0.013757
0.007943
0.000000
0.000000
0.015885
0.000000
0.000000
0.000000
0.018832
0.000000
0.000000
0.000000
Chattopadhyay, K.
Ramagopal, U.A.
Nathenson, S.G.
Almo, S.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
72.691
72.691
53.101
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
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
104
19452
19457
10.1073/pnas.0709264104
18040044
Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function.
2007
100
1
1
CCD
2006-04-08
ADSC QUANTUM 4
CCD
2006-04-16
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
1.009
1.0
6.10
180253
0.120
1.05
2.500
50.000
10652
100.00
16.90
X4A
NSLS
0.9795
SYNCHROTRON
NSLS BEAMLINE X4A
X29A
NSLS
1.009
SYNCHROTRON
NSLS BEAMLINE X29A
14687.742
Tumor necrosis factor ligand superfamily member 18
Extracellular, TNF homology domain
1
man
polymer
18.015
water
42
nat
water
Glucocorticoid-induced TNF-related ligand, hGITRL, Activation-inducible TNF-related ligand, AITRL
no
no
GSHMETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTL
TNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS
GSHMETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTL
TNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS
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
human
Homo
Escherichia
sample
TNFSF18, AITRL, GITRL, TL6
9606
Homo sapiens
562
Escherichia coli
Rosetta (DE3) pLysS
plasmid
pET-14b
1
2.76
55.37
VAPOR DIFFUSION, SITTING DROP
4.5
25% PEG 3350, 0.1 M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K
298
software
repository
Initial release
Version format compliance
Refinement description
1
0
2007-11-13
1
1
2011-07-13
1
2
2017-10-18
RCSB
Y
RCSB
2007-05-24
REL
REL
0.080
2.092
99.80
16.60
0.094
1.970
99.90
16.50
0.107
1.850
100.00
16.90
0.119
1.380
100.00
17.10
0.169
0.888
100.00
17.00
0.237
0.645
100.00
17.10
0.343
0.515
100.00
17.20
0.519
0.436
100.00
17.10
0.679
0.411
100.00
17.00
0.373
100.00
16.70
HOH
water
HOH
1
2
HOH
HOH
178
A
HOH
2
2
HOH
HOH
179
A
HOH
3
2
HOH
HOH
180
A
HOH
4
2
HOH
HOH
181
A
HOH
5
2
HOH
HOH
182
A
HOH
6
2
HOH
HOH
183
A
HOH
7
2
HOH
HOH
184
A
HOH
8
2
HOH
HOH
185
A
HOH
10
2
HOH
HOH
186
A
HOH
11
2
HOH
HOH
187
A
HOH
12
2
HOH
HOH
188
A
HOH
13
2
HOH
HOH
189
A
HOH
15
2
HOH
HOH
190
A
HOH
16
2
HOH
HOH
191
A
HOH
17
2
HOH
HOH
192
A
HOH
18
2
HOH
HOH
193
A
HOH
19
2
HOH
HOH
194
A
HOH
20
2
HOH
HOH
195
A
HOH
21
2
HOH
HOH
196
A
HOH
22
2
HOH
HOH
197
A
HOH
23
2
HOH
HOH
198
A
HOH
24
2
HOH
HOH
199
A
HOH
25
2
HOH
HOH
200
A
HOH
26
2
HOH
HOH
201
A
HOH
27
2
HOH
HOH
202
A
HOH
28
2
HOH
HOH
203
A
HOH
30
2
HOH
HOH
204
A
HOH
31
2
HOH
HOH
205
A
HOH
32
2
HOH
HOH
206
A
HOH
37
2
HOH
HOH
207
A
HOH
40
2
HOH
HOH
208
A
HOH
50
2
HOH
HOH
209
A
HOH
52
2
HOH
HOH
210
A
HOH
54
2
HOH
HOH
211
A
HOH
56
2
HOH
HOH
212
A
HOH
57
2
HOH
HOH
213
A
HOH
58
2
HOH
HOH
214
A
HOH
62
2
HOH
HOH
215
A
HOH
66
2
HOH
HOH
216
A
HOH
71
2
HOH
HOH
217
A
HOH
74
2
HOH
HOH
218
A
HOH
79
2
HOH
HOH
219
A
n
1
48
A
n
2
49
A
n
3
50
A
n
4
51
A
n
5
52
A
n
6
53
A
n
7
54
A
n
8
55
A
n
9
56
A
PRO
57
n
10
PRO
57
A
CYS
58
n
11
CYS
58
A
MET
59
n
12
MET
59
A
ALA
60
n
13
ALA
60
A
LYS
61
n
14
LYS
61
A
PHE
62
n
15
PHE
62
A
GLY
63
n
16
GLY
63
A
PRO
64
n
17
PRO
64
A
LEU
65
n
18
LEU
65
A
PRO
66
n
19
PRO
66
A
SER
67
n
20
SER
67
A
LYS
68
n
21
LYS
68
A
TRP
69
n
22
TRP
69
A
GLN
70
n
23
GLN
70
A
MET
71
n
24
MET
71
A
ALA
72
n
25
ALA
72
A
SER
73
n
26
SER
73
A
SER
74
n
27
SER
74
A
GLU
75
n
28
GLU
75
A
PRO
76
n
29
PRO
76
A
PRO
77
n
30
PRO
77
A
CYS
78
n
31
CYS
78
A
VAL
79
n
32
VAL
79
A
ASN
80
n
33
ASN
80
A
LYS
81
n
34
LYS
81
A
VAL
82
n
35
VAL
82
A
SER
83
n
36
SER
83
A
ASP
84
n
37
ASP
84
A
TRP
85
n
38
TRP
85
A
LYS
86
n
39
LYS
86
A
LEU
87
n
40
LEU
87
A
GLU
88
n
41
GLU
88
A
ILE
89
n
42
ILE
89
A
LEU
90
n
43
LEU
90
A
GLN
91
n
44
GLN
91
A
ASN
92
n
45
ASN
92
A
GLY
93
n
46
GLY
93
A
LEU
94
n
47
LEU
94
A
TYR
95
n
48
TYR
95
A
LEU
96
n
49
LEU
96
A
ILE
97
n
50
ILE
97
A
TYR
98
n
51
TYR
98
A
GLY
99
n
52
GLY
99
A
GLN
100
n
53
GLN
100
A
VAL
101
n
54
VAL
101
A
ALA
102
n
55
ALA
102
A
PRO
103
n
56
PRO
103
A
ASN
104
n
57
ASN
104
A
ALA
105
n
58
ALA
105
A
ASN
106
n
59
ASN
106
A
TYR
107
n
60
TYR
107
A
ASN
108
n
61
ASN
108
A
ASP
109
n
62
ASP
109
A
VAL
110
n
63
VAL
110
A
ALA
111
n
64
ALA
111
A
PRO
112
n
65
PRO
112
A
PHE
113
n
66
PHE
113
A
GLU
114
n
67
GLU
114
A
VAL
115
n
68
VAL
115
A
ARG
116
n
69
ARG
116
A
LEU
117
n
70
LEU
117
A
TYR
118
n
71
TYR
118
A
LYS
119
n
72
LYS
119
A
ASN
120
n
73
ASN
120
A
LYS
121
n
74
LYS
121
A
ASP
122
n
75
ASP
122
A
MET
123
n
76
MET
123
A
ILE
124
n
77
ILE
124
A
GLN
125
n
78
GLN
125
A
THR
126
n
79
THR
126
A
LEU
127
n
80
LEU
127
A
THR
128
n
81
THR
128
A
ASN
129
n
82
ASN
129
A
LYS
130
n
83
LYS
130
A
SER
131
n
84
SER
131
A
LYS
132
n
85
LYS
132
A
ILE
133
n
86
ILE
133
A
GLN
134
n
87
GLN
134
A
ASN
135
n
88
ASN
135
A
VAL
136
n
89
VAL
136
A
GLY
137
n
90
GLY
137
A
GLY
138
n
91
GLY
138
A
THR
139
n
92
THR
139
A
TYR
140
n
93
TYR
140
A
GLU
141
n
94
GLU
141
A
LEU
142
n
95
LEU
142
A
HIS
143
n
96
HIS
143
A
VAL
144
n
97
VAL
144
A
GLY
145
n
98
GLY
145
A
ASP
146
n
99
ASP
146
A
THR
147
n
100
THR
147
A
ILE
148
n
101
ILE
148
A
ASP
149
n
102
ASP
149
A
LEU
150
n
103
LEU
150
A
ILE
151
n
104
ILE
151
A
PHE
152
n
105
PHE
152
A
ASN
153
n
106
ASN
153
A
SER
154
n
107
SER
154
A
GLU
155
n
108
GLU
155
A
HIS
156
n
109
HIS
156
A
GLN
157
n
110
GLN
157
A
VAL
158
n
111
VAL
158
A
LEU
159
n
112
LEU
159
A
LYS
160
n
113
LYS
160
A
ASN
161
n
114
ASN
161
A
ASN
162
n
115
ASN
162
A
THR
163
n
116
THR
163
A
TYR
164
n
117
TYR
164
A
TRP
165
n
118
TRP
165
A
GLY
166
n
119
GLY
166
A
ILE
167
n
120
ILE
167
A
ILE
168
n
121
ILE
168
A
LEU
169
n
122
LEU
169
A
LEU
170
n
123
LEU
170
A
ALA
171
n
124
ALA
171
A
ASN
172
n
125
ASN
172
A
n
126
173
A
n
127
174
A
n
128
175
A
n
129
176
A
n
130
177
A
author_defined_assembly
3
trimeric
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_655
-y+1,x-y,z
crystal symmetry operation
72.6910000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_665
-x+y+1,-x+1,z
crystal symmetry operation
36.3455000000
62.9522526265
0.0000000000
A
O
GLN
70
A
O
GLN
23
A
N
LYS
61
A
N
LYS
14
A
N
PHE
62
A
N
PHE
15
A
O
TRP
165
A
O
TRP
118
A
O
LEU
170
A
O
LEU
123
A
N
LEU
94
A
N
LEU
47
A
N
VAL
101
A
N
VAL
54
A
O
GLN
134
A
O
GLN
87
A
O
GLN
70
A
O
GLN
23
A
N
LYS
61
A
N
LYS
14
A
N
PHE
62
A
N
PHE
15
A
O
TRP
165
A
O
TRP
118
A
O
LEU
170
A
O
LEU
123
A
N
LEU
94
A
N
LEU
47
A
N
ILE
97
A
N
ILE
50
A
O
GLY
138
A
O
GLY
91
A
N
SER
83
A
N
SER
36
A
O
LYS
86
A
O
LYS
39
A
N
LEU
87
A
N
LEU
40
A
O
ILE
148
A
O
ILE
101
A
O
ASP
149
A
O
ASP
102
A
N
TYR
118
A
N
TYR
71
A
N
LEU
117
A
N
LEU
70
A
O
ILE
124
A
O
ILE
77
1
A
GLY
48
A
GLY
1
1
Y
1
A
SER
49
A
SER
2
1
Y
1
A
HIS
50
A
HIS
3
1
Y
1
A
MET
51
A
MET
4
1
Y
1
A
GLU
52
A
GLU
5
1
Y
1
A
THR
53
A
THR
6
1
Y
1
A
ALA
54
A
ALA
7
1
Y
1
A
LYS
55
A
LYS
8
1
Y
1
A
GLU
56
A
GLU
9
1
Y
1
A
PRO
173
A
PRO
126
1
Y
1
A
GLN
174
A
GLN
127
1
Y
1
A
PHE
175
A
PHE
128
1
Y
1
A
ILE
176
A
ILE
129
1
Y
1
A
SER
177
A
SER
130
1
Y
1
A
LYS
68
-105.78
-125.69
1
A
ASN
106
-89.95
35.61
1
A
ASN
120
57.48
-123.92
1
A
ASN
162
-140.60
25.00
44.570
0.640
0.320
0.000
0.640
0.000
-0.960
0.949
0.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.257
0.215
0.217
0.217
2.300
21.7
331
7117
7117
4.700
99.410
6.671
0.164
RANDOM
1
THROUGHOUT
0.00
0
SAD
0.299
0.230
0.800
0.800
1.400
MAXIMUM LIKELIHOOD
MASK
2.300
21.7
42
989
0
0
947
0.012
0.022
974
1.431
1.950
1331
7.327
5.000
121
37.981
26.522
46
17.099
15.000
167
18.478
15.000
1
0.087
0.200
145
0.005
0.020
748
0.200
0.200
402
0.311
0.200
643
0.134
0.200
51
0.249
0.200
29
0.173
0.200
6
0.899
1.500
615
1.539
2.000
968
1.635
3.000
424
2.444
4.500
362
0.407
0.320
2.363
17
465
482
20
93.050
2.300
21.7
2Q1M
7131
7131
0
0
0.071
1.296
1,2
10.500
10.800
99.900
2.30
2.38
693
1.029
10.80
100.00
data reduction
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
DENZO
package
data scaling
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
SCALEPACK
package
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
April. 3, 2006
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
2.000
data collection
ADSC
Quantum
data reduction
HKL-2000
phasing
SHELXD
model building
SHELXE
Tumor necrosis factor ligand superfamily member 18
Crystal Structure of human GITRL
1
N
N
2
N
N
The biological unit is a trimer
disulf
2.025
A
CYS
58
A
SG
CYS
11
1_555
A
CYS
78
A
SG
CYS
31
1_555
SIGNALING PROTEIN
GITRL; Glucocorticoid-Induced TNF Receptor Ligand, SIGNALING PROTEIN
A
GLY
63
A
GLY
16
1
A
PRO
64
A
PRO
17
-2.15
A
LEU
65
A
LEU
18
1
A
PRO
66
A
PRO
19
4.77
A
GLU
75
A
GLU
28
1
A
PRO
76
A
PRO
29
-0.54
A
GLU
75
A
GLU
28
1
A
PRO
76
A
PRO
29
-2.66
TNF18_HUMAN
UNP
1
52
Q9UNG2
ETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTLTNKS
KIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS
52
177
2Q1M
52
177
Q9UNG2
A
1
5
130
1
EXPRESSION TAG
GLY
48
2Q1M
A
Q9UNG2
UNP
1
1
EXPRESSION TAG
SER
49
2Q1M
A
Q9UNG2
UNP
2
1
EXPRESSION TAG
HIS
50
2Q1M
A
Q9UNG2
UNP
3
1
EXPRESSION TAG
MET
51
2Q1M
A
Q9UNG2
UNP
4
5
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TRP
69
A
TRP
22
A
ALA
72
A
ALA
25
A
MET
59
A
MET
12
A
PHE
62
A
PHE
15
A
TYR
164
A
TYR
117
A
ALA
171
A
ALA
124
A
GLY
93
A
GLY
46
A
VAL
101
A
VAL
54
A
GLN
134
A
GLN
87
A
ASN
135
A
ASN
88
A
TRP
69
A
TRP
22
A
ALA
72
A
ALA
25
A
MET
59
A
MET
12
A
PHE
62
A
PHE
15
A
TYR
164
A
TYR
117
A
ALA
171
A
ALA
124
A
GLY
93
A
GLY
46
A
VAL
101
A
VAL
54
A
GLY
138
A
GLY
91
A
LEU
142
A
LEU
95
A
VAL
79
A
VAL
32
A
SER
83
A
SER
36
A
LYS
86
A
LYS
39
A
ILE
89
A
ILE
42
A
THR
147
A
THR
100
A
PHE
152
A
PHE
105
A
VAL
115
A
VAL
68
A
LYS
119
A
LYS
72
A
ASP
122
A
ASP
75
A
LEU
127
A
LEU
80
173
P 63