0.012747
0.007359
0.000000
0.000000
0.014719
0.000000
0.000000
0.000000
0.006285
0.00000
0.00000
0.00000
Ghosh, P.
Amaya, M.
Mellins, E.
Wiley, D.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
78.450
78.450
159.100
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta 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
Nature
NATUAS
0006
0028-0836
378
457
462
10.1038/378457a0
7477400
The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.
1995
10.2210/pdb1a6a/pdb
pdb_00001a6a
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
MIRRORS
IMAGE PLATE
1994-07
FUJI
SI(111)
M
x-ray
1
0.918
1.0
F1
CHESS
0.918
SYNCHROTRON
CHESS BEAMLINE F1
20469.172
HLA class II histocompatibility antigen, DR alpha chain
1
nat
polymer
21935.385
HLA class II histocompatibility antigen, DR-1 beta chain
1
nat
polymer
1676.118
HLA class II histocompatibility antigen, gamma chain
CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN
1
nat
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
2
man
non-polymer
18.015
water
22
nat
water
no
no
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
A
polypeptide(L)
no
no
PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG
VVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETV
PRSGEVYTCQVEHPSVTSPLTVEWRAR
PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG
VVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETV
PRSGEVYTCQVEHPSVTSPLTVEWRAR
B
polypeptide(L)
no
no
PVSKMRMATPLLMQA
PVSKMRMATPLLMQA
C
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
human
Homo
sample
B-LYMPHOCYTE
9.5.3
PLASMA MEMBRANE
9606
Homo sapiens
human
Homo
sample
B-LYMPHOCYTE
9.5.3
PLASMA MEMBRANE
9606
Homo sapiens
human
Homo
sample
B-LYMPHOCYTE
9.5.3
PLASMA MEMBRANE
9606
Homo sapiens
2
2.7
52.
4.5
12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
pdbx_unobs_or_zero_occ_atoms
software
struct_conn
struct_site
struct_site_gen
chem_comp
database_2
pdbx_initial_refinement_model
pdbx_unobs_or_zero_occ_atoms
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Advisory
Data collection
Derived calculations
Refinement description
Structure summary
Advisory
Database references
Refinement description
Structure summary
1
0
1998-05-27
1
1
2008-03-24
1
2
2011-07-13
1
3
2020-07-29
1
4
2023-08-02
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_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.ptnr1_label_seq_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
_struct_conn.ptnr2_label_seq_id
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
Y
BNL
1998-02-22
REL
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
HOH
water
1DLH
PDB ENTRY 1DLH
PDB
experimental model
NAG
100
4
NAG
NAG
181
A
NAG
200
4
NAG
NAG
200
A
HOH
6
5
HOH
HOH
201
A
HOH
8
5
HOH
HOH
202
A
HOH
9
5
HOH
HOH
203
A
HOH
16
5
HOH
HOH
204
A
HOH
17
5
HOH
HOH
205
A
HOH
20
5
HOH
HOH
206
A
HOH
21
5
HOH
HOH
207
A
HOH
22
5
HOH
HOH
208
A
HOH
1
5
HOH
HOH
192
B
HOH
2
5
HOH
HOH
193
B
HOH
3
5
HOH
HOH
194
B
HOH
4
5
HOH
HOH
195
B
HOH
5
5
HOH
HOH
196
B
HOH
7
5
HOH
HOH
197
B
HOH
11
5
HOH
HOH
198
B
HOH
12
5
HOH
HOH
199
B
HOH
13
5
HOH
HOH
200
B
HOH
14
5
HOH
HOH
201
B
HOH
15
5
HOH
HOH
202
B
HOH
18
5
HOH
HOH
203
B
HOH
19
5
HOH
HOH
204
B
HOH
10
5
HOH
HOH
10
C
HIS
5
n
1
HIS
5
A
VAL
6
n
2
VAL
6
A
ILE
7
n
3
ILE
7
A
ILE
8
n
4
ILE
8
A
GLN
9
n
5
GLN
9
A
ALA
10
n
6
ALA
10
A
GLU
11
n
7
GLU
11
A
PHE
12
n
8
PHE
12
A
TYR
13
n
9
TYR
13
A
LEU
14
n
10
LEU
14
A
ASN
15
n
11
ASN
15
A
PRO
16
n
12
PRO
16
A
ASP
17
n
13
ASP
17
A
GLN
18
n
14
GLN
18
A
SER
19
n
15
SER
19
A
GLY
20
n
16
GLY
20
A
GLU
21
n
17
GLU
21
A
PHE
22
n
18
PHE
22
A
MET
23
n
19
MET
23
A
PHE
24
n
20
PHE
24
A
ASP
25
n
21
ASP
25
A
PHE
26
n
22
PHE
26
A
ASP
27
n
23
ASP
27
A
GLY
28
n
24
GLY
28
A
ASP
29
n
25
ASP
29
A
GLU
30
n
26
GLU
30
A
ILE
31
n
27
ILE
31
A
PHE
32
n
28
PHE
32
A
HIS
33
n
29
HIS
33
A
VAL
34
n
30
VAL
34
A
ASP
35
n
31
ASP
35
A
MET
36
n
32
MET
36
A
ALA
37
n
33
ALA
37
A
LYS
38
n
34
LYS
38
A
LYS
39
n
35
LYS
39
A
GLU
40
n
36
GLU
40
A
THR
41
n
37
THR
41
A
VAL
42
n
38
VAL
42
A
TRP
43
n
39
TRP
43
A
ARG
44
n
40
ARG
44
A
LEU
45
n
41
LEU
45
A
GLU
46
n
42
GLU
46
A
GLU
47
n
43
GLU
47
A
PHE
48
n
44
PHE
48
A
GLY
49
n
45
GLY
49
A
ARG
50
n
46
ARG
50
A
PHE
51
n
47
PHE
51
A
ALA
52
n
48
ALA
52
A
SER
53
n
49
SER
53
A
PHE
54
n
50
PHE
54
A
GLU
55
n
51
GLU
55
A
ALA
56
n
52
ALA
56
A
GLN
57
n
53
GLN
57
A
GLY
58
n
54
GLY
58
A
ALA
59
n
55
ALA
59
A
LEU
60
n
56
LEU
60
A
ALA
61
n
57
ALA
61
A
ASN
62
n
58
ASN
62
A
ILE
63
n
59
ILE
63
A
ALA
64
n
60
ALA
64
A
VAL
65
n
61
VAL
65
A
ASP
66
n
62
ASP
66
A
LYS
67
n
63
LYS
67
A
ALA
68
n
64
ALA
68
A
ASN
69
n
65
ASN
69
A
LEU
70
n
66
LEU
70
A
GLU
71
n
67
GLU
71
A
ILE
72
n
68
ILE
72
A
MET
73
n
69
MET
73
A
THR
74
n
70
THR
74
A
LYS
75
n
71
LYS
75
A
ARG
76
n
72
ARG
76
A
SER
77
n
73
SER
77
A
ASN
78
n
74
ASN
78
A
TYR
79
n
75
TYR
79
A
THR
80
n
76
THR
80
A
PRO
81
n
77
PRO
81
A
ILE
82
n
78
ILE
82
A
THR
83
n
79
THR
83
A
ASN
84
n
80
ASN
84
A
VAL
85
n
81
VAL
85
A
PRO
86
n
82
PRO
86
A
PRO
87
n
83
PRO
87
A
GLU
88
n
84
GLU
88
A
VAL
89
n
85
VAL
89
A
THR
90
n
86
THR
90
A
VAL
91
n
87
VAL
91
A
LEU
92
n
88
LEU
92
A
THR
93
n
89
THR
93
A
ASN
94
n
90
ASN
94
A
SER
95
n
91
SER
95
A
PRO
96
n
92
PRO
96
A
VAL
97
n
93
VAL
97
A
GLU
98
n
94
GLU
98
A
LEU
99
n
95
LEU
99
A
ARG
100
n
96
ARG
100
A
GLU
101
n
97
GLU
101
A
PRO
102
n
98
PRO
102
A
ASN
103
n
99
ASN
103
A
VAL
104
n
100
VAL
104
A
LEU
105
n
101
LEU
105
A
ILE
106
n
102
ILE
106
A
CYS
107
n
103
CYS
107
A
PHE
108
n
104
PHE
108
A
ILE
109
n
105
ILE
109
A
ASP
110
n
106
ASP
110
A
LYS
111
n
107
LYS
111
A
PHE
112
n
108
PHE
112
A
THR
113
n
109
THR
113
A
PRO
114
n
110
PRO
114
A
PRO
115
n
111
PRO
115
A
VAL
116
n
112
VAL
116
A
VAL
117
n
113
VAL
117
A
ASN
118
n
114
ASN
118
A
VAL
119
n
115
VAL
119
A
THR
120
n
116
THR
120
A
TRP
121
n
117
TRP
121
A
LEU
122
n
118
LEU
122
A
ARG
123
n
119
ARG
123
A
ASN
124
n
120
ASN
124
A
GLY
125
n
121
GLY
125
A
LYS
126
n
122
LYS
126
A
PRO
127
n
123
PRO
127
A
VAL
128
n
124
VAL
128
A
THR
129
n
125
THR
129
A
THR
130
n
126
THR
130
A
GLY
131
n
127
GLY
131
A
VAL
132
n
128
VAL
132
A
SER
133
n
129
SER
133
A
GLU
134
n
130
GLU
134
A
THR
135
n
131
THR
135
A
VAL
136
n
132
VAL
136
A
PHE
137
n
133
PHE
137
A
LEU
138
n
134
LEU
138
A
PRO
139
n
135
PRO
139
A
ARG
140
n
136
ARG
140
A
GLU
141
n
137
GLU
141
A
ASP
142
n
138
ASP
142
A
HIS
143
n
139
HIS
143
A
LEU
144
n
140
LEU
144
A
PHE
145
n
141
PHE
145
A
ARG
146
n
142
ARG
146
A
LYS
147
n
143
LYS
147
A
PHE
148
n
144
PHE
148
A
HIS
149
n
145
HIS
149
A
TYR
150
n
146
TYR
150
A
LEU
151
n
147
LEU
151
A
PRO
152
n
148
PRO
152
A
PHE
153
n
149
PHE
153
A
LEU
154
n
150
LEU
154
A
PRO
155
n
151
PRO
155
A
SER
156
n
152
SER
156
A
THR
157
n
153
THR
157
A
GLU
158
n
154
GLU
158
A
ASP
159
n
155
ASP
159
A
VAL
160
n
156
VAL
160
A
TYR
161
n
157
TYR
161
A
ASP
162
n
158
ASP
162
A
CYS
163
n
159
CYS
163
A
ARG
164
n
160
ARG
164
A
VAL
165
n
161
VAL
165
A
GLU
166
n
162
GLU
166
A
HIS
167
n
163
HIS
167
A
TRP
168
n
164
TRP
168
A
GLY
169
n
165
GLY
169
A
LEU
170
n
166
LEU
170
A
ASP
171
n
167
ASP
171
A
GLU
172
n
168
GLU
172
A
PRO
173
n
169
PRO
173
A
LEU
174
n
170
LEU
174
A
LEU
175
n
171
LEU
175
A
LYS
176
n
172
LYS
176
A
HIS
177
n
173
HIS
177
A
TRP
178
n
174
TRP
178
A
GLU
179
n
175
GLU
179
A
PHE
180
n
176
PHE
180
A
PRO
5
n
1
PRO
5
B
ARG
6
n
2
ARG
6
B
PHE
7
n
3
PHE
7
B
LEU
8
n
4
LEU
8
B
GLU
9
n
5
GLU
9
B
TYR
10
n
6
TYR
10
B
SER
11
n
7
SER
11
B
THR
12
n
8
THR
12
B
SER
13
n
9
SER
13
B
GLU
14
n
10
GLU
14
B
CYS
15
n
11
CYS
15
B
HIS
16
n
12
HIS
16
B
PHE
17
n
13
PHE
17
B
PHE
18
n
14
PHE
18
B
ASN
19
n
15
ASN
19
B
GLY
20
n
16
GLY
20
B
THR
21
n
17
THR
21
B
GLU
22
n
18
GLU
22
B
ARG
23
n
19
ARG
23
B
VAL
24
n
20
VAL
24
B
ARG
25
n
21
ARG
25
B
TYR
26
n
22
TYR
26
B
LEU
27
n
23
LEU
27
B
ASP
28
n
24
ASP
28
B
ARG
29
n
25
ARG
29
B
TYR
30
n
26
TYR
30
B
PHE
31
n
27
PHE
31
B
HIS
32
n
28
HIS
32
B
ASN
33
n
29
ASN
33
B
GLN
34
n
30
GLN
34
B
GLU
35
n
31
GLU
35
B
GLU
36
n
32
GLU
36
B
ASN
37
n
33
ASN
37
B
VAL
38
n
34
VAL
38
B
ARG
39
n
35
ARG
39
B
PHE
40
n
36
PHE
40
B
ASP
41
n
37
ASP
41
B
SER
42
n
38
SER
42
B
ASP
43
n
39
ASP
43
B
VAL
44
n
40
VAL
44
B
GLY
45
n
41
GLY
45
B
GLU
46
n
42
GLU
46
B
PHE
47
n
43
PHE
47
B
ARG
48
n
44
ARG
48
B
ALA
49
n
45
ALA
49
B
VAL
50
n
46
VAL
50
B
THR
51
n
47
THR
51
B
GLU
52
n
48
GLU
52
B
LEU
53
n
49
LEU
53
B
GLY
54
n
50
GLY
54
B
ARG
55
n
51
ARG
55
B
PRO
56
n
52
PRO
56
B
ASP
57
n
53
ASP
57
B
ALA
58
n
54
ALA
58
B
GLU
59
n
55
GLU
59
B
TYR
60
n
56
TYR
60
B
TRP
61
n
57
TRP
61
B
ASN
62
n
58
ASN
62
B
SER
63
n
59
SER
63
B
GLN
64
n
60
GLN
64
B
LYS
65
n
61
LYS
65
B
ASP
66
n
62
ASP
66
B
LEU
67
n
63
LEU
67
B
LEU
68
n
64
LEU
68
B
GLU
69
n
65
GLU
69
B
GLN
70
n
66
GLN
70
B
LYS
71
n
67
LYS
71
B
ARG
72
n
68
ARG
72
B
GLY
73
n
69
GLY
73
B
ARG
74
n
70
ARG
74
B
VAL
75
n
71
VAL
75
B
ASP
76
n
72
ASP
76
B
ASN
77
n
73
ASN
77
B
TYR
78
n
74
TYR
78
B
CYS
79
n
75
CYS
79
B
ARG
80
n
76
ARG
80
B
HIS
81
n
77
HIS
81
B
ASN
82
n
78
ASN
82
B
TYR
83
n
79
TYR
83
B
GLY
84
n
80
GLY
84
B
VAL
85
n
81
VAL
85
B
VAL
86
n
82
VAL
86
B
GLU
87
n
83
GLU
87
B
SER
88
n
84
SER
88
B
PHE
89
n
85
PHE
89
B
THR
90
n
86
THR
90
B
VAL
91
n
87
VAL
91
B
GLN
92
n
88
GLN
92
B
ARG
93
n
89
ARG
93
B
ARG
94
n
90
ARG
94
B
VAL
95
n
91
VAL
95
B
HIS
96
n
92
HIS
96
B
PRO
97
n
93
PRO
97
B
LYS
98
n
94
LYS
98
B
VAL
99
n
95
VAL
99
B
THR
100
n
96
THR
100
B
VAL
101
n
97
VAL
101
B
TYR
102
n
98
TYR
102
B
PRO
103
n
99
PRO
103
B
SER
104
n
100
SER
104
B
LYS
105
n
101
LYS
105
B
THR
106
n
102
THR
106
B
GLN
107
n
103
GLN
107
B
PRO
108
n
104
PRO
108
B
LEU
109
n
105
LEU
109
B
GLN
110
n
106
GLN
110
B
HIS
111
n
107
HIS
111
B
HIS
112
n
108
HIS
112
B
ASN
113
n
109
ASN
113
B
LEU
114
n
110
LEU
114
B
LEU
115
n
111
LEU
115
B
VAL
116
n
112
VAL
116
B
CYS
117
n
113
CYS
117
B
SER
118
n
114
SER
118
B
VAL
119
n
115
VAL
119
B
SER
120
n
116
SER
120
B
GLY
121
n
117
GLY
121
B
PHE
122
n
118
PHE
122
B
TYR
123
n
119
TYR
123
B
PRO
124
n
120
PRO
124
B
GLY
125
n
121
GLY
125
B
SER
126
n
122
SER
126
B
ILE
127
n
123
ILE
127
B
GLU
128
n
124
GLU
128
B
VAL
129
n
125
VAL
129
B
ARG
130
n
126
ARG
130
B
TRP
131
n
127
TRP
131
B
PHE
132
n
128
PHE
132
B
ARG
133
n
129
ARG
133
B
ASN
134
n
130
ASN
134
B
GLY
135
n
131
GLY
135
B
GLN
136
n
132
GLN
136
B
GLU
137
n
133
GLU
137
B
GLU
138
n
134
GLU
138
B
LYS
139
n
135
LYS
139
B
THR
140
n
136
THR
140
B
GLY
141
n
137
GLY
141
B
VAL
142
n
138
VAL
142
B
VAL
143
n
139
VAL
143
B
SER
144
n
140
SER
144
B
THR
145
n
141
THR
145
B
GLY
146
n
142
GLY
146
B
LEU
147
n
143
LEU
147
B
ILE
148
n
144
ILE
148
B
HIS
149
n
145
HIS
149
B
ASN
150
n
146
ASN
150
B
GLY
151
n
147
GLY
151
B
ASP
152
n
148
ASP
152
B
TRP
153
n
149
TRP
153
B
THR
154
n
150
THR
154
B
PHE
155
n
151
PHE
155
B
GLN
156
n
152
GLN
156
B
THR
157
n
153
THR
157
B
LEU
158
n
154
LEU
158
B
VAL
159
n
155
VAL
159
B
MET
160
n
156
MET
160
B
LEU
161
n
157
LEU
161
B
GLU
162
n
158
GLU
162
B
THR
163
n
159
THR
163
B
VAL
164
n
160
VAL
164
B
PRO
165
n
161
PRO
165
B
ARG
166
n
162
ARG
166
B
SER
167
n
163
SER
167
B
GLY
168
n
164
GLY
168
B
GLU
169
n
165
GLU
169
B
VAL
170
n
166
VAL
170
B
TYR
171
n
167
TYR
171
B
THR
172
n
168
THR
172
B
CYS
173
n
169
CYS
173
B
GLN
174
n
170
GLN
174
B
VAL
175
n
171
VAL
175
B
GLU
176
n
172
GLU
176
B
HIS
177
n
173
HIS
177
B
PRO
178
n
174
PRO
178
B
SER
179
n
175
SER
179
B
VAL
180
n
176
VAL
180
B
THR
181
n
177
THR
181
B
SER
182
n
178
SER
182
B
PRO
183
n
179
PRO
183
B
LEU
184
n
180
LEU
184
B
THR
185
n
181
THR
185
B
VAL
186
n
182
VAL
186
B
GLU
187
n
183
GLU
187
B
TRP
188
n
184
TRP
188
B
ARG
189
n
185
ARG
189
B
ALA
190
n
186
ALA
190
B
ARG
191
n
187
ARG
191
B
PRO
87
n
1
PRO
87
C
VAL
88
n
2
VAL
88
C
SER
89
n
3
SER
89
C
LYS
90
n
4
LYS
90
C
MET
91
n
5
MET
91
C
ARG
92
n
6
ARG
92
C
MET
93
n
7
MET
93
C
ALA
94
n
8
ALA
94
C
THR
95
n
9
THR
95
C
PRO
96
n
10
PRO
96
C
LEU
97
n
11
LEU
97
C
LEU
98
n
12
LEU
98
C
MET
99
n
13
MET
99
C
GLN
100
n
14
GLN
100
C
ALA
101
n
15
ALA
101
C
author_and_software_defined_assembly
PISA
3
trimeric
software_defined_assembly
PISA
6
hexameric
7340
-42
17990
17000
-85
33650
A
ASN
78
GLYCOSYLATION SITE
A
ASN
74
ASN
A
ASN
118
GLYCOSYLATION SITE
A
ASN
114
ASN
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
6_555
x,x-y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
ILE
8
A
O
ILE
4
A
N
ASP
25
A
N
ASP
21
A
O
PHE
24
A
O
PHE
20
A
N
PHE
32
A
N
PHE
28
A
O
HIS
33
A
O
HIS
29
A
N
VAL
42
A
N
VAL
38
A
O
THR
90
A
O
THR
86
A
N
PHE
108
A
N
PHE
104
A
O
ASN
103
A
O
ASN
99
A
N
PHE
153
A
N
PHE
149
A
O
TYR
150
A
O
TYR
146
A
N
SER
133
A
N
SER
129
A
O
ASN
118
A
O
ASN
114
A
N
GLU
166
A
N
GLU
162
A
O
TYR
161
A
O
TYR
157
A
N
TRP
178
A
N
TRP
174
B
O
TYR
10
B
O
TYR
6
B
N
PHE
31
B
N
PHE
27
B
O
ASP
28
B
O
ASP
24
B
N
PHE
40
B
N
PHE
36
B
O
ARG
39
B
O
ARG
35
B
N
ARG
48
B
N
ARG
44
B
O
LYS
98
B
O
LYS
94
B
N
SER
120
B
N
SER
116
B
O
VAL
119
B
O
VAL
115
B
N
THR
157
B
N
THR
153
B
O
GLU
128
B
O
GLU
124
B
N
GLU
176
B
N
GLU
172
B
O
TYR
171
B
O
TYR
167
B
N
TRP
188
B
N
TRP
184
1
A
CG
ARG
123
A
CG
ARG
119
0
Y
1
A
CD
ARG
123
A
CD
ARG
119
0
Y
1
A
NE
ARG
123
A
NE
ARG
119
0
Y
1
A
CZ
ARG
123
A
CZ
ARG
119
0
Y
1
A
NH1
ARG
123
A
NH1
ARG
119
0
Y
1
A
NH2
ARG
123
A
NH2
ARG
119
0
Y
1
B
CG
ASN
19
B
CG
ASN
15
0
Y
1
B
OD1
ASN
19
B
OD1
ASN
15
0
Y
1
B
ND2
ASN
19
B
ND2
ASN
15
0
Y
1
B
CG
GLU
22
B
CG
GLU
18
0
Y
1
B
CD
GLU
22
B
CD
GLU
18
0
Y
1
B
OE1
GLU
22
B
OE1
GLU
18
0
Y
1
B
OE2
GLU
22
B
OE2
GLU
18
0
Y
1
B
CG
ARG
23
B
CG
ARG
19
0
Y
1
B
CD
ARG
23
B
CD
ARG
19
0
Y
1
B
NE
ARG
23
B
NE
ARG
19
0
Y
1
B
CZ
ARG
23
B
CZ
ARG
19
0
Y
1
B
NH1
ARG
23
B
NH1
ARG
19
0
Y
1
B
NH2
ARG
23
B
NH2
ARG
19
0
Y
1
B
CG
LYS
105
B
CG
LYS
101
0
Y
1
B
CD
LYS
105
B
CD
LYS
101
0
Y
1
B
CE
LYS
105
B
CE
LYS
101
0
Y
1
B
NZ
LYS
105
B
NZ
LYS
101
0
Y
1
B
CG
GLN
107
B
CG
GLN
103
0
Y
1
B
CD
GLN
107
B
CD
GLN
103
0
Y
1
B
OE1
GLN
107
B
OE1
GLN
103
0
Y
1
B
NE2
GLN
107
B
NE2
GLN
103
0
Y
1
B
CG
LEU
109
B
CG
LEU
105
0
Y
1
B
CD1
LEU
109
B
CD1
LEU
105
0
Y
1
B
CD2
LEU
109
B
CD2
LEU
105
0
Y
1
B
CG
GLN
110
B
CG
GLN
106
0
Y
1
B
CD
GLN
110
B
CD
GLN
106
0
Y
1
B
OE1
GLN
110
B
OE1
GLN
106
0
Y
1
B
NE2
GLN
110
B
NE2
GLN
106
0
Y
1
B
CG
HIS
111
B
CG
HIS
107
0
Y
1
B
ND1
HIS
111
B
ND1
HIS
107
0
Y
1
B
CD2
HIS
111
B
CD2
HIS
107
0
Y
1
B
CE1
HIS
111
B
CE1
HIS
107
0
Y
1
B
NE2
HIS
111
B
NE2
HIS
107
0
Y
1
B
CG
GLN
136
B
CG
GLN
132
0
Y
1
B
CD
GLN
136
B
CD
GLN
132
0
Y
1
B
OE1
GLN
136
B
OE1
GLN
132
0
Y
1
B
NE2
GLN
136
B
NE2
GLN
132
0
Y
1
B
CG
GLU
138
B
CG
GLU
134
0
Y
1
B
CD
GLU
138
B
CD
GLU
134
0
Y
1
B
OE1
GLU
138
B
OE1
GLU
134
0
Y
1
B
OE2
GLU
138
B
OE2
GLU
134
0
Y
1
B
CG
ARG
166
B
CG
ARG
162
0
Y
1
B
CD
ARG
166
B
CD
ARG
162
0
Y
1
B
NE
ARG
166
B
NE
ARG
162
0
Y
1
B
CZ
ARG
166
B
CZ
ARG
162
0
Y
1
B
NH1
ARG
166
B
NH1
ARG
162
0
Y
1
B
NH2
ARG
166
B
NH2
ARG
162
0
Y
1
B
OG
SER
167
B
OG
SER
163
0
Y
1
B
CG
ARG
189
B
CG
ARG
185
0
Y
1
B
CD
ARG
189
B
CD
ARG
185
0
Y
1
B
NE
ARG
189
B
NE
ARG
185
0
Y
1
B
CZ
ARG
189
B
CZ
ARG
185
0
Y
1
B
NH1
ARG
189
B
NH1
ARG
185
0
Y
1
B
NH2
ARG
189
B
NH2
ARG
185
0
Y
1
B
CG
ARG
191
B
CG
ARG
187
0
Y
1
B
CD
ARG
191
B
CD
ARG
187
0
Y
1
B
NE
ARG
191
B
NE
ARG
187
0
Y
1
B
CZ
ARG
191
B
CZ
ARG
187
0
Y
1
B
NH1
ARG
191
B
NH1
ARG
187
0
Y
1
B
NH2
ARG
191
B
NH2
ARG
187
0
Y
1
A
TYR
150
0.070
SIDE CHAIN
1
B
B
C
N
PHE
HIS
31
32
1.18
1
-10.04
1.60
122.70
112.66
B
B
B
O
C
N
PHE
PHE
HIS
31
31
32
Y
1
B
B
C
N
PHE
HIS
31
32
-0.159
0.023
1.336
1.177
Y
1
B
B
CD
OE2
GLU
GLU
87
87
0.083
0.011
1.252
1.335
N
1
A
PHE
32
-171.75
-176.31
1
A
THR
90
-163.29
116.89
1
A
LYS
111
46.38
73.71
1
A
THR
130
-66.28
76.22
1
A
HIS
143
39.60
43.33
1
A
LEU
144
-109.78
-166.23
1
A
LYS
147
177.85
133.60
1
A
SER
156
-125.40
-164.53
1
A
THR
157
-140.14
-2.32
1
A
LEU
170
-175.38
102.73
1
A
ASP
171
-35.99
-73.12
1
A
PRO
173
-60.90
99.39
1
A
GLU
179
-170.93
144.41
1
B
ASN
19
58.37
70.53
1
B
GLU
22
-52.47
-71.62
1
B
GLN
34
71.60
-7.37
1
B
SER
88
-52.62
-71.83
1
B
THR
90
-120.03
-74.71
1
B
HIS
112
-61.30
92.20
1
B
TYR
123
-175.42
130.30
1
B
PRO
124
-64.34
-172.28
1
B
ASN
134
49.43
21.48
1
B
GLU
138
-60.77
89.09
1
B
ASP
152
-99.97
36.13
1
B
SER
167
-63.12
67.98
PARHCSDX.PRO
TOPHCSDX.PRO
PARAM19.SOL
TOPH19.SOL
PARAM3_MOD.CHO
TOPH3.CHO
47.6
-10.
-10.
0.
-10.
0.
10.
RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191
OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON
DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY
OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109,
172, AND 189).
0.325
0.009
0.246
0.246
2.75
6.0
1323
13095
10.1
97.9
RANDOM
10000000.00
0.00
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1DLH
0.53
0.39
5.00
0.72
0.61
2.75
6.0
22
3158
28
0
3108
0.015
1.6
24.6
1.31
3.53
3.00
5.98
4.00
5.52
4.00
9.35
6.00
0.444
0.036
0.373
2.86
162
1442
8
10.1
96.7
30.8
2.75
15.
1A6A
14428
-3.
0.071
1
6.7
3.2
96.9
0.314
2.75
3.0
2.3
1
3.0
97.2
data reduction
DENZO
data reduction
ROTAVATA/AGROVATA
phasing
AMoRE
refinement
X-PLOR
3.1
data scaling
CCP4
(AGROVATA
data scaling
ROTAVATA
THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
A
GLU
46
A
GLU
42
HELX_P
A
PHE
51
A
PHE
47
1
1
6
A
ALA
56
A
ALA
52
HELX_P
A
ARG
76
A
ARG
72
1
2
21
B
GLU
52
B
GLU
48
HELX_P
B
SER
63
B
SER
59
5
3
12
B
LYS
65
B
LYS
61
HELX_P
B
ASN
77
B
ASN
73
1
4
13
B
CYS
79
B
CYS
75
HELX_P
B
VAL
86
B
VAL
82
1
5
8
disulf
2.029
A
CYS
107
A
SG
CYS
103
1_555
A
CYS
163
A
SG
CYS
159
1_555
disulf
2.032
B
CYS
15
B
SG
CYS
11
1_555
B
CYS
79
B
SG
CYS
75
1_555
disulf
2.054
B
CYS
117
B
SG
CYS
113
1_555
B
CYS
173
B
SG
CYS
169
1_555
covale
1.453
one
N-Glycosylation
A
ASN
78
A
ND2
ASN
74
1_555
A
NAG
181
D
C1
NAG
1_555
covale
1.440
one
N-Glycosylation
A
ASN
118
A
ND2
ASN
114
1_555
A
NAG
200
E
C1
NAG
1_555
COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)
MHC GLYCOPROTEIN, COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN), COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex
A
THR
113
A
THR
109
1
A
PRO
114
A
PRO
110
-0.11
B
TYR
123
B
TYR
119
1
B
PRO
124
B
PRO
120
-0.51
2DRA_HUMAN
UNP
1
1
P01903
MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFE
AQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSET
VFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIK
GVRKSNAAERRGPL
HB2B_HUMAN
UNP
2
1
P01912
MVCLRLPGGSCMAVLTVTLMVLSSPLALAGDTRPRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVT
ELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYGVVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRW
FRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL
FLGAGLFIYFRNQKGHSGLQPRGFLS
HG2A_HUMAN
UNP
3
1
P04233
MHRRRSRSCREDQKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQGRLDK
LTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGNMTEDHVMHLLQNADPLKVYPPLKG
SFPENLTHLKNTMETIDWKVFESWMHHWLLFEMSRHSLEQKPTDAPPKVLTKCQEEVSHIPAVHPGSFRPKCDENGNYLP
LQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSESLELEDPSSGLGVTKQDLGPVPM
30
205
1A6A
5
180
P01903
A
1
1
176
34
220
1A6A
5
191
P01912
B
2
1
187
103
117
1A6A
87
101
P04233
C
3
1
15
4
4
3
4
3
3
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
anti-parallel
A
ILE
7
A
ILE
3
A
LEU
14
A
LEU
10
A
SER
19
A
SER
15
A
PHE
26
A
PHE
22
A
ASP
29
A
ASP
25
A
ASP
35
A
ASP
31
A
GLU
40
A
GLU
36
A
TRP
43
A
TRP
39
A
THR
90
A
THR
86
A
THR
93
A
THR
89
A
ASN
103
A
ASN
99
A
ILE
109
A
ILE
105
A
LYS
147
A
LYS
143
A
PHE
153
A
PHE
149
A
VAL
132
A
VAL
128
A
GLU
134
A
GLU
130
A
ASN
118
A
ASN
114
A
ARG
123
A
ARG
119
A
VAL
160
A
VAL
156
A
GLU
166
A
GLU
162
A
LEU
174
A
LEU
170
A
GLU
179
A
GLU
175
B
GLU
9
B
GLU
5
B
PHE
18
B
PHE
14
B
ARG
23
B
ARG
19
B
HIS
32
B
HIS
28
B
GLU
35
B
GLU
31
B
ASP
41
B
ASP
37
B
PHE
47
B
PHE
43
B
ALA
49
B
ALA
45
B
LYS
98
B
LYS
94
B
PRO
103
B
PRO
99
B
LEU
115
B
LEU
111
B
SER
120
B
SER
116
B
GLN
156
B
GLN
152
B
LEU
158
B
LEU
154
B
ILE
127
B
ILE
123
B
ARG
133
B
ARG
129
B
VAL
170
B
VAL
166
B
HIS
177
B
HIS
173
B
LEU
184
B
LEU
180
B
ARG
189
B
ARG
185
153
P 32 1 2