1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Katoh, E.
Katoh, S.
Minami, E.
Yamazaki, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
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 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
C6 H13 N O2
131.173
y
LEUCINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
15341
15348
10.1074/jbc.M210531200
12588869
High Precision NMR Structure and Function of the RING-H2 Finger Domain of EL5, a Rice Protein Whose Expression Is Increased upon Exposure to Pathogen-derived Oligosaccharides
2003
10.2210/pdb1iym/pdb
pdb_00001iym
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
SINGLE WAVELENGTH
M
1
1.0
5985.849
EL5
RING-H2 finger domain
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
no
no
AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV
AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV
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
rice
Oryza
Escherichia
Escherichia coli
sample
4530
Oryza sativa
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pET32a
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
database_2
pdbx_database_status
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
Database references
Derived calculations
Other
1
0
2003-07-22
1
1
2008-04-27
1
2
2011-07-13
1
3
2020-02-26
1
4
2023-06-14
_pdbx_database_status.status_code_cs
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
5459 contains the chemical shifts
PDBJ
Y
PDBJ
2002-08-30
REL
REL
REL
REL
ZN
ZINC ION
50
15
3D_15N-separated_NOESY
4D_13C/15N-separated_NOESY
7.0
ambient
308
K
distance geometry simulated annealing
15
1mM RING-H2 finger domain of EL5 U-15N, 13C; 20mM Tris-HCl buffer, 100mM NaCl, 20uM ZnSO4, 1mM DTT; 90%H2O, 10% D2O
90% H2O/10% D2O
collection
XwinNMR
Deraglio
data analysis
NMRPipe
Brunger
refinement
X-PLOR
3.1
750
Bruker
DMX
ZN
182
2
ZN
ZN
182
A
ZN
183
2
ZN
ZN
183
A
ALA
127
n
1
ALA
127
A
MET
128
n
2
MET
128
A
ASP
129
n
3
ASP
129
A
ASP
130
n
4
ASP
130
A
GLY
131
n
5
GLY
131
A
VAL
132
n
6
VAL
132
A
GLU
133
n
7
GLU
133
A
CYS
134
n
8
CYS
134
A
ALA
135
n
9
ALA
135
A
VAL
136
n
10
VAL
136
A
CYS
137
n
11
CYS
137
A
LEU
138
n
12
LEU
138
A
ALA
139
n
13
ALA
139
A
GLU
140
n
14
GLU
140
A
LEU
141
n
15
LEU
141
A
GLU
142
n
16
GLU
142
A
ASP
143
n
17
ASP
143
A
GLY
144
n
18
GLY
144
A
GLU
145
n
19
GLU
145
A
GLU
146
n
20
GLU
146
A
ALA
147
n
21
ALA
147
A
ARG
148
n
22
ARG
148
A
PHE
149
n
23
PHE
149
A
LEU
150
n
24
LEU
150
A
PRO
151
n
25
PRO
151
A
ARG
152
n
26
ARG
152
A
CYS
153
n
27
CYS
153
A
GLY
154
n
28
GLY
154
A
HIS
155
n
29
HIS
155
A
GLY
156
n
30
GLY
156
A
PHE
157
n
31
PHE
157
A
HIS
158
n
32
HIS
158
A
ALA
159
n
33
ALA
159
A
GLU
160
n
34
GLU
160
A
CYS
161
n
35
CYS
161
A
VAL
162
n
36
VAL
162
A
ASP
163
n
37
ASP
163
A
MET
164
n
38
MET
164
A
TRP
165
n
39
TRP
165
A
LEU
166
n
40
LEU
166
A
GLY
167
n
41
GLY
167
A
SER
168
n
42
SER
168
A
HIS
169
n
43
HIS
169
A
SER
170
n
44
SER
170
A
THR
171
n
45
THR
171
A
CYS
172
n
46
CYS
172
A
PRO
173
n
47
PRO
173
A
LEU
174
n
48
LEU
174
A
CYS
175
n
49
CYS
175
A
ARG
176
n
50
ARG
176
A
LEU
177
n
51
LEU
177
A
THR
178
n
52
THR
178
A
VAL
179
n
53
VAL
179
A
VAL
180
n
54
VAL
180
A
VAL
181
n
55
VAL
181
A
author_defined_assembly
1
monomeric
A
CYS
134
A
SG
CYS
8
1_555
A
ZN
182
B
ZN
ZN
1_555
A
CYS
137
A
SG
CYS
11
1_555
108.1
A
CYS
134
A
SG
CYS
8
1_555
A
ZN
182
B
ZN
ZN
1_555
A
HIS
158
A
ND1
HIS
32
1_555
108.5
A
CYS
137
A
SG
CYS
11
1_555
A
ZN
182
B
ZN
ZN
1_555
A
HIS
158
A
ND1
HIS
32
1_555
111.0
A
CYS
134
A
SG
CYS
8
1_555
A
ZN
182
B
ZN
ZN
1_555
A
CYS
161
A
SG
CYS
35
1_555
112.1
A
CYS
137
A
SG
CYS
11
1_555
A
ZN
182
B
ZN
ZN
1_555
A
CYS
161
A
SG
CYS
35
1_555
108.2
A
HIS
158
A
ND1
HIS
32
1_555
A
ZN
182
B
ZN
ZN
1_555
A
CYS
161
A
SG
CYS
35
1_555
108.9
A
CYS
153
A
SG
CYS
27
1_555
A
ZN
183
C
ZN
ZN
1_555
A
HIS
155
A
ND1
HIS
29
1_555
107.5
A
CYS
153
A
SG
CYS
27
1_555
A
ZN
183
C
ZN
ZN
1_555
A
CYS
172
A
SG
CYS
46
1_555
109.9
A
HIS
155
A
ND1
HIS
29
1_555
A
ZN
183
C
ZN
ZN
1_555
A
CYS
172
A
SG
CYS
46
1_555
109.9
A
CYS
153
A
SG
CYS
27
1_555
A
ZN
183
C
ZN
ZN
1_555
A
CYS
175
A
SG
CYS
49
1_555
107.5
A
HIS
155
A
ND1
HIS
29
1_555
A
ZN
183
C
ZN
ZN
1_555
A
CYS
175
A
SG
CYS
49
1_555
113.6
A
CYS
172
A
SG
CYS
46
1_555
A
ZN
183
C
ZN
ZN
1_555
A
CYS
175
A
SG
CYS
49
1_555
108.5
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ARG
148
A
N
ARG
22
A
O
PHE
157
A
O
PHE
31
1
A
ARG
148
0.268
SIDE CHAIN
1
A
ARG
152
0.122
SIDE CHAIN
1
A
ARG
176
0.272
SIDE CHAIN
2
A
ARG
148
0.079
SIDE CHAIN
2
A
ARG
152
0.253
SIDE CHAIN
2
A
ARG
176
0.178
SIDE CHAIN
3
A
ARG
152
0.218
SIDE CHAIN
3
A
ARG
176
0.318
SIDE CHAIN
4
A
ARG
148
0.206
SIDE CHAIN
4
A
ARG
152
0.258
SIDE CHAIN
4
A
ARG
176
0.298
SIDE CHAIN
5
A
ARG
148
0.230
SIDE CHAIN
5
A
ARG
152
0.212
SIDE CHAIN
5
A
ARG
176
0.249
SIDE CHAIN
6
A
ARG
148
0.178
SIDE CHAIN
6
A
ARG
152
0.251
SIDE CHAIN
6
A
ARG
176
0.307
SIDE CHAIN
7
A
ARG
148
0.259
SIDE CHAIN
7
A
ARG
152
0.317
SIDE CHAIN
7
A
ARG
176
0.316
SIDE CHAIN
8
A
ARG
148
0.222
SIDE CHAIN
8
A
ARG
152
0.170
SIDE CHAIN
8
A
ARG
176
0.196
SIDE CHAIN
9
A
ARG
148
0.291
SIDE CHAIN
9
A
ARG
176
0.311
SIDE CHAIN
10
A
ARG
148
0.297
SIDE CHAIN
10
A
ARG
152
0.311
SIDE CHAIN
10
A
ARG
176
0.256
SIDE CHAIN
11
A
ARG
148
0.305
SIDE CHAIN
11
A
ARG
152
0.237
SIDE CHAIN
11
A
ARG
176
0.246
SIDE CHAIN
12
A
ARG
148
0.305
SIDE CHAIN
12
A
ARG
152
0.318
SIDE CHAIN
12
A
ARG
176
0.309
SIDE CHAIN
13
A
ARG
148
0.274
SIDE CHAIN
13
A
ARG
152
0.289
SIDE CHAIN
13
A
ARG
176
0.280
SIDE CHAIN
14
A
ARG
148
0.310
SIDE CHAIN
14
A
ARG
152
0.255
SIDE CHAIN
14
A
ARG
176
0.282
SIDE CHAIN
15
A
ARG
148
0.175
SIDE CHAIN
15
A
ARG
152
0.318
SIDE CHAIN
15
A
ARG
176
0.316
SIDE CHAIN
1
A
ASP
129
-85.32
45.64
1
A
VAL
136
-98.85
-66.38
1
A
LEU
141
-58.68
107.26
1
A
CYS
153
-120.97
-50.60
1
A
LEU
166
-70.84
-73.37
1
A
SER
168
140.96
-62.61
1
A
SER
170
-94.95
49.27
1
A
ARG
176
102.28
35.46
1
A
THR
178
-41.98
154.92
2
A
LEU
138
73.50
42.07
2
A
LEU
141
-58.39
106.59
2
A
CYS
153
-120.51
-51.78
2
A
SER
168
92.64
-53.71
2
A
SER
170
-102.12
52.70
2
A
ARG
176
101.92
35.72
2
A
THR
178
-41.89
154.73
3
A
VAL
136
-98.97
-66.37
3
A
GLU
146
-114.56
73.44
3
A
CYS
153
-120.40
-52.86
3
A
LEU
166
-64.60
-71.15
3
A
SER
168
127.08
-63.41
3
A
SER
170
-95.82
51.15
3
A
ARG
176
101.31
37.07
3
A
THR
178
-41.99
155.13
4
A
MET
128
-178.65
78.92
4
A
VAL
136
-98.68
-66.34
4
A
LEU
141
-58.63
98.20
4
A
GLU
146
-118.19
79.87
4
A
CYS
153
-120.51
-51.23
4
A
LEU
166
-68.76
-72.47
4
A
SER
168
136.23
-64.81
4
A
SER
170
-95.23
50.59
4
A
ARG
176
102.68
35.29
4
A
THR
178
-41.82
155.22
5
A
MET
128
71.76
82.77
5
A
VAL
136
-98.59
-66.28
5
A
LEU
141
-60.30
97.42
5
A
LEU
166
-77.11
-74.09
5
A
SER
168
144.67
-61.45
5
A
SER
170
-94.58
44.71
5
A
ARG
176
99.25
31.90
6
A
VAL
136
-98.57
-66.13
6
A
LEU
141
-58.32
95.82
6
A
CYS
153
-120.88
-50.63
6
A
PHE
157
-120.38
-169.55
6
A
SER
168
91.27
-52.66
6
A
SER
170
-101.85
43.74
6
A
ARG
176
101.76
42.12
6
A
THR
178
-41.48
153.79
7
A
MET
128
56.56
-173.22
7
A
VAL
136
-98.73
-66.18
7
A
LEU
141
-58.53
95.74
7
A
CYS
153
-120.68
-51.13
7
A
LEU
166
-73.55
-72.84
7
A
SER
168
137.72
-64.45
7
A
SER
170
-96.43
50.49
7
A
ARG
176
102.07
38.03
7
A
THR
178
-41.60
154.96
8
A
VAL
136
-98.73
-66.33
8
A
CYS
153
-120.91
-50.23
8
A
HIS
158
-49.17
154.68
8
A
SER
168
90.96
-53.03
8
A
SER
170
-101.34
48.36
8
A
ARG
176
101.49
41.14
8
A
THR
178
-41.65
150.52
9
A
ASP
130
-104.43
65.33
9
A
VAL
136
-98.76
-66.11
9
A
LEU
141
-58.16
95.63
9
A
CYS
153
-120.99
-51.34
9
A
PHE
157
-123.58
-168.99
9
A
LEU
166
-75.96
-73.98
9
A
SER
168
143.71
-60.48
9
A
SER
170
-94.61
48.35
9
A
ARG
176
101.82
37.67
9
A
THR
178
-42.17
154.80
10
A
CYS
134
-50.85
109.67
10
A
VAL
136
-98.59
-66.31
10
A
CYS
153
-120.47
-51.26
10
A
LEU
166
-68.51
-72.22
10
A
SER
168
134.12
-63.39
10
A
SER
170
-94.87
48.91
10
A
ARG
176
102.12
35.46
10
A
THR
178
-42.04
155.16
11
A
MET
128
52.28
-174.23
11
A
VAL
136
-98.66
-66.37
11
A
CYS
153
-120.73
-52.09
11
A
SER
168
88.88
-52.02
11
A
SER
170
-99.56
53.58
11
A
ARG
176
102.00
36.37
11
A
THR
178
-42.05
154.95
12
A
MET
128
-160.35
64.73
12
A
VAL
136
-98.69
-66.34
12
A
CYS
153
-120.48
-51.66
12
A
SER
168
91.33
-53.21
12
A
SER
170
-99.29
52.11
12
A
ARG
176
101.41
36.20
12
A
THR
178
-42.14
155.17
13
A
MET
128
-156.42
69.19
13
A
LEU
138
78.10
41.55
13
A
LEU
166
-77.66
-74.17
13
A
SER
168
144.02
-58.74
13
A
SER
170
-96.37
42.52
13
A
ARG
176
100.29
32.96
14
A
MET
128
47.44
95.74
14
A
ASP
130
-98.52
40.53
14
A
VAL
136
-98.69
-66.47
14
A
LEU
141
-58.26
101.26
14
A
CYS
153
-120.99
-51.85
14
A
HIS
158
-49.00
157.25
14
A
LEU
166
-74.06
-73.39
14
A
SER
168
139.54
-62.51
14
A
SER
170
-95.03
36.15
14
A
ARG
176
100.24
29.82
15
A
MET
128
67.84
123.50
15
A
VAL
136
-98.85
-66.25
15
A
LEU
141
-58.28
96.99
15
A
CYS
153
-120.79
-51.94
15
A
LEU
166
-74.63
-73.62
15
A
SER
168
143.00
-60.74
15
A
SER
170
-94.46
48.91
15
A
ARG
176
101.88
36.17
15
A
THR
178
-41.95
154.68
RING-H2 finger domain of EL5
1
N
N
2
N
N
2
N
N
A
GLU
160
A
GLU
34
HELX_P
A
TRP
165
A
TRP
39
1
1
6
metalc
2.293
A
CYS
134
A
SG
CYS
8
1_555
A
ZN
182
B
ZN
ZN
1_555
metalc
2.278
A
CYS
137
A
SG
CYS
11
1_555
A
ZN
182
B
ZN
ZN
1_555
metalc
2.277
A
CYS
153
A
SG
CYS
27
1_555
A
ZN
183
C
ZN
ZN
1_555
metalc
2.099
A
HIS
155
A
ND1
HIS
29
1_555
A
ZN
183
C
ZN
ZN
1_555
metalc
2.082
A
HIS
158
A
ND1
HIS
32
1_555
A
ZN
182
B
ZN
ZN
1_555
metalc
2.300
A
CYS
161
A
SG
CYS
35
1_555
A
ZN
182
B
ZN
ZN
1_555
metalc
2.301
A
CYS
172
A
SG
CYS
46
1_555
A
ZN
183
C
ZN
ZN
1_555
metalc
2.309
A
CYS
175
A
SG
CYS
49
1_555
A
ZN
183
C
ZN
ZN
1_555
DNA BINDING PROTEIN
RING-H2 finger, ubiquitin ligase, DNA binding protein
EL5_ORYSA
UNP
1
129
Q9LRB7
DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV
129
181
1IYM
129
181
Q9LRB7
A
1
3
55
1
cloning artifact
ALA
127
1IYM
A
Q9LRB7
UNP
1
1
cloning artifact
MET
128
1IYM
A
Q9LRB7
UNP
2
2
anti-parallel
A
ARG
148
A
ARG
22
A
PHE
149
A
PHE
23
A
GLY
156
A
GLY
30
A
PHE
157
A
PHE
31
BINDING SITE FOR RESIDUE ZN A 182
A
ZN
182
Software
4
BINDING SITE FOR RESIDUE ZN A 183
A
ZN
183
Software
4
A
CYS
134
A
CYS
8
4
1_555
A
CYS
137
A
CYS
11
4
1_555
A
HIS
158
A
HIS
32
4
1_555
A
CYS
161
A
CYS
35
4
1_555
A
CYS
153
A
CYS
27
4
1_555
A
HIS
155
A
HIS
29
4
1_555
A
CYS
172
A
CYS
46
4
1_555
A
CYS
175
A
CYS
49
4
1_555