0.031328
0.000000
0.000000
0.000000
0.024219
0.000000
0.000000
0.000000
0.013080
0.00000
0.00000
0.00000
Harata, K.
Muraki, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.0
90.0
90.0
31.92
41.29
76.45
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
297
673
681
10.1006/jmbi.2000.3594
10731420
Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose.
2000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
286
1
DIFFRACTOMETER
1999-05-07
ENRAF-NONIUS FAST
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS FR571
9349.346
AGGLUTININ ISOLECTIN VI
1
nat
polymer
18.015
water
54
nat
water
no
yes
(PCA)RCGSQGGGATCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDY
CSGGKCQYRCSSS
QRCGSQGGGATCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG
KCQYRCSSS
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
great nettle
Urtica
sample
3501
Urtica dioica
3
2.69
54.33
VAPOR DIFFUSION, HANGING DROP
5.6
PEG1000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
software
diffrn_detector
entity_poly
pdbx_struct_mod_residue
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Polymer sequence
1
0
2000-04-05
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2018-04-18
2
0
2019-12-25
_software.name
_diffrn_detector.detector
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_struct_mod_residue.parent_comp_id
_struct_conn.pdbx_leaving_atom_flag
URTICA DIOICA AGGLUTININ IN COMPLEX WITH TRI-N-ACETYLCHITOTRIOSE
RCSB
Y
RCSB
2000-02-20
REL
REL
HOH
water
HOH
101
2
HOH
HOH
101
A
HOH
102
2
HOH
HOH
102
A
HOH
103
2
HOH
HOH
103
A
HOH
104
2
HOH
HOH
104
A
HOH
105
2
HOH
HOH
105
A
HOH
106
2
HOH
HOH
106
A
HOH
107
2
HOH
HOH
107
A
HOH
108
2
HOH
HOH
108
A
HOH
109
2
HOH
HOH
109
A
HOH
110
2
HOH
HOH
110
A
HOH
111
2
HOH
HOH
111
A
HOH
112
2
HOH
HOH
112
A
HOH
113
2
HOH
HOH
113
A
HOH
114
2
HOH
HOH
114
A
HOH
115
2
HOH
HOH
115
A
HOH
116
2
HOH
HOH
116
A
HOH
117
2
HOH
HOH
117
A
HOH
118
2
HOH
HOH
118
A
HOH
119
2
HOH
HOH
119
A
HOH
120
2
HOH
HOH
120
A
HOH
121
2
HOH
HOH
121
A
HOH
122
2
HOH
HOH
122
A
HOH
123
2
HOH
HOH
123
A
HOH
124
2
HOH
HOH
124
A
HOH
125
2
HOH
HOH
125
A
HOH
126
2
HOH
HOH
126
A
HOH
127
2
HOH
HOH
127
A
HOH
128
2
HOH
HOH
128
A
HOH
129
2
HOH
HOH
129
A
HOH
130
2
HOH
HOH
130
A
HOH
131
2
HOH
HOH
131
A
HOH
132
2
HOH
HOH
132
A
HOH
133
2
HOH
HOH
133
A
HOH
134
2
HOH
HOH
134
A
HOH
135
2
HOH
HOH
135
A
HOH
136
2
HOH
HOH
136
A
HOH
137
2
HOH
HOH
137
A
HOH
138
2
HOH
HOH
138
A
HOH
139
2
HOH
HOH
139
A
HOH
140
2
HOH
HOH
140
A
HOH
141
2
HOH
HOH
141
A
HOH
142
2
HOH
HOH
142
A
HOH
143
2
HOH
HOH
143
A
HOH
144
2
HOH
HOH
144
A
HOH
145
2
HOH
HOH
145
A
HOH
146
2
HOH
HOH
146
A
HOH
147
2
HOH
HOH
147
A
HOH
148
2
HOH
HOH
148
A
HOH
149
2
HOH
HOH
149
A
HOH
150
2
HOH
HOH
150
A
HOH
151
2
HOH
HOH
151
A
HOH
152
2
HOH
HOH
152
A
HOH
153
2
HOH
HOH
153
A
HOH
154
2
HOH
HOH
154
A
PGL
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
ALA
10
n
10
ALA
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
GLU
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
LYS
81
n
81
LYS
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
SER
87
n
87
SER
87
A
SER
88
n
88
SER
88
A
SER
89
n
89
SER
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
3.69
0.50
120.30
123.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
1
-3.66
0.50
120.30
116.64
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
16
16
16
N
1
6.67
0.80
106.30
112.97
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
21
21
21
N
1
-5.57
0.80
107.30
101.73
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
21
21
21
N
1
7.05
0.80
106.30
113.35
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
23
23
23
N
1
-6.12
0.80
107.30
101.18
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
23
23
23
N
1
5.52
0.80
106.30
111.82
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
40
40
40
N
1
-5.19
0.80
107.30
102.11
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
40
40
40
N
1
3.07
0.50
120.30
123.37
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
44
44
44
N
1
4.44
0.50
120.30
124.74
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
48
48
48
N
1
-3.05
0.50
120.30
117.25
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
62
62
62
N
1
6.45
0.80
106.30
112.75
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
69
69
69
N
1
-5.77
0.80
107.30
101.53
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
69
69
69
N
1
-4.75
0.60
121.00
116.25
A
A
A
CB
CG
CD2
TYR
TYR
TYR
84
84
84
N
1
-17.37
2.70
111.00
93.63
A
A
A
N
CA
C
SER
SER
SER
88
88
88
N
1
A
A
NE2
CD2
HIS
HIS
67
67
-0.066
0.011
1.373
1.307
N
1
A
THR
34
-91.90
30.29
1
A
HIS
47
59.92
16.70
1
A
SER
87
22.55
52.06
1
A
SER
88
151.79
-99.58
0.267
0.229
1.5
8.0
1212
13142
1
2.0
1.5
8.0
54
695
0
0
641
0.015
3.01
20.9
1.4
24.5
1EHD
19125
19125
0.0
0.0
0.031
1
7.98
8.3
89.0
0.323
1.40
1.427
859
76.1
data collection
MADNESS
data reduction
MERGEF
model building
MIRPHS
refinement
X-PLOR
3.1
data reduction
MADNESS
data scaling
MERGEF
phasing
MIRPHS
AGGLUTININ ISOLECTIN VI
CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI
1
N
N
2
N
N
A
GLY
4
A
GLY
4
HELX_P
A
GLY
8
A
GLY
8
5
1
5
A
CYS
12
A
CYS
12
HELX_P
A
ARG
16
A
ARG
16
5
2
5
A
SER
27
A
SER
27
HELX_P
A
GLY
32
A
GLY
32
1
3
6
A
CYS
39
A
CYS
39
HELX_P
A
GLU
43
A
GLU
43
5
4
5
A
GLY
50
A
GLY
50
HELX_P
A
GLY
54
A
GLY
54
5
5
5
A
GLY
73
A
GLY
73
HELX_P
A
SER
78
A
SER
78
1
6
6
disulf
2.035
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
18
A
SG
CYS
18
1_555
disulf
2.035
A
CYS
12
A
SG
CYS
12
1_555
A
CYS
24
A
SG
CYS
24
1_555
disulf
1.952
A
CYS
17
A
SG
CYS
17
1_555
A
CYS
31
A
SG
CYS
31
1_555
disulf
1.998
A
CYS
35
A
SG
CYS
35
1_555
A
CYS
39
A
SG
CYS
39
1_555
disulf
2.020
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
64
A
SG
CYS
64
1_555
disulf
2.038
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
70
A
SG
CYS
70
1_555
disulf
2.023
A
CYS
63
A
SG
CYS
63
1_555
A
CYS
77
A
SG
CYS
77
1_555
disulf
2.044
A
CYS
82
A
SG
CYS
82
1_555
A
CYS
86
A
SG
CYS
86
1_555
covale
1.310
both
A
PCA
1
A
C
PCA
1
1_555
A
ARG
2
A
N
ARG
2
1_555
PLANT PROTEIN
Two homologous hevein-like domains, PLANT PROTEIN
Q9S7B3_URTDI
UNP
1
24
Q9S7B3
QRCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGERSDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGG
NCQYRCSSS
24
112
1EHD
1
89
Q9S7B3
A
1
1
89
1
SER
conflict
ALA
10
1EHD
A
Q9S7B3
UNP
33
10
1
ASN
conflict
LYS
81
1EHD
A
Q9S7B3
UNP
104
81
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