0.018995
0.000000
0.000000
0.000000
0.017756
0.000000
0.000000
0.000000
0.023940
0.00000
0.00000
0.00000
Leonidas, D.D.
Boix, E.
Prill, R.
Suzuki, M.
Turton, R.
Minson, K.
Swaminathan, G.J.
Youle, R.J.
Acharya, K.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
52.646
56.318
41.771
C10 H15 N5 O10 P2
427.201
n
ADENOSINE-5'-DIPHOSPHATE
non-polymer
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
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
276
15009
10.1074/JBC.M010585200
11154698
Mapping the Ribonucleolytic Active Site of Eosinophil-Derived Neurotoxin (Edn): High Resolution Crystal Structures of Edn Complexes with Adenylic Nucleotide Inhibitors
2001
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
260
540
10.1006/JMBI.1996.0420
8759319
X-Ray Crystallographic Structure of Recombinant Eosinophil-Derived Neurotoxin at 1.83 A Resolution
1996
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
IMAGE PLATE
1999-03-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS
15611.750
EOSINOPHIL-DERIVED NEUROTOXIN
3.1.27.5
1
man
polymer
427.201
ADENOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
18.015
water
132
nat
water
RNASE-2, RNASE-US, EDN
no
no
MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVP
LIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII
MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVP
LIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII
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
HUMAN
BLOOD
sample
EOSINOPHIL
SECRETORY GRANULES
9606
GRANULE
HOMO SAPIENS
562
ESCHERICHIA COLI
1
1.34
44
6.50
1.5M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5, 5% ETHANOL
struct
repository
Initial release
Version format compliance
Version format compliance
Data collection
Structure summary
1
0
2001-05-31
1
1
2011-05-08
1
2
2011-07-13
1
3
2018-05-30
_struct.title
EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - SULPHATE COMPLEX
EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-2'-5'-DIPHOSPHATE COMPLEX
EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-3'-5'-DIPHOSPHATE COMPLEX
PDBE
Y
PDBE
2001-01-02
REL
ADP
ADENOSINE-5'-DIPHOSPHATE
HOH
water
ADP
999
2
ADP
ADP
999
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2077
3
HOH
HOH
2077
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2084
3
HOH
HOH
2084
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2092
3
HOH
HOH
2092
A
HOH
2093
3
HOH
HOH
2093
A
HOH
2094
3
HOH
HOH
2094
A
HOH
2095
3
HOH
HOH
2095
A
HOH
2096
3
HOH
HOH
2096
A
HOH
2097
3
HOH
HOH
2097
A
HOH
2098
3
HOH
HOH
2098
A
HOH
2099
3
HOH
HOH
2099
A
HOH
2100
3
HOH
HOH
2100
A
HOH
2101
3
HOH
HOH
2101
A
HOH
2102
3
HOH
HOH
2102
A
HOH
2103
3
HOH
HOH
2103
A
HOH
2104
3
HOH
HOH
2104
A
HOH
2105
3
HOH
HOH
2105
A
HOH
2106
3
HOH
HOH
2106
A
HOH
2107
3
HOH
HOH
2107
A
HOH
2108
3
HOH
HOH
2108
A
HOH
2109
3
HOH
HOH
2109
A
HOH
2110
3
HOH
HOH
2110
A
HOH
2111
3
HOH
HOH
2111
A
HOH
2112
3
HOH
HOH
2112
A
HOH
2113
3
HOH
HOH
2113
A
HOH
2114
3
HOH
HOH
2114
A
HOH
2115
3
HOH
HOH
2115
A
HOH
2116
3
HOH
HOH
2116
A
HOH
2117
3
HOH
HOH
2117
A
HOH
2118
3
HOH
HOH
2118
A
HOH
2119
3
HOH
HOH
2119
A
HOH
2120
3
HOH
HOH
2120
A
HOH
2121
3
HOH
HOH
2121
A
HOH
2122
3
HOH
HOH
2122
A
HOH
2123
3
HOH
HOH
2123
A
HOH
2124
3
HOH
HOH
2124
A
HOH
2125
3
HOH
HOH
2125
A
HOH
2126
3
HOH
HOH
2126
A
HOH
2127
3
HOH
HOH
2127
A
HOH
2128
3
HOH
HOH
2128
A
HOH
2129
3
HOH
HOH
2129
A
HOH
2130
3
HOH
HOH
2130
A
HOH
2131
3
HOH
HOH
2131
A
HOH
2132
3
HOH
HOH
2132
A
MET
0
n
1
MET
0
A
LYS
1
n
2
LYS
1
A
PRO
2
n
3
PRO
2
A
PRO
3
n
4
PRO
3
A
GLN
4
n
5
GLN
4
A
PHE
5
n
6
PHE
5
A
THR
6
n
7
THR
6
A
TRP
7
n
8
TRP
7
A
ALA
8
n
9
ALA
8
A
GLN
9
n
10
GLN
9
A
TRP
10
n
11
TRP
10
A
PHE
11
n
12
PHE
11
A
GLU
12
n
13
GLU
12
A
THR
13
n
14
THR
13
A
GLN
14
n
15
GLN
14
A
HIS
15
n
16
HIS
15
A
ILE
16
n
17
ILE
16
A
ASN
17
n
18
ASN
17
A
MET
18
n
19
MET
18
A
THR
19
n
20
THR
19
A
SER
20
n
21
SER
20
A
GLN
21
n
22
GLN
21
A
GLN
22
n
23
GLN
22
A
CYS
23
n
24
CYS
23
A
THR
24
n
25
THR
24
A
ASN
25
n
26
ASN
25
A
ALA
26
n
27
ALA
26
A
MET
27
n
28
MET
27
A
GLN
28
n
29
GLN
28
A
VAL
29
n
30
VAL
29
A
ILE
30
n
31
ILE
30
A
ASN
31
n
32
ASN
31
A
ASN
32
n
33
ASN
32
A
TYR
33
n
34
TYR
33
A
GLN
34
n
35
GLN
34
A
ARG
35
n
36
ARG
35
A
ARG
36
n
37
ARG
36
A
CYS
37
n
38
CYS
37
A
LYS
38
n
39
LYS
38
A
ASN
39
n
40
ASN
39
A
GLN
40
n
41
GLN
40
A
ASN
41
n
42
ASN
41
A
THR
42
n
43
THR
42
A
PHE
43
n
44
PHE
43
A
LEU
44
n
45
LEU
44
A
LEU
45
n
46
LEU
45
A
THR
46
n
47
THR
46
A
THR
47
n
48
THR
47
A
PHE
48
n
49
PHE
48
A
ALA
49
n
50
ALA
49
A
ASN
50
n
51
ASN
50
A
VAL
51
n
52
VAL
51
A
VAL
52
n
53
VAL
52
A
ASN
53
n
54
ASN
53
A
VAL
54
n
55
VAL
54
A
CYS
55
n
56
CYS
55
A
GLY
56
n
57
GLY
56
A
ASN
57
n
58
ASN
57
A
PRO
58
n
59
PRO
58
A
ASN
59
n
60
ASN
59
A
MET
60
n
61
MET
60
A
THR
61
n
62
THR
61
A
CYS
62
n
63
CYS
62
A
PRO
63
n
64
PRO
63
A
SER
64
n
65
SER
64
A
ASN
65
n
66
ASN
65
A
LYS
66
n
67
LYS
66
A
THR
67
n
68
THR
67
A
ARG
68
n
69
ARG
68
A
LYS
69
n
70
LYS
69
A
ASN
70
n
71
ASN
70
A
CYS
71
n
72
CYS
71
A
HIS
72
n
73
HIS
72
A
HIS
73
n
74
HIS
73
A
SER
74
n
75
SER
74
A
GLY
75
n
76
GLY
75
A
SER
76
n
77
SER
76
A
GLN
77
n
78
GLN
77
A
VAL
78
n
79
VAL
78
A
PRO
79
n
80
PRO
79
A
LEU
80
n
81
LEU
80
A
ILE
81
n
82
ILE
81
A
HIS
82
n
83
HIS
82
A
CYS
83
n
84
CYS
83
A
ASN
84
n
85
ASN
84
A
LEU
85
n
86
LEU
85
A
THR
86
n
87
THR
86
A
THR
87
n
88
THR
87
A
PRO
88
n
89
PRO
88
A
SER
89
n
90
SER
89
A
PRO
90
n
91
PRO
90
A
GLN
91
n
92
GLN
91
A
ASN
92
n
93
ASN
92
A
ILE
93
n
94
ILE
93
A
SER
94
n
95
SER
94
A
ASN
95
n
96
ASN
95
A
CYS
96
n
97
CYS
96
A
ARG
97
n
98
ARG
97
A
TYR
98
n
99
TYR
98
A
ALA
99
n
100
ALA
99
A
GLN
100
n
101
GLN
100
A
THR
101
n
102
THR
101
A
PRO
102
n
103
PRO
102
A
ALA
103
n
104
ALA
103
A
ASN
104
n
105
ASN
104
A
MET
105
n
106
MET
105
A
PHE
106
n
107
PHE
106
A
TYR
107
n
108
TYR
107
A
ILE
108
n
109
ILE
108
A
VAL
109
n
110
VAL
109
A
ALA
110
n
111
ALA
110
A
CYS
111
n
112
CYS
111
A
ASP
112
n
113
ASP
112
A
ASN
113
n
114
ASN
113
A
ARG
114
n
115
ARG
114
A
ASP
115
n
116
ASP
115
A
GLN
116
n
117
GLN
116
A
ARG
117
n
118
ARG
117
A
ARG
118
n
119
ARG
118
A
ASP
119
n
120
ASP
119
A
PRO
120
n
121
PRO
120
A
PRO
121
n
122
PRO
121
A
GLN
122
n
123
GLN
122
A
TYR
123
n
124
TYR
123
A
PRO
124
n
125
PRO
124
A
VAL
125
n
126
VAL
125
A
VAL
126
n
127
VAL
126
A
PRO
127
n
128
PRO
127
A
VAL
128
n
129
VAL
128
A
HIS
129
n
130
HIS
129
A
LEU
130
n
131
LEU
130
A
ASP
131
n
132
ASP
131
A
ARG
132
n
133
ARG
132
A
ILE
133
n
134
ILE
133
A
ILE
134
n
135
ILE
134
A
author_and_software_defined_assembly
PQS
1
monomeric
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
PHE
43
A
N
PHE
44
A
O
ILE
81
A
O
ILE
82
A
N
THR
86
A
N
THR
87
A
O
ARG
97
A
O
ARG
98
A
N
HIS
72
A
N
HIS
73
A
O
VAL
109
A
O
VAL
110
A
N
ASP
112
A
N
ASP
113
A
O
VAL
126
A
O
VAL
127
1
A
ARG
36
175.57
146.04
1
A
LYS
66
-48.86
-18.68
1
A
ASN
92
-178.37
103.74
PROTEIN_REP
TOPHCSDX.PR
PAR
TOP
LIG
LIG
16.3
0.00
0.00
0.00
0.00
0.00
0.00
BULK SOLVENT MODEL USED
0.253
0.010
0.193
0.193
1.80
30.00
604
11720
5.2
97.7
RANDOM
10000000.00
0.001000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.26
0.19
5.00
0.24
0.19
1.80
30.00
132
1248
27
0
1089
0.009
1.5
27.7
0.79
1.40
1.50
2.09
2.00
2.54
2.00
3.83
2.50
0.328
0.038
0.281
1.91
76
1674
6
4.3
89.9
14.1
1.800
30.000
1HI5
11749
2.000
0.06400
1
10.7000
5.000
97.4
1.80
1.86
4.200
0.26300
1
82.9
refinement
X-PLOR
3.851
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
EOSINOPHIL-DERIVED NEUROTOXIN (E.C.3.1.27.5)
Eosinophil-derived Neurotoxin (EDN) - Adenosine-5'-Diphosphate Complex
1
N
N
2
N
N
3
N
N
A
THR
6
A
THR
7
HELX_P
A
ILE
16
A
ILE
17
1
1
11
A
GLN
22
A
GLN
23
HELX_P
A
ARG
35
A
ARG
36
1
2
14
A
THR
47
A
THR
48
HELX_P
A
CYS
55
A
CYS
56
1
3
9
A
ASN
92
A
ASN
93
HELX_P
A
CYS
96
A
CYS
97
5
4
5
disulf
2.032
A
CYS
23
A
SG
CYS
24
1_555
A
CYS
83
A
SG
CYS
84
1_555
disulf
2.033
A
CYS
37
A
SG
CYS
38
1_555
A
CYS
96
A
SG
CYS
97
1_555
disulf
2.037
A
CYS
55
A
SG
CYS
56
1_555
A
CYS
111
A
SG
CYS
112
1_555
disulf
2.031
A
CYS
62
A
SG
CYS
63
1_555
A
CYS
71
A
SG
CYS
72
1_555
HYDROLASE
HYDROLASE, RNASE-2, RNASE US, RIBONUCLEASE
RNKD_HUMAN
UNP
1
P10153
27
161
1HI5
0
134
P10153
A
1
1
135
1
cloning artifact
MET
0
1HI5
A
P10153
UNP
1
3
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
40
A
GLN
41
A
LEU
44
A
LEU
45
A
VAL
78
A
VAL
79
A
THR
87
A
THR
88
A
ARG
97
A
ARG
98
A
MET
105
A
MET
106
A
ASN
59
A
ASN
60
A
MET
60
A
MET
61
A
CYS
71
A
CYS
72
A
HIS
73
A
HIS
74
A
TYR
107
A
TYR
108
A
ASN
113
A
ASN
114
A
VAL
125
A
VAL
126
A
ILE
133
A
ILE
134
BINDING SITE FOR RESIDUE ADP A 999
Software
12
A
GLN
14
A
GLN
15
12
1_555
A
HIS
15
A
HIS
16
12
1_555
A
LYS
38
A
LYS
39
12
1_555
A
GLN
40
A
GLN
41
12
1_555
A
HIS
82
A
HIS
83
12
1_555
A
HIS
129
A
HIS
130
12
1_555
A
LEU
130
A
LEU
131
12
1_555
A
HOH
2016
C
HOH
12
1_555
A
HOH
2052
C
HOH
12
1_555
A
HOH
2123
C
HOH
12
1_555
A
HOH
2128
C
HOH
12
1_555
A
HOH
2131
C
HOH
12
1_555
19
P 21 21 21