0.03195
0.00000
0.00000
0.00000
0.02404
0.00000
0.00000
0.00000
0.01297
0.00000
0.00000
0.00000
Saul, F.A.
Rovira, P.
Boulot, G.
Van Damme, E.J.M.
Peumans, W.J.
Truffa-Bachi, P.
Bentley, G.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
31.300
41.600
77.100
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 H7 N O3
129.114
n
PYROGLUTAMIC ACID
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 Fold.Des.
FODEFH
1263
0969-2126
8
593
603
10.1016/S0969-2126(00)00142-8
10873861
Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
2000
NE
Plant Mol.Biol.
PMBIDB
2006
0167-4412
39
335
347
10.1023/A:1006134932290
Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family
1999
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
IMAGE PLATE
1998-09-21
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.375
1.0
D41A
LURE
1.375
SYNCHROTRON
LURE BEAMLINE D41A
TWO ISOFORMS ARE PRESENT IN THE CRYSTAL: ISOLECTIN VI AND ISOLECTIN V
9350.269
PROTEIN (AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V)
1
nat
polymer
18.015
water
49
nat
water
UDA
no
yes
(PCA)RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDY
CSGGNCQYRCSSS
QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG
NCQYRCSSS
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
y
y
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
great nettle
PURIFIED FROM THE RHIZOMES
Urtica
sample
3501
Urtica dioica
3
2.68
54.16
VAPOR DIFFUSION, SITTING DROP
6.0
PEG 6000, sodium acetate, sodium chloride , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
290.0
entity_poly
pdbx_struct_mod_residue
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Advisory
Database references
Derived calculations
Polymer sequence
1
0
2000-06-21
1
1
2008-04-27
1
2
2011-07-13
2
0
2019-12-25
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_struct_mod_residue.parent_comp_id
_struct_conn.pdbx_leaving_atom_flag
UDA TETRASACCHARIDE COMPLEX
UDA TRISACCHARIDE COMPLEX
RCSB
Y
RCSB
2000-02-28
REL
REL
HOH
water
The structure comprises two hevein-like domains,
each homologous to those of Wheat Germ Agglutinin
(PDB code: 9wga). Each domain contains a
saccharide-binding site. The N-terminal residue is
pyrrolidone carboxylic acid (PCA). A dual conformation
is seen at Gly79, Gly80. No electron density is seen
for the side chain of Arg33 beyond the CB atom. No
interpretable density is seen for C-terminal residues
Ser87, Ser88, and Ser89.
WAT
1
2
HOH
HOH
90
A
WAT
2
2
HOH
HOH
91
A
WAT
3
2
HOH
HOH
92
A
WAT
4
2
HOH
HOH
93
A
WAT
5
2
HOH
HOH
94
A
WAT
6
2
HOH
HOH
95
A
WAT
7
2
HOH
HOH
96
A
WAT
8
2
HOH
HOH
97
A
WAT
9
2
HOH
HOH
98
A
WAT
10
2
HOH
HOH
99
A
WAT
11
2
HOH
HOH
100
A
WAT
12
2
HOH
HOH
101
A
WAT
13
2
HOH
HOH
102
A
WAT
14
2
HOH
HOH
103
A
WAT
15
2
HOH
HOH
104
A
WAT
16
2
HOH
HOH
105
A
WAT
17
2
HOH
HOH
106
A
WAT
18
2
HOH
HOH
107
A
WAT
19
2
HOH
HOH
108
A
WAT
20
2
HOH
HOH
109
A
WAT
21
2
HOH
HOH
110
A
WAT
23
2
HOH
HOH
111
A
WAT
24
2
HOH
HOH
112
A
WAT
25
2
HOH
HOH
113
A
WAT
26
2
HOH
HOH
114
A
WAT
27
2
HOH
HOH
115
A
WAT
28
2
HOH
HOH
116
A
WAT
29
2
HOH
HOH
117
A
WAT
30
2
HOH
HOH
118
A
WAT
31
2
HOH
HOH
119
A
WAT
32
2
HOH
HOH
120
A
WAT
33
2
HOH
HOH
121
A
WAT
34
2
HOH
HOH
122
A
WAT
35
2
HOH
HOH
123
A
WAT
36
2
HOH
HOH
124
A
WAT
37
2
HOH
HOH
125
A
WAT
38
2
HOH
HOH
126
A
WAT
39
2
HOH
HOH
127
A
WAT
40
2
HOH
HOH
128
A
WAT
42
2
HOH
HOH
129
A
WAT
43
2
HOH
HOH
130
A
WAT
46
2
HOH
HOH
131
A
WAT
47
2
HOH
HOH
132
A
WAT
48
2
HOH
HOH
133
A
WAT
49
2
HOH
HOH
134
A
WAT
50
2
HOH
HOH
135
A
WAT
51
2
HOH
HOH
136
A
WAT
52
2
HOH
HOH
137
A
WAT
53
2
HOH
HOH
138
A
PCA
1
n
1
PCA
1
A
ARG
2
n
2
ARG
2
A
CYS
3
n
3
CYS
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
GLN
6
n
6
GLN
6
A
GLY
7
n
7
GLY
7
A
GLY
8
n
8
GLY
8
A
GLY
9
n
9
GLY
9
A
SER
10
y
10
SER
10
A
GLY
10
y
10
GLY
10
A
THR
11
n
11
THR
11
A
CYS
12
n
12
CYS
12
A
PRO
13
n
13
PRO
13
A
GLY
14
n
14
GLY
14
A
LEU
15
n
15
LEU
15
A
ARG
16
n
16
ARG
16
A
CYS
17
n
17
CYS
17
A
CYS
18
n
18
CYS
18
A
SER
19
n
19
SER
19
A
ILE
20
n
20
ILE
20
A
TRP
21
n
21
TRP
21
A
GLY
22
n
22
GLY
22
A
TRP
23
n
23
TRP
23
A
CYS
24
n
24
CYS
24
A
GLY
25
n
25
GLY
25
A
ASP
26
n
26
ASP
26
A
SER
27
n
27
SER
27
A
GLU
28
n
28
GLU
28
A
PRO
29
n
29
PRO
29
A
TYR
30
n
30
TYR
30
A
CYS
31
n
31
CYS
31
A
GLY
32
n
32
GLY
32
A
ARG
33
n
33
ARG
33
A
THR
34
n
34
THR
34
A
CYS
35
n
35
CYS
35
A
GLN
36
n
36
GLU
36
A
ASN
37
n
37
ASN
37
A
LYS
38
n
38
LYS
38
A
CYS
39
n
39
CYS
39
A
TRP
40
n
40
TRP
40
A
SER
41
n
41
SER
41
A
GLY
42
n
42
GLY
42
A
GLU
43
n
43
GLU
43
A
ARG
44
n
44
ARG
44
A
SER
45
n
45
SER
45
A
ASP
46
n
46
ASP
46
A
HIS
47
n
47
HIS
47
A
ARG
48
n
48
ARG
48
A
CYS
49
n
49
CYS
49
A
GLY
50
n
50
GLY
50
A
ALA
51
n
51
ALA
51
A
ALA
52
n
52
ALA
52
A
VAL
53
n
53
VAL
53
A
GLY
54
n
54
GLY
54
A
ASN
55
n
55
ASN
55
A
PRO
56
n
56
PRO
56
A
PRO
57
n
57
PRO
57
A
CYS
58
n
58
CYS
58
A
GLY
59
n
59
GLY
59
A
GLN
60
n
60
GLN
60
A
ASP
61
n
61
ASP
61
A
ARG
62
n
62
ARG
62
A
CYS
63
n
63
CYS
63
A
CYS
64
n
64
CYS
64
A
SER
65
n
65
SER
65
A
VAL
66
n
66
VAL
66
A
HIS
67
n
67
HIS
67
A
GLY
68
n
68
GLY
68
A
TRP
69
n
69
TRP
69
A
CYS
70
n
70
CYS
70
A
GLY
71
n
71
GLY
71
A
GLY
72
n
72
GLY
72
A
GLY
73
n
73
GLY
73
A
ASN
74
n
74
ASN
74
A
ASP
75
n
75
ASP
75
A
TYR
76
n
76
TYR
76
A
CYS
77
n
77
CYS
77
A
SER
78
n
78
SER
78
A
GLY
79
n
79
GLY
79
A
GLY
80
n
80
GLY
80
A
ASN
81
n
81
ASN
81
A
CYS
82
n
82
CYS
82
A
GLN
83
n
83
GLN
83
A
TYR
84
n
84
TYR
84
A
ARG
85
n
85
ARG
85
A
CYS
86
n
86
CYS
86
A
n
87
87
A
n
88
88
A
n
89
89
A
author_defined_assembly
1
monomeric
A
PCA
1
PYROGLUTAMIC ACID
A
PCA
1
GLN
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
GLY
25
A
N
GLY
25
A
O
CYS
17
A
O
CYS
17
A
O
CYS
18
A
O
CYS
18
A
N
GLU
36
A
N
GLU
36
A
O
GLY
71
A
O
GLY
71
A
N
CYS
63
A
N
CYS
63
A
O
CYS
64
A
O
CYS
64
A
N
GLN
83
A
N
GLN
83
1
A
SER
87
A
SER
87
1
Y
1
A
SER
88
A
SER
88
1
Y
1
A
SER
89
A
SER
89
1
Y
1
A
A
OG
O
SER
HOH
10
97
1.97
A
1
3.65
0.50
120.30
123.95
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
33
33
33
N
The structure was determined to 2.45A resolution by MIR methods based on 4 Hg derivatives (rotating-anode X-ray source) with solvent flattening, and refined to 1.66A resolution with synchrotron data using a bulk solvent correction and anisotropic scale factor.
0.249
0.191
0.207
0.207
1.66
18.0
602
11689
11689
95.4
RANDOM
1
0
0
MIR
Engh & Huber
1.66
18.0
49
680
0
0
631
0.017
0.02
0.016
0.02
0.0220
0.03
0.0116
0.02
0.185
0.15
0.149
0.30
0.162
0.30
0.00
15.0
4.90
7.00
13.7
15.0
27.4
20.0
1.814
2.00
2.864
3.00
3.397
3.00
4.916
4.00
30.8
1.66
18.0
1EIS
11689
11689
0.0
0.0
0.056
1
24.7
12.5
95.4
0.352
1.66
1.72
1015
8.9
84.7
data reduction
DENZO
data scaling
SCALEPACK
phasing
MLPHARE
model building
DM
refinement
REFMAC
phasing
DM
AGGLUTININ ISOLECTIN VI/AGGLUTININ ISOLECTIN V
UDA UNCOMPLEXED FORM. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II
1
N
N
2
N
N
A
CYS
12
A
CYS
12
HELX_P
A
ARG
16
A
ARG
16
5
1
5
A
SER
27
A
SER
27
HELX_P
A
GLY
32
A
GLY
32
1
2
6
A
CYS
39
A
CYS
39
HELX_P
A
GLU
43
A
GLU
43
5
3
5
A
GLY
50
A
GLY
50
HELX_P
A
GLY
54
A
GLY
54
5
4
5
A
GLY
73
A
GLY
73
HELX_P
A
SER
78
A
SER
78
1
5
6
disulf
2.012
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
18
A
SG
CYS
18
1_555
disulf
2.029
A
CYS
12
A
SG
CYS
12
1_555
A
CYS
24
A
SG
CYS
24
1_555
disulf
2.030
A
CYS
17
A
SG
CYS
17
1_555
A
CYS
31
A
SG
CYS
31
1_555
disulf
2.010
A
CYS
35
A
SG
CYS
35
1_555
A
CYS
39
A
SG
CYS
39
1_555
disulf
2.038
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
64
A
SG
CYS
64
1_555
disulf
2.017
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
70
A
SG
CYS
70
1_555
disulf
2.041
A
CYS
63
A
SG
CYS
63
1_555
A
CYS
77
A
SG
CYS
77
1_555
disulf
2.026
A
CYS
82
A
SG
CYS
82
1_555
A
CYS
86
A
SG
CYS
86
1_555
covale
1.360
both
A
PCA
1
A
C
PCA
1
1_555
A
ARG
2
A
N
ARG
2
1_555
SUGAR BINDING PROTEIN
LECTIN, HEVEIN DOMAIN, UDA, SUPERANTIGEN, SUGAR BINDING PROTEIN
Q9SYR5_URTDI
UNP
1
24
Q9SYR5
QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG
NCQYRCSSS
24
112
1EIS
1
89
Q9SYR5
A
1
1
89
1
SER
microheterogeneity
GLY
10
1EIS
A
Q9SYR5
UNP
33
10
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
CYS
24
A
CYS
24
A
GLY
25
A
GLY
25
A
CYS
17
A
CYS
17
A
SER
19
A
SER
19
A
CYS
35
A
CYS
35
A
ASN
37
A
ASN
37
A
CYS
70
A
CYS
70
A
GLY
71
A
GLY
71
A
CYS
63
A
CYS
63
A
SER
65
A
SER
65
A
CYS
82
A
CYS
82
A
TYR
84
A
TYR
84
19
P 21 21 21