0.011325
0.006539
0.000000
0.000000
0.013077
0.000000
0.000000
0.000000
0.019493
0.00000
0.00000
0.00000
THE IDENTITY OF THE NA 629 ION HAS NOT BEEN CONFIRMED.
Bodian, D.L.
Jones, E.Y.
Harlos, K.
Stuart, D.I.
Davis, S.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
88.300
88.300
51.300
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
Na 1
22.990
SODIUM ION
non-polymer
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
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
Structure
STRUE6
2005
0969-2126
2
755
766
10.1016/S0969-2126(94)00076-X
7994575
Crystal structure of the extracellular region of the human cell adhesion molecule CD2 at 2.5 A resolution.
1994
To be Published
0353
Ligand Binding by the Immunoglobulin Superfamily Recognition Molecule Cd2 is Glycosylation Independent
UK
Nature
NATUAS
0006
0028-0836
360
232
Crystal Structure at 2.8 Angstroms Resolution of a Soluble Form of the Cell Adhesion Molecule Cd2
1992
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
21002.076
CD2
1
man
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
3
man
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
22
nat
water
no
no
KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDI
YKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTTLTCEVMNGTDPELNLYQDGKHLKLSQRVITHKWTTSLSAKF
KCTAGNKVSKESSVEPVSCPEK
KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDI
YKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTTLTCEVMNGTDPELNLYQDGKHLKLSQRVITHKWTTSLSAKF
KCTAGNKVSKESSVEPVSCPEK
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
9606
OVARY
Homo sapiens
2.75
55.24
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_database_status
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Data collection
Derived calculations
Other
Structure summary
1
0
1995-02-07
1
1
2008-03-24
1
2
2011-07-13
1
3
2020-07-29
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_database_status.process_site
_pdbx_entity_nonpoly.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
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
Y
BNL
1994-08-10
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
NA
SODIUM ION
HOH
water
THE AUTHOR STATES THAT THE IDENTITY OF THE NA 629 ION HAS NOT BEEN CONFIRMED
NAG
500
2
NAG
NAG
500
A
NAG
501
2
NAG
NAG
501
A
NAG
502
2
NAG
NAG
502
A
NA
629
3
NA
NA
629
A
HOH
600
4
HOH
HOH
600
A
HOH
601
4
HOH
HOH
601
A
HOH
602
4
HOH
HOH
602
A
HOH
603
4
HOH
HOH
603
A
HOH
604
4
HOH
HOH
604
A
HOH
605
4
HOH
HOH
605
A
HOH
609
4
HOH
HOH
609
A
HOH
610
4
HOH
HOH
610
A
HOH
611
4
HOH
HOH
611
A
HOH
617
4
HOH
HOH
617
A
HOH
618
4
HOH
HOH
618
A
HOH
619
4
HOH
HOH
619
A
HOH
621
4
HOH
HOH
621
A
HOH
622
4
HOH
HOH
622
A
HOH
623
4
HOH
HOH
623
A
HOH
625
4
HOH
HOH
625
A
HOH
630
4
HOH
HOH
630
A
HOH
631
4
HOH
HOH
631
A
HOH
632
4
HOH
HOH
632
A
HOH
642
4
HOH
HOH
642
A
HOH
643
4
HOH
HOH
643
A
HOH
646
4
HOH
HOH
646
A
n
1
1
A
n
2
2
A
n
3
3
A
THR
4
n
4
THR
4
A
ASN
5
n
5
ASN
5
A
ALA
6
n
6
ALA
6
A
LEU
7
n
7
LEU
7
A
GLU
8
n
8
GLU
8
A
THR
9
n
9
THR
9
A
TRP
10
n
10
TRP
10
A
GLY
11
n
11
GLY
11
A
ALA
12
n
12
ALA
12
A
LEU
13
n
13
LEU
13
A
GLY
14
n
14
GLY
14
A
GLN
15
n
15
GLN
15
A
ASP
16
n
16
ASP
16
A
ILE
17
n
17
ILE
17
A
ASN
18
n
18
ASN
18
A
LEU
19
n
19
LEU
19
A
ASP
20
n
20
ASP
20
A
ILE
21
n
21
ILE
21
A
PRO
22
n
22
PRO
22
A
SER
23
n
23
SER
23
A
PHE
24
n
24
PHE
24
A
GLN
25
n
25
GLN
25
A
MET
26
n
26
MET
26
A
SER
27
n
27
SER
27
A
ASP
28
n
28
ASP
28
A
ASP
29
n
29
ASP
29
A
ILE
30
n
30
ILE
30
A
ASP
31
n
31
ASP
31
A
ASP
32
n
32
ASP
32
A
ILE
33
n
33
ILE
33
A
LYS
34
n
34
LYS
34
A
TRP
35
n
35
TRP
35
A
GLU
36
n
36
GLU
36
A
LYS
37
n
37
LYS
37
A
THR
38
n
38
THR
38
A
SER
39
n
39
SER
39
A
ASP
40
n
40
ASP
40
A
LYS
41
n
41
LYS
41
A
LYS
42
n
42
LYS
42
A
LYS
43
n
43
LYS
43
A
ILE
44
n
44
ILE
44
A
ALA
45
n
45
ALA
45
A
GLN
46
n
46
GLN
46
A
PHE
47
n
47
PHE
47
A
ARG
48
n
48
ARG
48
A
LYS
49
n
49
LYS
49
A
GLU
50
n
50
GLU
50
A
LYS
51
n
51
LYS
51
A
GLU
52
n
52
GLU
52
A
THR
53
n
53
THR
53
A
PHE
54
n
54
PHE
54
A
LYS
55
n
55
LYS
55
A
GLU
56
n
56
GLU
56
A
LYS
57
n
57
LYS
57
A
ASP
58
n
58
ASP
58
A
THR
59
n
59
THR
59
A
TYR
60
n
60
TYR
60
A
LYS
61
n
61
LYS
61
A
LEU
62
n
62
LEU
62
A
PHE
63
n
63
PHE
63
A
LYS
64
n
64
LYS
64
A
ASN
65
n
65
ASN
65
A
GLY
66
n
66
GLY
66
A
THR
67
n
67
THR
67
A
LEU
68
n
68
LEU
68
A
LYS
69
n
69
LYS
69
A
ILE
70
n
70
ILE
70
A
LYS
71
n
71
LYS
71
A
HIS
72
n
72
HIS
72
A
LEU
73
n
73
LEU
73
A
LYS
74
n
74
LYS
74
A
THR
75
n
75
THR
75
A
ASP
76
n
76
ASP
76
A
ASP
77
n
77
ASP
77
A
GLN
78
n
78
GLN
78
A
ASP
79
n
79
ASP
79
A
ILE
80
n
80
ILE
80
A
TYR
81
n
81
TYR
81
A
LYS
82
n
82
LYS
82
A
VAL
83
n
83
VAL
83
A
SER
84
n
84
SER
84
A
ILE
85
n
85
ILE
85
A
TYR
86
n
86
TYR
86
A
ASP
87
n
87
ASP
87
A
THR
88
n
88
THR
88
A
LYS
89
n
89
LYS
89
A
GLY
90
n
90
GLY
90
A
LYS
91
n
91
LYS
91
A
ASN
92
n
92
ASN
92
A
VAL
93
n
93
VAL
93
A
LEU
94
n
94
LEU
94
A
GLU
95
n
95
GLU
95
A
LYS
96
n
96
LYS
96
A
ILE
97
n
97
ILE
97
A
PHE
98
n
98
PHE
98
A
ASP
99
n
99
ASP
99
A
LEU
100
n
100
LEU
100
A
LYS
101
n
101
LYS
101
A
ILE
102
n
102
ILE
102
A
GLN
103
n
103
GLN
103
A
GLU
104
n
104
GLU
104
A
ARG
105
n
105
ARG
105
A
VAL
106
n
106
VAL
106
A
SER
107
n
107
SER
107
A
LYS
108
n
108
LYS
108
A
PRO
109
n
109
PRO
109
A
LYS
110
n
110
LYS
110
A
ILE
111
n
111
ILE
111
A
SER
112
n
112
SER
112
A
TRP
113
n
113
TRP
113
A
THR
114
n
114
THR
114
A
CYS
115
n
115
CYS
115
A
ILE
116
n
116
ILE
116
A
ASN
117
n
117
ASN
117
A
THR
118
n
118
THR
118
A
THR
119
n
119
THR
119
A
LEU
120
n
120
LEU
120
A
THR
121
n
121
THR
121
A
CYS
122
n
122
CYS
122
A
GLU
123
n
123
GLU
123
A
VAL
124
n
124
VAL
124
A
MET
125
n
125
MET
125
A
ASN
126
n
126
ASN
126
A
GLY
127
n
127
GLY
127
A
THR
128
n
128
THR
128
A
ASP
129
n
129
ASP
129
A
PRO
130
n
130
PRO
130
A
GLU
131
n
131
GLU
131
A
LEU
132
n
132
LEU
132
A
ASN
133
n
133
ASN
133
A
LEU
134
n
134
LEU
134
A
TYR
135
n
135
TYR
135
A
GLN
136
n
136
GLN
136
A
ASP
137
n
137
ASP
137
A
GLY
138
n
138
GLY
138
A
LYS
139
n
139
LYS
139
A
HIS
140
n
140
HIS
140
A
LEU
141
n
141
LEU
141
A
LYS
142
n
142
LYS
142
A
LEU
143
n
143
LEU
143
A
SER
144
n
144
SER
144
A
GLN
145
n
145
GLN
145
A
ARG
146
n
146
ARG
146
A
VAL
147
n
147
VAL
147
A
ILE
148
n
148
ILE
148
A
THR
149
n
149
THR
149
A
HIS
150
n
150
HIS
150
A
LYS
151
n
151
LYS
151
A
TRP
152
n
152
TRP
152
A
THR
153
n
153
THR
153
A
THR
154
n
154
THR
154
A
SER
155
n
155
SER
155
A
LEU
156
n
156
LEU
156
A
SER
157
n
157
SER
157
A
ALA
158
n
158
ALA
158
A
LYS
159
n
159
LYS
159
A
PHE
160
n
160
PHE
160
A
LYS
161
n
161
LYS
161
A
CYS
162
n
162
CYS
162
A
THR
163
n
163
THR
163
A
ALA
164
n
164
ALA
164
A
GLY
165
n
165
GLY
165
A
ASN
166
n
166
ASN
166
A
LYS
167
n
167
LYS
167
A
VAL
168
n
168
VAL
168
A
SER
169
n
169
SER
169
A
LYS
170
n
170
LYS
170
A
GLU
171
n
171
GLU
171
A
SER
172
n
172
SER
172
A
SER
173
n
173
SER
173
A
VAL
174
n
174
VAL
174
A
GLU
175
n
175
GLU
175
A
PRO
176
n
176
PRO
176
A
VAL
177
n
177
VAL
177
A
SER
178
n
178
SER
178
A
CYS
179
n
179
CYS
179
A
PRO
180
n
180
PRO
180
A
GLU
181
n
181
GLU
181
A
LYS
182
n
182
LYS
182
A
author_defined_assembly
1
monomeric
A
TYR
60
A
OH
TYR
60
1_555
A
NA
629
E
NA
NA
1_555
A
ASP
77
A
OD1
ASP
77
1_555
111.7
A
TYR
60
A
OH
TYR
60
1_555
A
NA
629
E
NA
NA
1_555
A
TYR
81
A
OH
TYR
81
1_555
145.2
A
ASP
77
A
OD1
ASP
77
1_555
A
NA
629
E
NA
NA
1_555
A
TYR
81
A
OH
TYR
81
1_555
102.7
A
ASN
65
GLYCOSYLATION SITE
A
ASN
65
ASN
A
ASN
117
GLYCOSYLATION SITE
A
ASN
117
ASN
A
ASN
126
GLYCOSYLATION SITE
A
ASN
126
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
A
N
LEU
7
A
N
LEU
7
A
O
ILE
97
A
O
ILE
97
A
N
LEU
100
A
N
LEU
100
A
O
ASP
79
A
O
ASP
79
A
O
TYR
86
A
O
TYR
86
A
N
ASP
31
A
N
ASP
31
A
O
TRP
35
A
O
TRP
35
A
N
ILE
44
A
N
ILE
44
A
N
GLN
46
A
N
GLN
46
A
O
PHE
54
A
O
PHE
54
A
N
LEU
19
A
N
LEU
19
A
O
LEU
68
A
O
LEU
68
A
N
LYS
69
A
N
LYS
69
A
O
LYS
61
A
O
LYS
61
A
N
THR
114
A
N
THR
114
A
O
THR
119
A
O
THR
119
A
N
CYS
122
A
N
CYS
122
A
O
ILE
148
A
O
ILE
148
A
O
SER
144
A
O
SER
144
A
N
LEU
132
A
N
LEU
132
A
N
TYR
135
A
N
TYR
135
A
O
LYS
161
A
O
LYS
161
A
O
ALA
164
A
O
ALA
164
A
N
GLU
171
A
N
GLU
171
1
A
LYS
1
A
LYS
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
ILE
3
A
ILE
3
1
Y
1
-12.68
1.90
111.40
98.72
A
A
A
CB
CA
C
VAL
VAL
VAL
83
83
83
N
1
A
GLN
25
-161.80
107.37
1
A
SER
27
-170.43
-166.53
1
A
LYS
41
44.32
83.69
1
A
LYS
49
58.00
-176.45
1
A
GLU
52
159.89
148.60
1
A
HIS
72
46.70
70.22
1
A
ASP
129
35.21
58.55
1
A
LEU
141
-104.89
-64.38
1
A
THR
153
-130.61
-40.55
1
A
GLU
181
40.80
73.35
36.
0.193
0.193
2.5
24.
7181
1
2.5
24.
22
1512
43
0
1447
1.97
1HNF
7181
1
87.
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
CD2 (HUMAN)
CRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL ADHESION MOLECULE CD2 AT 2.5 ANGSTROMS RESOLUTION
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
SER
39
A
SER
39
HELX_P
A
LYS
41
A
LYS
41
5
1
3
A
LYS
49
A
LYS
49
HELX_P
A
LYS
51
A
LYS
51
5
2
3
A
LYS
74
A
LYS
74
HELX_P
A
GLN
78
A
GLN
78
5
3
5
disulf
2.005
A
CYS
115
A
SG
CYS
115
1_555
A
CYS
179
A
SG
CYS
179
1_555
disulf
2.014
A
CYS
122
A
SG
CYS
122
1_555
A
CYS
162
A
SG
CYS
162
1_555
covale
1.459
one
N-Glycosylation
A
ASN
65
A
ND2
ASN
65
1_555
A
NAG
500
B
C1
NAG
1_555
covale
1.450
one
N-Glycosylation
A
ASN
117
A
ND2
ASN
117
1_555
A
NAG
501
C
C1
NAG
1_555
covale
1.440
one
N-Glycosylation
A
ASN
126
A
ND2
ASN
126
1_555
A
NAG
502
D
C1
NAG
1_555
metalc
2.494
A
TYR
60
A
OH
TYR
60
1_555
A
NA
629
E
NA
NA
1_555
metalc
2.781
A
ASP
77
A
OD1
ASP
77
1_555
A
NA
629
E
NA
NA
1_555
metalc
2.634
A
TYR
81
A
OH
TYR
81
1_555
A
NA
629
E
NA
NA
1_555
T LYMPHOCYTE ADHESION GLYCOPROTEIN
T LYMPHOCYTE ADHESION GLYCOPROTEIN
CD2_HUMAN
UNP
1
1
P06729
MSFPCKFVASFLLIFNVSSKGAVSKEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKE
KDTYKLFKNGTLKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTTLTCEVMNGTDPELNLYQ
DGKHLKLSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVSCPEKGLDIYLIIGICGGGSLLMVFVALLVFYITKRKKQ
RSRRNDEELETRAHRVATEERGRKPQQIPASTPQNPATSQHPPPPPGHRSQAPSHRPPPPGHRVQHQPQKRPPAPSGTQV
HQQKGPPLPRPRVQPKPPHGAAENSLSPSSN
25
206
1HNF
1
182
P06729
A
1
1
182
6
3
3
4
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
7
A
LEU
7
A
ALA
12
A
ALA
12
A
ASN
92
A
ASN
92
A
GLN
103
A
GLN
103
A
ASP
79
A
ASP
79
A
ASP
87
A
ASP
87
A
ILE
30
A
ILE
30
A
LYS
37
A
LYS
37
A
LYS
43
A
LYS
43
A
PHE
47
A
PHE
47
A
THR
53
A
THR
53
A
LYS
55
A
LYS
55
A
ILE
17
A
ILE
17
A
LEU
19
A
LEU
19
A
LEU
68
A
LEU
68
A
ILE
70
A
ILE
70
A
TYR
60
A
TYR
60
A
LEU
62
A
LEU
62
A
LYS
110
A
LYS
110
A
THR
114
A
THR
114
A
THR
119
A
THR
119
A
GLU
123
A
GLU
123
A
ILE
148
A
ILE
148
A
LYS
151
A
LYS
151
A
HIS
140
A
HIS
140
A
SER
144
A
SER
144
A
GLU
131
A
GLU
131
A
GLN
136
A
GLN
136
A
LEU
156
A
LEU
156
A
GLY
165
A
GLY
165
A
LYS
170
A
LYS
170
A
CYS
179
A
CYS
179
152
P 31 2 1