
EXTRACELLULAR
10090
Mus musculus
INCLUSION BODY
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
BACTERIAL
PET3A
house mouse
Mus
Escherichia
Escherichia coli
sample
BL21
EXTRACELLULAR
10090
Mus musculus
INCLUSION BODY
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
BACTERIAL
PET21D
Lentivirus
sample
11676
Human immunodeficiency virus 1
1
2.53
58
6.5
pH 6.5
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Refinement description
1
0
1999-01-13
1
1
2008-03-24
1
2
2011-07-13
1
3
2023-08-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
BNL
1998-06-22
REL
REL
HOH
water
1VAD
PDB ENTRY 1VAD
PDB
experimental model
HOH
1
4
HOH
HOH
275
A
HOH
2
4
HOH
HOH
276
A
HOH
3
4
HOH
HOH
277
A
HOH
4
4
HOH
HOH
278
A
MET
1
n
1
MET
1
A
SER
2
n
2
SER
2
A
HIS
3
n
3
HIS
3
A
SER
4
n
4
SER
4
A
LEU
5
n
5
LEU
5
A
ARG
6
n
6
ARG
6
A
TYR
7
n
7
TYR
7
A
PHE
8
n
8
PHE
8
A
VAL
9
n
9
VAL
9
A
THR
10
n
10
THR
10
A
ALA
11
n
11
ALA
11
A
VAL
12
n
12
VAL
12
A
SER
13
n
13
SER
13
A
ARG
14
n
14
ARG
14
A
PRO
15
n
15
PRO
15
A
GLY
16
n
16
GLY
16
A
PHE
17
n
17
PHE
17
A
GLY
18
n
18
GLY
18
A
GLU
19
n
19
GLU
19
A
PRO
20
n
20
PRO
20
A
ARG
21
n
21
ARG
21
A
TYR
22
n
22
TYR
22
A
MET
23
n
23
MET
23
A
GLU
24
n
24
GLU
24
A
VAL
25
n
25
VAL
25
A
GLY
26
n
26
GLY
26
A
TYR
27
n
27
TYR
27
A
VAL
28
n
28
VAL
28
A
ASP
29
n
29
ASP
29
A
ASN
30
n
30
ASN
30
A
THR
31
n
31
THR
31
A
GLU
32
n
32
GLU
32
A
PHE
33
n
33
PHE
33
A
VAL
34
n
34
VAL
34
A
ARG
35
n
35
ARG
35
A
PHE
36
n
36
PHE
36
A
ASP
37
n
37
ASP
37
A
SER
38
n
38
SER
38
A
ASP
39
n
39
ASP
39
A
ALA
40
n
40
ALA
40
A
GLU
41
n
41
GLU
41
A
ASN
42
n
42
ASN
42
A
PRO
43
n
43
PRO
43
A
ARG
44
n
44
ARG
44
A
TYR
45
n
45
TYR
45
A
GLU
46
n
46
GLU
46
A
PRO
47
n
47
PRO
47
A
ARG
48
n
48
ARG
48
A
ALA
49
n
49
ALA
49
A
ARG
50
n
50
ARG
50
A
TRP
51
n
51
TRP
51
A
ILE
52
n
52
ILE
52
A
GLU
53
n
53
GLU
53
A
GLN
54
n
54
GLN
54
A
GLU
55
n
55
GLU
55
A
GLY
56
n
56
GLY
56
A
PRO
57
n
57
PRO
57
A
GLU
58
n
58
GLU
58
A
TYR
59
n
59
TYR
59
A
TRP
60
n
60
TRP
60
A
GLU
61
n
61
GLU
61
A
ARG
62
n
62
ARG
62
A
GLU
63
n
63
GLU
63
A
THR
64
n
64
THR
64
A
ARG
65
n
65
ARG
65
A
ARG
66
n
66
ARG
66
A
ALA
67
n
67
ALA
67
A
ASN
68
n
68
ASN
68
A
GLY
69
n
69
GLY
69
A
ASN
70
n
70
ASN
70
A
GLU
71
n
71
GLU
71
A
GLN
72
n
72
GLN
72
A
SER
73
n
73
SER
73
A
PHE
74
n
74
PHE
74
A
ARG
75
n
75
ARG
75
A
VAL
76
n
76
VAL
76
A
ASP
77
n
77
ASP
77
A
LEU
78
n
78
LEU
78
A
ARG
79
n
79
ARG
79
A
THR
80
n
80
THR
80
A
ALA
81
n
81
ALA
81
A
LEU
82
n
82
LEU
82
A
ARG
83
n
83
ARG
83
A
TYR
84
n
84
TYR
84
A
TYR
85
n
85
TYR
85
A
ASN
86
n
86
ASN
86
A
GLN
87
n
87
GLN
87
A
SER
88
n
88
SER
88
A
ALA
89
n
89
ALA
89
A
GLY
90
n
90
GLY
90
A
GLY
91
n
91
GLY
91
A
SER
92
n
92
SER
92
A
HIS
93
n
93
HIS
93
A
THR
94
n
94
THR
94
A
LEU
95
n
95
LEU
95
A
GLN
96
n
96
GLN
96
A
TRP
97
n
97
TRP
97
A
MET
98
n
98
MET
98
A
ALA
99
n
99
ALA
99
A
GLY
100
n
100
GLY
100
A
CYS
101
n
101
CYS
101
A
ASP
102
n
102
ASP
102
A
VAL
103
n
103
VAL
103
A
GLU
104
n
104
GLU
104
A
SER
105
n
105
SER
105
A
ASP
106
n
106
ASP
106
A
GLY
107
n
107
GLY
107
A
ARG
108
n
108
ARG
108
A
LEU
109
n
109
LEU
109
A
LEU
110
n
110
LEU
110
A
ARG
111
n
111
ARG
111
A
GLY
112
n
112
GLY
112
A
TYR
113
n
113
TYR
113
A
TRP
114
n
114
TRP
114
A
GLN
115
n
115
GLN
115
A
PHE
116
n
116
PHE
116
A
ALA
117
n
117
ALA
117
A
TYR
118
n
118
TYR
118
A
ASP
119
n
119
ASP
119
A
GLY
120
n
120
GLY
120
A
CYS
121
n
121
CYS
121
A
ASP
122
n
122
ASP
122
A
TYR
123
n
123
TYR
123
A
ILE
124
n
124
ILE
124
A
ALA
125
n
125
ALA
125
A
LEU
126
n
126
LEU
126
A
ASN
127
n
127
ASN
127
A
GLU
128
n
128
GLU
128
A
ASP
129
n
129
ASP
129
A
LEU
130
n
130
LEU
130
A
LYS
131
n
131
LYS
131
A
THR
132
n
132
THR
132
A
TRP
133
n
133
TRP
133
A
THR
134
n
134
THR
134
A
ALA
135
n
135
ALA
135
A
ALA
136
n
136
ALA
136
A
ASP
137
n
137
ASP
137
A
MET
138
n
138
MET
138
A
ALA
139
n
139
ALA
139
A
ALA
140
n
140
ALA
140
A
GLN
141
n
141
GLN
141
A
ILE
142
n
142
ILE
142
A
THR
143
n
143
THR
143
A
ARG
144
n
144
ARG
144
A
ARG
145
n
145
ARG
145
A
LYS
146
n
146
LYS
146
A
TRP
147
n
147
TRP
147
A
GLU
148
n
148
GLU
148
A
GLN
149
n
149
GLN
149
A
ALA
150
n
150
ALA
150
A
GLY
151
n
151
GLY
151
A
ALA
152
n
152
ALA
152
A
ALA
153
n
153
ALA
153
A
GLU
154
n
154
GLU
154
A
ARG
155
n
155
ARG
155
A
ASP
156
n
156
ASP
156
A
ARG
157
n
157
ARG
157
A
ALA
158
n
158
ALA
158
A
TYR
159
n
159
TYR
159
A
LEU
160
n
160
LEU
160
A
GLU
161
n
161
GLU
161
A
GLY
162
n
162
GLY
162
A
GLU
163
n
163
GLU
163
A
CYS
164
n
164
CYS
164
A
VAL
165
n
165
VAL
165
A
GLU
166
n
166
GLU
166
A
TRP
167
n
167
TRP
167
A
LEU
168
n
168
LEU
168
A
ARG
169
n
169
ARG
169
A
ARG
170
n
170
ARG
170
A
TYR
171
n
171
TYR
171
A
LEU
172
n
172
LEU
172
A
LYS
173
n
173
LYS
173
A
ASN
174
n
174
ASN
174
A
GLY
175
n
175
GLY
175
A
ASN
176
n
176
ASN
176
A
ALA
177
n
177
ALA
177
A
THR
178
n
178
THR
178
A
LEU
179
n
179
LEU
179
A
LEU
180
n
180
LEU
180
A
ALA
181
n
181
ALA
181
A
THR
182
n
182
THR
182
A
ASP
183
n
183
ASP
183
A
PRO
184
n
184
PRO
184
A
PRO
185
n
185
PRO
185
A
LYS
186
n
186
LYS
186
A
ALA
187
n
187
ALA
187
A
HIS
188
n
188
HIS
188
A
VAL
189
n
189
VAL
189
A
THR
190
n
190
THR
190
A
HIS
191
n
191
HIS
191
A
HIS
192
n
192
HIS
192
A
ARG
193
n
193
ARG
193
A
ARG
194
n
194
ARG
194
A
PRO
195
n
195
PRO
195
A
GLU
196
n
196
GLU
196
A
GLY
197
n
197
GLY
197
A
ASP
198
n
198
ASP
198
A
VAL
199
n
199
VAL
199
A
THR
200
n
200
THR
200
A
LEU
201
n
201
LEU
201
A
ARG
202
n
202
ARG
202
A
CYS
203
n
203
CYS
203
A
TRP
204
n
204
TRP
204
A
ALA
205
n
205
ALA
205
A
LEU
206
n
206
LEU
206
A
GLY
207
n
207
GLY
207
A
PHE
208
n
208
PHE
208
A
TYR
209
n
209
TYR
209
A
PRO
210
n
210
PRO
210
A
ALA
211
n
211
ALA
211
A
GLU
212
n
212
GLU
212
A
ILE
213
n
213
ILE
213
A
THR
214
n
214
THR
214
A
LEU
215
n
215
LEU
215
A
THR
216
n
216
THR
216
A
TRP
217
n
217
TRP
217
A
GLN
218
n
218
GLN
218
A
LEU
219
n
219
LEU
219
A
ASN
220
n
220
ASN
220
A
GLY
221
n
221
GLY
221
A
GLU
222
n
222
GLU
222
A
GLU
223
n
223
GLU
223
A
LEU
224
n
224
LEU
224
A
THR
225
n
225
THR
225
A
GLN
226
n
226
GLN
226
A
GLU
227
n
227
GLU
227
A
MET
228
n
228
MET
228
A
GLU
229
n
229
GLU
229
A
LEU
230
n
230
LEU
230
A
VAL
231
n
231
VAL
231
A
GLU
232
n
232
GLU
232
A
THR
233
n
233
THR
233
A
ARG
234
n
234
ARG
234
A
PRO
235
n
235
PRO
235
A
ALA
236
n
236
ALA
236
A
GLY
237
n
237
GLY
237
A
ASP
238
n
238
ASP
238
A
GLY
239
n
239
GLY
239
A
THR
240
n
240
THR
240
A
PHE
241
n
241
PHE
241
A
GLN
242
n
242
GLN
242
A
LYS
243
n
243
LYS
243
A
TRP
244
n
244
TRP
244
A
ALA
245
n
245
ALA
245
A
SER
246
n
246
SER
246
A
VAL
247
n
247
VAL
247
A
VAL
248
n
248
VAL
248
A
VAL
249
n
249
VAL
249
A
PRO
250
n
250
PRO
250
A
LEU
251
n
251
LEU
251
A
GLY
252
n
252
GLY
252
A
LYS
253
n
253
LYS
253
A
GLN
254
n
254
GLN
254
A
GLN
255
n
255
GLN
255
A
LYS
256
n
256
LYS
256
A
TYR
257
n
257
TYR
257
A
THR
258
n
258
THR
258
A
CYS
259
n
259
CYS
259
A
HIS
260
n
260
HIS
260
A
VAL
261
n
261
VAL
261
A
GLU
262
n
262
GLU
262
A
HIS
263
n
263
HIS
263
A
GLU
264
n
264
GLU
264
A
GLY
265
n
265
GLY
265
A
LEU
266
n
266
LEU
266
A
PRO
267
n
267
PRO
267
A
GLU
268
n
268
GLU
268
A
PRO
269
n
269
PRO
269
A
LEU
270
n
270
LEU
270
A
THR
271
n
271
THR
271
A
LEU
272
n
272
LEU
272
A
ARG
273
n
273
ARG
273
A
TRP
274
n
274
TRP
274
A
MET
1
n
1
MET
1
B
GLN
2
n
2
GLN
2
B
LYS
3
n
3
LYS
3
B
THR
4
n
4
THR
4
B
PRO
5
n
5
PRO
5
B
GLN
6
n
6
GLN
6
B
ILE
7
n
7
ILE
7
B
GLN
8
n
8
GLN
8
B
VAL
9
n
9
VAL
9
B
TYR
10
n
10
TYR
10
B
SER
11
n
11
SER
11
B
ARG
12
n
12
ARG
12
B
HIS
13
n
13
HIS
13
B
PRO
14
n
14
PRO
14
B
PRO
15
n
15
PRO
15
B
GLU
16
n
16
GLU
16
B
ASN
17
n
17
ASN
17
B
GLY
18
n
18
GLY
18
B
LYS
19
n
19
LYS
19
B
PRO
20
n
20
PRO
20
B
ASN
21
n
21
ASN
21
B
ILE
22
n
22
ILE
22
B
LEU
23
n
23
LEU
23
B
ASN
24
n
24
ASN
24
B
CYS
25
n
25
CYS
25
B
TYR
26
n
26
TYR
26
B
VAL
27
n
27
VAL
27
B
THR
28
n
28
THR
28
B
GLN
29
n
29
GLN
29
B
PHE
30
n
30
PHE
30
B
HIS
31
n
31
HIS
31
B
PRO
32
n
32
PRO
32
B
PRO
33
n
33
PRO
33
B
HIS
34
n
34
HIS
34
B
ILE
35
n
35
ILE
35
B
GLU
36
n
36
GLU
36
B
ILE
37
n
37
ILE
37
B
GLN
38
n
38
GLN
38
B
MET
39
n
39
MET
39
B
LEU
40
n
40
LEU
40
B
LYS
41
n
41
LYS
41
B
ASN
42
n
42
ASN
42
B
GLY
43
n
43
GLY
43
B
LYS
44
n
44
LYS
44
B
LYS
45
n
45
LYS
45
B
ILE
46
n
46
ILE
46
B
PRO
47
n
47
PRO
47
B
LYS
48
n
48
LYS
48
B
VAL
49
n
49
VAL
49
B
GLU
50
n
50
GLU
50
B
MET
51
n
51
MET
51
B
SER
52
n
52
SER
52
B
ASP
53
n
53
ASP
53
B
MET
54
n
54
MET
54
B
SER
55
n
55
SER
55
B
PHE
56
n
56
PHE
56
B
SER
57
n
57
SER
57
B
LYS
58
n
58
LYS
58
B
ASP
59
n
59
ASP
59
B
TRP
60
n
60
TRP
60
B
SER
61
n
61
SER
61
B
PHE
62
n
62
PHE
62
B
TYR
63
n
63
TYR
63
B
ILE
64
n
64
ILE
64
B
LEU
65
n
65
LEU
65
B
ALA
66
n
66
ALA
66
B
HIS
67
n
67
HIS
67
B
THR
68
n
68
THR
68
B
GLU
69
n
69
GLU
69
B
PHE
70
n
70
PHE
70
B
THR
71
n
71
THR
71
B
PRO
72
n
72
PRO
72
B
THR
73
n
73
THR
73
B
GLU
74
n
74
GLU
74
B
THR
75
n
75
THR
75
B
ASP
76
n
76
ASP
76
B
THR
77
n
77
THR
77
B
TYR
78
n
78
TYR
78
B
ALA
79
n
79
ALA
79
B
CYS
80
n
80
CYS
80
B
ARG
81
n
81
ARG
81
B
VAL
82
n
82
VAL
82
B
LYS
83
n
83
LYS
83
B
HIS
84
n
84
HIS
84
B
ALA
85
n
85
ALA
85
B
SER
86
n
86
SER
86
B
MET
87
n
87
MET
87
B
ALA
88
n
88
ALA
88
B
GLU
89
n
89
GLU
89
B
PRO
90
n
90
PRO
90
B
LYS
91
n
91
LYS
91
B
THR
92
n
92
THR
92
B
VAL
93
n
93
VAL
93
B
TYR
94
n
94
TYR
94
B
TRP
95
n
95
TRP
95
B
ASP
96
n
96
ASP
96
B
ARG
97
n
97
ARG
97
B
ASP
98
n
98
ASP
98
B
MET
99
n
99
MET
99
B
ARG
1
n
1
ARG
1
P
GLY
2
n
2
GLY
2
P
PRO
3
n
3
PRO
3
P
GLY
4
n
4
GLY
4
P
ARG
5
n
5
ARG
5
P
ALA
6
n
6
ALA
6
P
PHE
7
n
7
PHE
7
P
VAL
8
n
8
VAL
8
P
THR
9
n
9
THR
9
P
ILE
10
n
10
ILE
10
P
author_and_software_defined_assembly
PISA
3
trimeric
4330
-18
18780
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
THR
31
A
O
THR
31
A
N
VAL
28
A
N
VAL
28
A
O
ARG
21
A
O
ARG
21
A
N
VAL
12
A
N
VAL
12
A
O
HIS
3
A
O
HIS
3
A
N
VAL
103
A
N
VAL
103
A
O
GLN
96
A
O
GLN
96
A
N
ALA
117
A
N
ALA
117
A
O
ALA
125
A
O
ALA
125
A
N
THR
134
A
N
THR
134
A
O
HIS
188
A
O
HIS
188
A
N
TRP
204
A
N
TRP
204
A
O
VAL
199
A
O
VAL
199
A
N
VAL
249
A
N
VAL
249
A
O
TRP
244
A
O
TRP
244
A
N
VAL
231
A
N
VAL
231
A
O
THR
214
A
O
THR
214
A
N
GLU
262
A
N
GLU
262
A
O
CYS
259
A
O
CYS
259
A
N
LEU
272
A
N
LEU
272
B
O
ASN
21
B
O
ASN
21
B
N
PHE
70
B
N
PHE
70
B
O
GLU
36
B
O
GLU
36
B
N
LYS
83
B
N
LYS
83
B
O
CYS
80
B
O
CYS
80
B
N
VAL
93
B
N
VAL
93
B
O
SER
52
B
O
SER
52
B
N
LEU
65
B
N
LEU
65
1
A
CB
SER
2
A
CB
SER
2
1
Y
1
A
OG
SER
2
A
OG
SER
2
1
Y
1
A
CB
SER
88
A
CB
SER
88
1
Y
1
A
OG
SER
88
A
OG
SER
88
1
Y
1
A
CB
ALA
89
A
CB
ALA
89
1
Y
1
A
CB
SER
105
A
CB
SER
105
1
Y
1
A
OG
SER
105
A
OG
SER
105
1
Y
1
A
CB
ALA
117
A
CB
ALA
117
1
Y
1
A
CB
LYS
131
A
CB
LYS
131
1
Y
1
A
CG
LYS
131
A
CG
LYS
131
1
Y
1
A
CD
LYS
131
A
CD
LYS
131
1
Y
1
A
CE
LYS
131
A
CE
LYS
131
1
Y
1
A
NZ
LYS
131
A
NZ
LYS
131
1
Y
1
A
CG
LYS
186
A
CG
LYS
186
1
Y
1
A
CD
LYS
186
A
CD
LYS
186
1
Y
1
A
CE
LYS
186
A
CE
LYS
186
1
Y
1
A
NZ
LYS
186
A
NZ
LYS
186
1
Y
1
A
CB
ARG
193
A
CB
ARG
193
1
Y
1
A
CG
ARG
193
A
CG
ARG
193
1
Y
1
A
CD
ARG
193
A
CD
ARG
193
1
Y
1
A
NE
ARG
193
A
NE
ARG
193
1
Y
1
A
CZ
ARG
193
A
CZ
ARG
193
1
Y
1
A
NH1
ARG
193
A
NH1
ARG
193
1
Y
1
A
NH2
ARG
193
A
NH2
ARG
193
1
Y
1
A
CB
ARG
194
A
CB
ARG
194
0
Y
1
A
CG
ARG
194
A
CG
ARG
194
0
Y
1
A
CD
ARG
194
A
CD
ARG
194
0
Y
1
A
NE
ARG
194
A
NE
ARG
194
0
Y
1
A
CZ
ARG
194
A
CZ
ARG
194
0
Y
1
A
NH1
ARG
194
A
NH1
ARG
194
0
Y
1
A
NH2
ARG
194
A
NH2
ARG
194
0
Y
1
A
CB
GLU
196
A
CB
GLU
196
1
Y
1
A
CG
GLU
196
A
CG
GLU
196
1
Y
1
A
CD
GLU
196
A
CD
GLU
196
1
Y
1
A
OE1
GLU
196
A
OE1
GLU
196
1
Y
1
A
OE2
GLU
196
A
OE2
GLU
196
1
Y
1
A
CB
VAL
199
A
CB
VAL
199
1
Y
1
A
CG1
VAL
199
A
CG1
VAL
199
1
Y
1
A
CG2
VAL
199
A
CG2
VAL
199
1
Y
1
A
CB
LEU
224
A
CB
LEU
224
1
Y
1
A
CG
LEU
224
A
CG
LEU
224
1
Y
1
A
CD1
LEU
224
A
CD1
LEU
224
1
Y
1
A
CD2
LEU
224
A
CD2
LEU
224
1
Y
1
A
CG
LYS
253
A
CG
LYS
253
1
Y
1
A
CD
LYS
253
A
CD
LYS
253
1
Y
1
A
CE
LYS
253
A
CE
LYS
253
1
Y
1
A
NZ
LYS
253
A
NZ
LYS
253
1
Y
1
A
CB
LYS
256
A
CB
LYS
256
1
Y
1
A
CG
LYS
256
A
CG
LYS
256
1
Y
1
A
CD
LYS
256
A
CD
LYS
256
1
Y
1
A
CE
LYS
256
A
CE
LYS
256
1
Y
1
A
NZ
LYS
256
A
NZ
LYS
256
1
Y
1
A
CB
ARG
273
A
CB
ARG
273
1
Y
1
A
CG
ARG
273
A
CG
ARG
273
1
Y
1
A
CD
ARG
273
A
CD
ARG
273
1
Y
1
A
NE
ARG
273
A
NE
ARG
273
1
Y
1
A
CZ
ARG
273
A
CZ
ARG
273
1
Y
1
A
NH1
ARG
273
A
NH1
ARG
273
1
Y
1
A
NH2
ARG
273
A
NH2
ARG
273
1
Y
1
A
CB
TRP
274
A
CB
TRP
274
1
Y
1
A
CG
TRP
274
A
CG
TRP
274
1
Y
1
A
CD1
TRP
274
A
CD1
TRP
274
1
Y
1
A
CD2
TRP
274
A
CD2
TRP
274
1
Y
1
A
NE1
TRP
274
A
NE1
TRP
274
1
Y
1
A
CE2
TRP
274
A
CE2
TRP
274
1
Y
1
A
CE3
TRP
274
A
CE3
TRP
274
1
Y
1
A
CZ2
TRP
274
A
CZ2
TRP
274
1
Y
1
A
CZ3
TRP
274
A
CZ3
TRP
274
1
Y
1
A
CH2
TRP
274
A
CH2
TRP
274
1
Y
1
A
OXT
TRP
274
A
OXT
TRP
274
0
Y
1
B
CB
LYS
3
B
CB
LYS
3
1
Y
1
B
CG
LYS
3
B
CG
LYS
3
1
Y
1
B
CD
LYS
3
B
CD
LYS
3
1
Y
1
B
CE
LYS
3
B
CE
LYS
3
1
Y
1
B
NZ
LYS
3
B
NZ
LYS
3
1
Y
1
B
CB
GLN
6
B
CB
GLN
6
1
Y
1
B
CG
GLN
6
B
CG
GLN
6
1
Y
1
B
CD
GLN
6
B
CD
GLN
6
1
Y
1
B
OE1
GLN
6
B
OE1
GLN
6
1
Y
1
B
NE2
GLN
6
B
NE2
GLN
6
1
Y
1
B
CB
LYS
19
B
CB
LYS
19
1
Y
1
B
CG
LYS
19
B
CG
LYS
19
1
Y
1
B
CD
LYS
19
B
CD
LYS
19
1
Y
1
B
CE
LYS
19
B
CE
LYS
19
1
Y
1
B
NZ
LYS
19
B
NZ
LYS
19
1
Y
1
B
CB
LYS
45
B
CB
LYS
45
1
Y
1
B
CG
LYS
45
B
CG
LYS
45
1
Y
1
B
CD
LYS
45
B
CD
LYS
45
1
Y
1
B
CE
LYS
45
B
CE
LYS
45
1
Y
1
B
NZ
LYS
45
B
NZ
LYS
45
1
Y
1
B
CB
LYS
48
B
CB
LYS
48
1
Y
1
B
CG
LYS
48
B
CG
LYS
48
1
Y
1
B
CD
LYS
48
B
CD
LYS
48
1
Y
1
B
CE
LYS
48
B
CE
LYS
48
1
Y
1
B
NZ
LYS
48
B
NZ
LYS
48
1
Y
1
B
CB
SER
57
B
CB
SER
57
1
Y
1
B
OG
SER
57
B
OG
SER
57
1
Y
1
B
CB
GLU
74
B
CB
GLU
74
1
Y
1
B
CG
GLU
74
B
CG
GLU
74
1
Y
1
B
CD
GLU
74
B
CD
GLU
74
1
Y
1
B
OE1
GLU
74
B
OE1
GLU
74
1
Y
1
B
OE2
GLU
74
B
OE2
GLU
74
1
Y
1
A
SER
2
-139.77
-72.96
1
A
SER
13
-66.29
99.26
1
A
ASP
29
55.93
-130.86
1
A
ASN
30
-104.72
51.80
1
A
GLU
41
-52.79
-76.82
1
A
PRO
43
-85.06
49.23
1
A
ARG
48
-84.67
48.04
1
A
ALA
49
175.33
147.13
1
A
GLU
53
-45.70
-19.01
1
A
ASN
86
57.59
13.38
1
A
TRP
114
-161.25
88.32
1
A
ASP
119
78.38
-73.46
1
A
TYR
123
-104.22
-74.61
1
A
ASN
127
-52.99
174.15
1
A
ASP
129
-58.13
-3.61
1
A
LEU
179
-81.00
-117.13
1
A
LEU
180
10.06
-55.16
1
A
ALA
181
-18.31
80.80
1
A
LYS
186
-115.65
66.91
1
A
ALA
187
-58.19
173.68
1
A
HIS
188
163.55
137.99
1
A
PRO
195
-69.21
-123.71
1
A
GLU
196
31.09
33.18
1
A
TYR
209
-175.97
133.10
1
A
GLU
212
-39.24
126.26
1
A
THR
225
-127.57
-67.95
1
A
GLN
226
-64.12
67.18
1
A
GLU
227
176.70
-26.04
1
A
THR
233
-61.20
94.09
1
A
LYS
243
162.44
172.65
1
A
LEU
251
-50.54
97.21
1
A
GLN
254
10.41
-64.45
1
A
ARG
273
-173.43
-177.71
1
B
GLN
2
-162.20
103.74
1
B
PRO
20
-42.57
163.44
1
B
ASN
21
-172.35
-167.85
1
B
TYR
26
-44.67
107.02
1
B
GLN
29
38.96
28.53
1
B
PRO
47
-44.97
-71.71
1
B
VAL
49
-64.70
75.73
1
B
ASP
53
103.72
-133.81
1
B
MET
54
95.49
79.10
1
B
SER
55
-156.12
-158.01
1
B
TRP
60
70.03
-27.11
1
B
HIS
67
-164.78
109.37
1
B
ASP
76
-33.72
110.85
1
B
ASP
98
-52.16
98.35
1
P
ALA
6
-69.95
40.21
1
P
THR
9
-57.89
-167.53
PARHCSDX.PRO
TOPHCSDX.PRO
0.337
0.229
0.229
3.1
8.0
641
7863
7.0
86.4
RANDOM
0
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
PDB ENTRY 1VAD
3.1
8.0
4
3051
0
0
3047
0.010
1.72
23.9
1.35
0.476
0.309
3.2
64
7267
10
7.0
79.8
3.1
1DDH
33412
0.081
0.081
1
12.7
3.6
86.8
0.389
3.1
3.2
2.4
0.389
75.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
X-PLOR
3.1
MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120
1
N
N
2
N
N
3
N
N
4
N
N
A
TRP
51
A
TRP
51
HELX_P
A
GLN
54
A
GLN
54
5
1
4
A
PRO
57
A
PRO
57
HELX_P
A
TYR
85
A
TYR
85
1
2
29
A
MET
138
A
MET
138
HELX_P
A
GLN
149
A
GLN
149
1
3
12
A
ALA
152
A
ALA
152
HELX_P
A
GLU
161
A
GLU
161
1
4
10
A
GLU
163
A
GLU
163
HELX_P
A
LYS
173
A
LYS
173
1
5
11
A
GLN
254
A
GLN
254
HELX_P
A
LYS
256
A
LYS
256
5
6
3
disulf
2.034
A
CYS
101
A
SG
CYS
101
1_555
A
CYS
164
A
SG
CYS
164
1_555
disulf
2.034
A
CYS
203
A
SG
CYS
203
1_555
A
CYS
259
A
SG
CYS
259
1_555
disulf
2.020
B
CYS
25
B
SG
CYS
25
1_555
B
CYS
80
B
SG
CYS
80
1_555
COMPLEX (HISTOCOMPATIBILITY/ANTIGEN)
COMPLEX (HISTOCOMPATIBILITY-ANTIGEN), HISTOCOMPATIBILITY ANTIGEN, CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX, MHC I, COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) complex
A
TYR
209
A
TYR
209
1
A
PRO
210
A
PRO
210
-0.11
B
HIS
31
B
HIS
31
1
B
PRO
32
B
PRO
32
1.69
HA12_MOUSE
UNP
1
26
P01900
B2MG_MOUSE
UNP
2
22
P01887
ENV_HV1B8
UNP
3
311
P04582
26
298
1DDH
2
274
P01900
A
1
2
274
22
119
1DDH
2
99
P01887
B
2
2
99
311
320
1DDH
1
10
P04582
P
3
1
10
1
LYS
conflict
ASN
68
1DDH
A
P01900
UNP
92
68
1
ARG
conflict
ALA
181
1DDH
A
P01900
UNP
205
181
1
ASP
conflict
GLU
212
1DDH
A
P01900
UNP
236
212
1
GLU
conflict
GLN
254
1DDH
A
P01900
UNP
278
254
2
ASP
conflict
ALA
85
1DDH
B
P01887
UNP
105
85
5
2
4
3
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
31
A
THR
31
A
ASP
37
A
ASP
37
A
ARG
21
A
ARG
21
A
VAL
28
A
VAL
28
A
HIS
3
A
HIS
3
A
SER
13
A
SER
13
A
HIS
93
A
HIS
93
A
VAL
103
A
VAL
103
A
LEU
109
A
LEU
109
A
TYR
118
A
TYR
118
A
ILE
124
A
ILE
124
A
LEU
126
A
LEU
126
A
TRP
133
A
TRP
133
A
ALA
135
A
ALA
135
A
HIS
188
A
HIS
188
A
HIS
192
A
HIS
192
A
ASP
198
A
ASP
198
A
TRP
204
A
TRP
204
A
TRP
244
A
TRP
244
A
PRO
250
A
PRO
250
A
MET
228
A
MET
228
A
VAL
231
A
VAL
231
A
THR
214
A
THR
214
A
LEU
219
A
LEU
219
A
TYR
257
A
TYR
257
A
GLU
262
A
GLU
262
A
LEU
270
A
LEU
270
A
LEU
272
A
LEU
272
B
PRO
20
B
PRO
20
B
ASN
24
B
ASN
24
B
HIS
67
B
HIS
67
B
THR
71
B
THR
71
B
GLU
36
B
GLU
36
B
LYS
41
B
LYS
41
B
TYR
78
B
TYR
78
B
LYS
83
B
LYS
83
B
LYS
91
B
LYS
91
B
TYR
94
B
TYR
94
B
MET
51
B
MET
51
B
PHE
56
B
PHE
56
B
PHE
62
B
PHE
62
B
ALA
66
B
ALA
66
19
P 21 21 21