0.014988
0.008653
0.000000
0.000000
0.017307
0.000000
0.000000
0.000000
0.011752
0.00000
0.00000
0.00000
Cha, S.-S.
Kim, J.-S.
Cho, H.-S.
Oh, B.-H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
9
90.00
90.00
120.00
66.720
66.720
85.090
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
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
273
2153
2160
10.1074/jbc.273.4.2153
9442056
High resolution crystal structure of a human tumor necrosis factor-alpha mutant with low systemic toxicity.
1998
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
264
17595
The Structure of Tumor Necrosis Factor-Alpha at 2.6 A Resolution. Implications for Receptor Binding
1989
10.2210/pdb4tsv/pdb
pdb_00004tsv
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
1
IMAGE PLATE
1995-12
MACSCIENCE
GRAPHITE(002)
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
MACSCIENCE M18X
16578.797
TUMOR NECROSIS FACTOR-ALPHA
DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F
1
man
polymer
18.015
water
70
nat
water
no
no
PSDKPVAHVVANPQAEGQLQWSNRRANALLANGVELRDNQLVVPIEGLFLIYSQVLFKGQGCPSTHVLLTHTISRIAVSY
QTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
PSDKPVAHVVANPQAEGQLQWSNRRANALLANGVELRDNQLVVPIEGLFLIYSQVLFKGQGCPSTHVLLTHTISRIAVSY
QTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
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
human
Homo
Escherichia
Escherichia coli
sample
BL21
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
BL21
1
2.20
44.02
6.8
1.4 M SODIUM FORMATE, pH 6.8
diffrn_source
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Data collection
Database references
1
0
1998-12-30
1
1
2008-03-25
1
2
2011-07-13
1
3
2018-04-04
1
4
2021-11-03
_diffrn_source.type
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
BNL
1997-10-29
REL
REL
HOH
water
HOH
201
2
HOH
HOH
201
A
HOH
202
2
HOH
HOH
202
A
HOH
204
2
HOH
HOH
204
A
HOH
205
2
HOH
HOH
205
A
HOH
206
2
HOH
HOH
206
A
HOH
207
2
HOH
HOH
207
A
HOH
208
2
HOH
HOH
208
A
HOH
209
2
HOH
HOH
209
A
HOH
210
2
HOH
HOH
210
A
HOH
211
2
HOH
HOH
211
A
HOH
212
2
HOH
HOH
212
A
HOH
213
2
HOH
HOH
213
A
HOH
214
2
HOH
HOH
214
A
HOH
215
2
HOH
HOH
215
A
HOH
216
2
HOH
HOH
216
A
HOH
217
2
HOH
HOH
217
A
HOH
218
2
HOH
HOH
218
A
HOH
219
2
HOH
HOH
219
A
HOH
220
2
HOH
HOH
220
A
HOH
221
2
HOH
HOH
221
A
HOH
222
2
HOH
HOH
222
A
HOH
223
2
HOH
HOH
223
A
HOH
224
2
HOH
HOH
224
A
HOH
225
2
HOH
HOH
225
A
HOH
226
2
HOH
HOH
226
A
HOH
227
2
HOH
HOH
227
A
HOH
228
2
HOH
HOH
228
A
HOH
229
2
HOH
HOH
229
A
HOH
230
2
HOH
HOH
230
A
HOH
231
2
HOH
HOH
231
A
HOH
232
2
HOH
HOH
232
A
HOH
233
2
HOH
HOH
233
A
HOH
234
2
HOH
HOH
234
A
HOH
235
2
HOH
HOH
235
A
HOH
236
2
HOH
HOH
236
A
HOH
237
2
HOH
HOH
237
A
HOH
238
2
HOH
HOH
238
A
HOH
239
2
HOH
HOH
239
A
HOH
240
2
HOH
HOH
240
A
HOH
241
2
HOH
HOH
241
A
HOH
242
2
HOH
HOH
242
A
HOH
243
2
HOH
HOH
243
A
HOH
244
2
HOH
HOH
244
A
HOH
245
2
HOH
HOH
245
A
HOH
246
2
HOH
HOH
246
A
HOH
247
2
HOH
HOH
247
A
HOH
248
2
HOH
HOH
248
A
HOH
249
2
HOH
HOH
249
A
HOH
250
2
HOH
HOH
250
A
HOH
251
2
HOH
HOH
251
A
HOH
252
2
HOH
HOH
252
A
HOH
253
2
HOH
HOH
253
A
HOH
254
2
HOH
HOH
254
A
HOH
255
2
HOH
HOH
255
A
HOH
256
2
HOH
HOH
256
A
HOH
257
2
HOH
HOH
257
A
HOH
258
2
HOH
HOH
258
A
HOH
259
2
HOH
HOH
259
A
HOH
260
2
HOH
HOH
260
A
HOH
261
2
HOH
HOH
261
A
HOH
262
2
HOH
HOH
262
A
HOH
263
2
HOH
HOH
263
A
HOH
264
2
HOH
HOH
264
A
HOH
265
2
HOH
HOH
265
A
HOH
266
2
HOH
HOH
266
A
HOH
267
2
HOH
HOH
267
A
HOH
268
2
HOH
HOH
268
A
HOH
269
2
HOH
HOH
269
A
HOH
270
2
HOH
HOH
270
A
HOH
271
2
HOH
HOH
271
A
n
1
8
A
n
2
9
A
ASP
10
n
3
ASP
10
A
LYS
11
n
4
LYS
11
A
PRO
12
n
5
PRO
12
A
VAL
13
n
6
VAL
13
A
ALA
14
n
7
ALA
14
A
HIS
15
n
8
HIS
15
A
VAL
16
n
9
VAL
16
A
VAL
17
n
10
VAL
17
A
ALA
18
n
11
ALA
18
A
ASN
19
n
12
ASN
19
A
PRO
20
n
13
PRO
20
A
GLN
21
n
14
GLN
21
A
ALA
22
n
15
ALA
22
A
GLU
23
n
16
GLU
23
A
GLY
24
n
17
GLY
24
A
GLN
25
n
18
GLN
25
A
LEU
26
n
19
LEU
26
A
GLN
27
n
20
GLN
27
A
TRP
28
n
21
TRP
28
A
SER
29
n
22
SER
29
A
ASN
30
n
23
ASN
30
A
ARG
31
n
24
ARG
31
A
ARG
32
n
25
ARG
32
A
ALA
33
n
26
ALA
33
A
ASN
34
n
27
ASN
34
A
ALA
35
n
28
ALA
35
A
LEU
36
n
29
LEU
36
A
LEU
37
n
30
LEU
37
A
ALA
38
n
31
ALA
38
A
ASN
39
n
32
ASN
39
A
GLY
40
n
33
GLY
40
A
VAL
41
n
34
VAL
41
A
GLU
42
n
35
GLU
42
A
LEU
43
n
36
LEU
43
A
ARG
44
n
37
ARG
44
A
ASP
45
n
38
ASP
45
A
ASN
46
n
39
ASN
46
A
GLN
47
n
40
GLN
47
A
LEU
48
n
41
LEU
48
A
VAL
49
n
42
VAL
49
A
VAL
50
n
43
VAL
50
A
PRO
51
n
44
PRO
51
A
ILE
52
n
45
ILE
52
A
GLU
53
n
46
GLU
53
A
GLY
54
n
47
GLY
54
A
LEU
55
n
48
LEU
55
A
PHE
56
n
49
PHE
56
A
LEU
57
n
50
LEU
57
A
ILE
58
n
51
ILE
58
A
TYR
59
n
52
TYR
59
A
SER
60
n
53
SER
60
A
GLN
61
n
54
GLN
61
A
VAL
62
n
55
VAL
62
A
LEU
63
n
56
LEU
63
A
PHE
64
n
57
PHE
64
A
LYS
65
n
58
LYS
65
A
GLY
66
n
59
GLY
66
A
GLN
67
n
60
GLN
67
A
GLY
68
n
61
GLY
68
A
CYS
69
n
62
CYS
69
A
PRO
70
n
63
PRO
70
A
SER
71
n
64
SER
71
A
THR
72
n
65
THR
72
A
HIS
73
n
66
HIS
73
A
VAL
74
n
67
VAL
74
A
LEU
75
n
68
LEU
75
A
LEU
76
n
69
LEU
76
A
THR
77
n
70
THR
77
A
HIS
78
n
71
HIS
78
A
THR
79
n
72
THR
79
A
ILE
80
n
73
ILE
80
A
SER
81
n
74
SER
81
A
ARG
82
n
75
ARG
82
A
ILE
83
n
76
ILE
83
A
ALA
84
n
77
ALA
84
A
VAL
85
n
78
VAL
85
A
SER
86
n
79
SER
86
A
TYR
87
n
80
TYR
87
A
GLN
88
n
81
GLN
88
A
THR
89
n
82
THR
89
A
LYS
90
n
83
LYS
90
A
VAL
91
n
84
VAL
91
A
ASN
92
n
85
ASN
92
A
LEU
93
n
86
LEU
93
A
LEU
94
n
87
LEU
94
A
SER
95
n
88
SER
95
A
ALA
96
n
89
ALA
96
A
ILE
97
n
90
ILE
97
A
LYS
98
n
91
LYS
98
A
SER
99
n
92
SER
99
A
PRO
100
n
93
PRO
100
A
CYS
101
n
94
CYS
101
A
GLN
102
n
95
GLN
102
A
ARG
103
n
96
ARG
103
A
GLU
104
n
97
GLU
104
A
THR
105
n
98
THR
105
A
PRO
106
n
99
PRO
106
A
GLU
107
n
100
GLU
107
A
GLY
108
n
101
GLY
108
A
ALA
109
n
102
ALA
109
A
GLU
110
n
103
GLU
110
A
ALA
111
n
104
ALA
111
A
LYS
112
n
105
LYS
112
A
PRO
113
n
106
PRO
113
A
TRP
114
n
107
TRP
114
A
TYR
115
n
108
TYR
115
A
GLU
116
n
109
GLU
116
A
PRO
117
n
110
PRO
117
A
ILE
118
n
111
ILE
118
A
TYR
119
n
112
TYR
119
A
LEU
120
n
113
LEU
120
A
GLY
121
n
114
GLY
121
A
GLY
122
n
115
GLY
122
A
VAL
123
n
116
VAL
123
A
PHE
124
n
117
PHE
124
A
GLN
125
n
118
GLN
125
A
LEU
126
n
119
LEU
126
A
GLU
127
n
120
GLU
127
A
LYS
128
n
121
LYS
128
A
GLY
129
n
122
GLY
129
A
ASP
130
n
123
ASP
130
A
ARG
131
n
124
ARG
131
A
LEU
132
n
125
LEU
132
A
SER
133
n
126
SER
133
A
ALA
134
n
127
ALA
134
A
GLU
135
n
128
GLU
135
A
ILE
136
n
129
ILE
136
A
ASN
137
n
130
ASN
137
A
ARG
138
n
131
ARG
138
A
PRO
139
n
132
PRO
139
A
ASP
140
n
133
ASP
140
A
TYR
141
n
134
TYR
141
A
LEU
142
n
135
LEU
142
A
ASP
143
n
136
ASP
143
A
PHE
144
n
137
PHE
144
A
ALA
145
n
138
ALA
145
A
GLU
146
n
139
GLU
146
A
SER
147
n
140
SER
147
A
GLY
148
n
141
GLY
148
A
GLN
149
n
142
GLN
149
A
VAL
150
n
143
VAL
150
A
TYR
151
n
144
TYR
151
A
PHE
152
n
145
PHE
152
A
GLY
153
n
146
GLY
153
A
ILE
154
n
147
ILE
154
A
ILE
155
n
148
ILE
155
A
ALA
156
n
149
ALA
156
A
LEU
157
n
150
LEU
157
A
author_and_software_defined_assembly
PISA,PQS
3
trimeric
5860
-36
18080
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_845
-y+3,x-y-1,z
crystal symmetry operation
233.5200000000
-57.7812149405
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_985
-x+y+4,-x+3,z
crystal symmetry operation
166.8000000000
173.3436448215
0.0000000000
A
O
LEU
36
A
O
LEU
29
A
N
HIS
15
A
N
HIS
8
A
O
ALA
14
A
O
ALA
7
A
N
ILE
154
A
N
ILE
147
A
O
TYR
151
A
O
TYR
144
A
N
GLN
61
A
N
GLN
54
A
O
GLY
54
A
O
GLY
47
A
N
LEU
126
A
N
LEU
119
A
O
GLU
42
A
O
GLU
35
A
N
VAL
49
A
N
VAL
42
A
O
ARG
131
A
O
ARG
124
A
N
ILE
83
A
N
ILE
76
A
O
LEU
76
A
O
LEU
69
A
N
LYS
98
A
N
LYS
91
1
A
CG
ASP
10
A
CG
ASP
3
1
Y
1
A
OD1
ASP
10
A
OD1
ASP
3
1
Y
1
A
OD2
ASP
10
A
OD2
ASP
3
1
Y
1
A
CG
GLU
23
A
CG
GLU
16
1
Y
1
A
CD
GLU
23
A
CD
GLU
16
1
Y
1
A
OE1
GLU
23
A
OE1
GLU
16
1
Y
1
A
OE2
GLU
23
A
OE2
GLU
16
1
Y
1
A
CG
GLN
25
A
CG
GLN
18
1
Y
1
A
CD
GLN
25
A
CD
GLN
18
1
Y
1
A
OE1
GLN
25
A
OE1
GLN
18
1
Y
1
A
NE2
GLN
25
A
NE2
GLN
18
1
Y
1
A
CG
TYR
87
A
CG
TYR
80
1
Y
1
A
CD1
TYR
87
A
CD1
TYR
80
1
Y
1
A
CD2
TYR
87
A
CD2
TYR
80
1
Y
1
A
CE1
TYR
87
A
CE1
TYR
80
1
Y
1
A
CE2
TYR
87
A
CE2
TYR
80
1
Y
1
A
CZ
TYR
87
A
CZ
TYR
80
1
Y
1
A
OH
TYR
87
A
OH
TYR
80
1
Y
1
A
CG
GLN
88
A
CG
GLN
81
1
Y
1
A
CD
GLN
88
A
CD
GLN
81
1
Y
1
A
OE1
GLN
88
A
OE1
GLN
81
1
Y
1
A
NE2
GLN
88
A
NE2
GLN
81
1
Y
1
A
CG
ARG
103
A
CG
ARG
96
1
Y
1
A
CD
ARG
103
A
CD
ARG
96
1
Y
1
A
NE
ARG
103
A
NE
ARG
96
1
Y
1
A
CZ
ARG
103
A
CZ
ARG
96
1
Y
1
A
NH1
ARG
103
A
NH1
ARG
96
1
Y
1
A
NH2
ARG
103
A
NH2
ARG
96
1
Y
1
A
CG
GLU
107
A
CG
GLU
100
1
Y
1
A
CD
GLU
107
A
CD
GLU
100
1
Y
1
A
OE1
GLU
107
A
OE1
GLU
100
1
Y
1
A
OE2
GLU
107
A
OE2
GLU
100
1
Y
1
A
CG
GLU
110
A
CG
GLU
103
1
Y
1
A
CD
GLU
110
A
CD
GLU
103
1
Y
1
A
OE1
GLU
110
A
OE1
GLU
103
1
Y
1
A
OE2
GLU
110
A
OE2
GLU
103
1
Y
1
A
CG
GLU
146
A
CG
GLU
139
1
Y
1
A
CD
GLU
146
A
CD
GLU
139
1
Y
1
A
OE1
GLU
146
A
OE1
GLU
139
1
Y
1
A
OE2
GLU
146
A
OE2
GLU
139
1
Y
1
A
O
LEU
157
A
O
LEU
150
1
Y
1
A
PRO
8
A
PRO
1
1
Y
1
A
SER
9
A
SER
2
1
Y
1
A
A
O
N
PRO
SER
70
71
0.70
1
A
A
O
N
ILE
ALA
83
84
1.74
1
A
A
CA
O
THR
HOH
105
261
2.18
1
A
A
NZ
O
LYS
PRO
98
117
2.19
1
A
PRO
70
-126.21
1
A
ILE
83
43.22
1
A
A
C
N
THR
HIS
72
73
2.87
1
A
A
C
N
GLU
THR
104
105
1.99
1
A
A
C
N
GLU
ALA
110
111
1.74
1
30.55
2.20
117.20
147.75
A
A
A
CA
C
N
PRO
PRO
SER
70
70
71
Y
1
-89.70
1.60
122.70
33.00
A
A
A
O
C
N
PRO
PRO
SER
70
70
71
Y
1
18.94
2.50
121.70
140.64
A
A
A
C
N
CA
PRO
SER
SER
70
71
71
Y
1
-43.78
1.60
122.70
78.92
A
A
A
O
C
N
ILE
ILE
ALA
83
83
84
Y
1
A
A
C
N
ILE
ALA
83
84
0.158
0.023
1.336
1.494
Y
1
A
A
NH2
OG
ARG
SER
32
71
1.91
1_555
6_985
1
A
LEU
37
-161.09
77.22
1
A
CYS
69
-117.55
60.01
1
A
PRO
70
-26.97
105.26
1
A
SER
71
56.56
-31.86
1
A
ILE
83
-115.95
64.85
1
A
ALA
84
-42.43
153.91
1
A
VAL
85
78.36
-95.80
1
A
SER
86
176.89
79.49
1
A
TYR
87
80.46
50.82
1
A
GLN
88
-108.22
-155.63
1
A
PRO
106
-23.99
87.93
1
A
GLU
107
45.82
-158.61
1
A
SER
147
57.07
-151.16
0.262
0.2
0.2
1.8
8
13102
10
99.9
1
1
0.3
1.8
8
70
1187
0
0
1117
0.015
2.177
1.8
10
4TSV
13102
1.0
0.04
1
99.9
data reduction
DENZO
data scaling
SCALEPACK
model building
X-PLOR
3.0
refinement
X-PLOR
3.01
phasing
X-PLOR
3.0
HIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT
1
N
N
2
N
N
A
PRO
139
A
PRO
132
HELX_P
A
TYR
141
A
TYR
134
5
1
3
disulf
1.963
A
CYS
69
A
SG
CYS
62
1_555
A
CYS
101
A
SG
CYS
94
1_555
LYMPHOKINE
LYMPHOKINE, TNF
TNFA_HUMAN
UNP
1
1
P01375
MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFGVIGPQREEFPRDLSLISPLAQAVRSS
SRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIA
VSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
84
233
4TSV
8
157
P01375
A
1
1
150
1
LEU
engineered mutation
SER
29
4TSV
A
P01375
UNP
105
22
1
SER
engineered mutation
ILE
52
4TSV
A
P01375
UNP
128
45
1
TYR
engineered mutation
PHE
56
4TSV
A
P01375
UNP
132
49
5
2
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
36
A
LEU
29
A
ALA
38
A
ALA
31
A
VAL
13
A
VAL
6
A
VAL
17
A
VAL
10
A
TYR
151
A
TYR
144
A
ALA
156
A
ALA
149
A
GLY
54
A
GLY
47
A
GLN
67
A
GLN
60
A
PRO
113
A
PRO
106
A
LEU
126
A
LEU
119
A
GLU
42
A
GLU
35
A
ARG
44
A
ARG
37
A
GLN
47
A
GLN
40
A
VAL
49
A
VAL
42
A
ARG
131
A
ARG
124
A
ILE
136
A
ILE
129
A
LEU
75
A
LEU
68
A
ILE
83
A
ILE
76
A
LYS
90
A
LYS
83
A
SER
99
A
SER
92
146
H 3