0.010226
0.000000
0.000000
0.000000
0.010226
0.000000
0.000000
0.000000
0.006279
0.00000
0.00000
0.00000
Cuff, M.E.
Skarina, T.
Savchenko, A.
Edwards, A.
Joachimiak, A.
Midwest Center for Structural Genomics (MCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
97.788
97.788
159.270
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C8 H15 N O6
221.208
2-acetamido-2-deoxy-alpha-D-glucopyranose
D-saccharide, alpha 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
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
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
To be Published
0353
putative nagD protein
150
1
CCD
2002-07-26
SBC-2
double crystal Si(111)
MAD
M
x-ray
1
0.97929
1.0
0.97918
1.0
0.96396
1.0
19-ID
APS
0.97929,0.97918,0.96396
SYNCHROTRON
APS BEAMLINE 19-ID
28559.908
nagD protein, putative
1
man
polymer
221.208
2-acetamido-2-deoxy-alpha-D-glucopyranose
1
man
non-polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
88
nat
water
no
yes
(MSE)LDKIELFILD(MSE)DGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRN(MSE)GVDVPDD
AVVTSGEITAEH(MSE)LKRFGRCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYERLKKACILLRKGKFYI
ATHPDINCPSKEGPVPDAGSI(MSE)AAIEASTGRKPDLIAGKPNPLVVDVISEKFGVPKER(MSE)A(MSE)VGDRLYT
DVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGE
MLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSGEITAEH
MLKRFGRCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYERLKKACILLRKGKFYIATHPDINCPSKEGPVP
DAGSIMAAIEASTGRKPDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERA
ETKPDFVFKNLGE
A
APC4903
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Thermotoga
Escherichia
sample
TM1742
2336
Thermotoga maritima
562
Escherichia coli
1
VAPOR DIFFUSION, HANGING DROP
6.5
amonium sulfate, sodium cacodylate, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
Midwest Center for Structural Genomics
MCSG
PSI, Protein Structure Initiative
software
atom_site
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_ref_seq_dif
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Refinement description
Atomic model
Data collection
Database references
Derived calculations
Structure summary
1
0
2004-03-02
1
1
2008-04-29
1
2
2011-07-13
1
3
2017-10-11
2
0
2020-07-29
_software.name
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
DGlcpNAca
N-acetyl-a-D-glucopyranosamine
a-D-GlcpNAc
GlcNAc
Y
RCSB
Y
RCSB
2003-06-30
REL
REL
NDG
2-acetamido-2-deoxy-alpha-D-glucopyranose
SO4
SULFATE ION
HOH
water
NAG
200
2
NDG
NDG
254
A
SO4
301
3
SO4
SO4
301
A
SO4
302
3
SO4
SO4
302
A
HOH
1
4
HOH
HOH
303
A
HOH
2
4
HOH
HOH
304
A
HOH
3
4
HOH
HOH
305
A
HOH
4
4
HOH
HOH
306
A
HOH
5
4
HOH
HOH
307
A
HOH
6
4
HOH
HOH
308
A
HOH
7
4
HOH
HOH
309
A
HOH
8
4
HOH
HOH
310
A
HOH
9
4
HOH
HOH
311
A
HOH
10
4
HOH
HOH
312
A
HOH
11
4
HOH
HOH
313
A
HOH
12
4
HOH
HOH
314
A
HOH
13
4
HOH
HOH
315
A
HOH
14
4
HOH
HOH
316
A
HOH
15
4
HOH
HOH
317
A
HOH
16
4
HOH
HOH
318
A
HOH
17
4
HOH
HOH
319
A
HOH
18
4
HOH
HOH
320
A
HOH
19
4
HOH
HOH
321
A
HOH
20
4
HOH
HOH
322
A
HOH
21
4
HOH
HOH
323
A
HOH
22
4
HOH
HOH
324
A
HOH
23
4
HOH
HOH
325
A
HOH
24
4
HOH
HOH
326
A
HOH
25
4
HOH
HOH
327
A
HOH
26
4
HOH
HOH
328
A
HOH
27
4
HOH
HOH
329
A
HOH
28
4
HOH
HOH
330
A
HOH
29
4
HOH
HOH
331
A
HOH
30
4
HOH
HOH
332
A
HOH
31
4
HOH
HOH
333
A
HOH
32
4
HOH
HOH
334
A
HOH
33
4
HOH
HOH
335
A
HOH
34
4
HOH
HOH
336
A
HOH
35
4
HOH
HOH
337
A
HOH
36
4
HOH
HOH
338
A
HOH
37
4
HOH
HOH
339
A
HOH
38
4
HOH
HOH
340
A
HOH
39
4
HOH
HOH
341
A
HOH
40
4
HOH
HOH
342
A
HOH
41
4
HOH
HOH
343
A
HOH
42
4
HOH
HOH
344
A
HOH
43
4
HOH
HOH
345
A
HOH
44
4
HOH
HOH
346
A
HOH
45
4
HOH
HOH
347
A
HOH
46
4
HOH
HOH
348
A
HOH
47
4
HOH
HOH
349
A
HOH
48
4
HOH
HOH
350
A
HOH
49
4
HOH
HOH
351
A
HOH
50
4
HOH
HOH
352
A
HOH
51
4
HOH
HOH
353
A
HOH
52
4
HOH
HOH
354
A
HOH
53
4
HOH
HOH
355
A
HOH
54
4
HOH
HOH
356
A
HOH
55
4
HOH
HOH
357
A
HOH
56
4
HOH
HOH
358
A
HOH
57
4
HOH
HOH
359
A
HOH
58
4
HOH
HOH
360
A
HOH
59
4
HOH
HOH
361
A
HOH
60
4
HOH
HOH
362
A
HOH
61
4
HOH
HOH
363
A
HOH
62
4
HOH
HOH
364
A
HOH
63
4
HOH
HOH
365
A
HOH
64
4
HOH
HOH
366
A
HOH
65
4
HOH
HOH
367
A
HOH
66
4
HOH
HOH
368
A
HOH
67
4
HOH
HOH
369
A
HOH
68
4
HOH
HOH
370
A
HOH
69
4
HOH
HOH
371
A
HOH
70
4
HOH
HOH
372
A
HOH
71
4
HOH
HOH
373
A
HOH
72
4
HOH
HOH
374
A
HOH
73
4
HOH
HOH
375
A
HOH
74
4
HOH
HOH
376
A
HOH
75
4
HOH
HOH
377
A
HOH
76
4
HOH
HOH
378
A
HOH
77
4
HOH
HOH
379
A
HOH
78
4
HOH
HOH
380
A
HOH
79
4
HOH
HOH
381
A
HOH
80
4
HOH
HOH
382
A
HOH
81
4
HOH
HOH
383
A
HOH
82
4
HOH
HOH
384
A
HOH
83
4
HOH
HOH
385
A
HOH
84
4
HOH
HOH
386
A
HOH
85
4
HOH
HOH
387
A
HOH
86
4
HOH
HOH
388
A
HOH
87
4
HOH
HOH
389
A
HOH
88
4
HOH
HOH
390
A
MSE
1
n
1
MSE
1
A
LEU
2
n
2
LEU
2
A
ASP
3
n
3
ASP
3
A
LYS
4
n
4
LYS
4
A
ILE
5
n
5
ILE
5
A
GLU
6
n
6
GLU
6
A
LEU
7
n
7
LEU
7
A
PHE
8
n
8
PHE
8
A
ILE
9
n
9
ILE
9
A
LEU
10
n
10
LEU
10
A
ASP
11
n
11
ASP
11
A
MSE
12
n
12
MSE
12
A
ASP
13
n
13
ASP
13
A
GLY
14
n
14
GLY
14
A
THR
15
n
15
THR
15
A
PHE
16
n
16
PHE
16
A
TYR
17
n
17
TYR
17
A
LEU
18
n
18
LEU
18
A
ASP
19
n
19
ASP
19
A
ASP
20
n
20
ASP
20
A
SER
21
n
21
SER
21
A
LEU
22
n
22
LEU
22
A
LEU
23
n
23
LEU
23
A
PRO
24
n
24
PRO
24
A
GLY
25
n
25
GLY
25
A
SER
26
n
26
SER
26
A
LEU
27
n
27
LEU
27
A
GLU
28
n
28
GLU
28
A
PHE
29
n
29
PHE
29
A
LEU
30
n
30
LEU
30
A
GLU
31
n
31
GLU
31
A
THR
32
n
32
THR
32
A
LEU
33
n
33
LEU
33
A
LYS
34
n
34
LYS
34
A
GLU
35
n
35
GLU
35
A
LYS
36
n
36
LYS
36
A
ASN
37
n
37
ASN
37
A
LYS
38
n
38
LYS
38
A
ARG
39
n
39
ARG
39
A
PHE
40
n
40
PHE
40
A
VAL
41
n
41
VAL
41
A
PHE
42
n
42
PHE
42
A
PHE
43
n
43
PHE
43
A
THR
44
n
44
THR
44
A
ASN
45
n
45
ASN
45
A
ASN
46
n
46
ASN
46
A
SER
47
n
47
SER
47
A
SER
48
n
48
SER
48
A
LEU
49
n
49
LEU
49
A
GLY
50
n
50
GLY
50
A
ALA
51
n
51
ALA
51
A
GLN
52
n
52
GLN
52
A
ASP
53
n
53
ASP
53
A
TYR
54
n
54
TYR
54
A
VAL
55
n
55
VAL
55
A
ARG
56
n
56
ARG
56
A
LYS
57
n
57
LYS
57
A
LEU
58
n
58
LEU
58
A
ARG
59
n
59
ARG
59
A
ASN
60
n
60
ASN
60
A
MSE
61
n
61
MSE
61
A
GLY
62
n
62
GLY
62
A
VAL
63
n
63
VAL
63
A
ASP
64
n
64
ASP
64
A
VAL
65
n
65
VAL
65
A
PRO
66
n
66
PRO
66
A
ASP
67
n
67
ASP
67
A
ASP
68
n
68
ASP
68
A
ALA
69
n
69
ALA
69
A
VAL
70
n
70
VAL
70
A
VAL
71
n
71
VAL
71
A
THR
72
n
72
THR
72
A
SER
73
n
73
SER
73
A
GLY
74
n
74
GLY
74
A
GLU
75
n
75
GLU
75
A
ILE
76
n
76
ILE
76
A
THR
77
n
77
THR
77
A
ALA
78
n
78
ALA
78
A
GLU
79
n
79
GLU
79
A
HIS
80
n
80
HIS
80
A
MSE
81
n
81
MSE
81
A
LEU
82
n
82
LEU
82
A
LYS
83
n
83
LYS
83
A
ARG
84
n
84
ARG
84
A
PHE
85
n
85
PHE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
CYS
88
n
88
CYS
88
A
ARG
89
n
89
ARG
89
A
ILE
90
n
90
ILE
90
A
PHE
91
n
91
PHE
91
A
LEU
92
n
92
LEU
92
A
LEU
93
n
93
LEU
93
A
GLY
94
n
94
GLY
94
A
THR
95
n
95
THR
95
A
PRO
96
n
96
PRO
96
A
GLN
97
n
97
GLN
97
A
LEU
98
n
98
LEU
98
A
LYS
99
n
99
LYS
99
A
LYS
100
n
100
LYS
100
A
VAL
101
n
101
VAL
101
A
PHE
102
n
102
PHE
102
A
GLU
103
n
103
GLU
103
A
ALA
104
n
104
ALA
104
A
TYR
105
n
105
TYR
105
A
GLY
106
n
106
GLY
106
A
HIS
107
n
107
HIS
107
A
VAL
108
n
108
VAL
108
A
ILE
109
n
109
ILE
109
A
ASP
110
n
110
ASP
110
A
GLU
111
n
111
GLU
111
A
GLU
112
n
112
GLU
112
A
ASN
113
n
113
ASN
113
A
PRO
114
n
114
PRO
114
A
ASP
115
n
115
ASP
115
A
PHE
116
n
116
PHE
116
A
VAL
117
n
117
VAL
117
A
VAL
118
n
118
VAL
118
A
LEU
119
n
119
LEU
119
A
GLY
120
n
120
GLY
120
A
PHE
121
n
121
PHE
121
A
ASP
122
n
122
ASP
122
A
LYS
123
n
123
LYS
123
A
THR
124
n
124
THR
124
A
LEU
125
n
125
LEU
125
A
THR
126
n
126
THR
126
A
TYR
127
n
127
TYR
127
A
GLU
128
n
128
GLU
128
A
ARG
129
n
129
ARG
129
A
LEU
130
n
130
LEU
130
A
LYS
131
n
131
LYS
131
A
LYS
132
n
132
LYS
132
A
ALA
133
n
133
ALA
133
A
CYS
134
n
134
CYS
134
A
ILE
135
n
135
ILE
135
A
LEU
136
n
136
LEU
136
A
LEU
137
n
137
LEU
137
A
ARG
138
n
138
ARG
138
A
LYS
139
n
139
LYS
139
A
GLY
140
n
140
GLY
140
A
LYS
141
n
141
LYS
141
A
PHE
142
n
142
PHE
142
A
TYR
143
n
143
TYR
143
A
ILE
144
n
144
ILE
144
A
ALA
145
n
145
ALA
145
A
THR
146
n
146
THR
146
A
HIS
147
n
147
HIS
147
A
PRO
148
n
148
PRO
148
A
ASP
149
n
149
ASP
149
A
ILE
150
n
150
ILE
150
A
ASN
151
n
151
ASN
151
A
CYS
152
n
152
CYS
152
A
PRO
153
n
153
PRO
153
A
SER
154
n
154
SER
154
A
LYS
155
n
155
LYS
155
A
GLU
156
n
156
GLU
156
A
GLY
157
n
157
GLY
157
A
PRO
158
n
158
PRO
158
A
VAL
159
n
159
VAL
159
A
PRO
160
n
160
PRO
160
A
ASP
161
n
161
ASP
161
A
ALA
162
n
162
ALA
162
A
GLY
163
n
163
GLY
163
A
SER
164
n
164
SER
164
A
ILE
165
n
165
ILE
165
A
MSE
166
n
166
MSE
166
A
ALA
167
n
167
ALA
167
A
ALA
168
n
168
ALA
168
A
ILE
169
n
169
ILE
169
A
GLU
170
n
170
GLU
170
A
ALA
171
n
171
ALA
171
A
SER
172
n
172
SER
172
A
THR
173
n
173
THR
173
A
GLY
174
n
174
GLY
174
A
ARG
175
n
175
ARG
175
A
LYS
176
n
176
LYS
176
A
PRO
177
n
177
PRO
177
A
ASP
178
n
178
ASP
178
A
LEU
179
n
179
LEU
179
A
ILE
180
n
180
ILE
180
A
ALA
181
n
181
ALA
181
A
GLY
182
n
182
GLY
182
A
LYS
183
n
183
LYS
183
A
PRO
184
n
184
PRO
184
A
ASN
185
n
185
ASN
185
A
PRO
186
n
186
PRO
186
A
LEU
187
n
187
LEU
187
A
VAL
188
n
188
VAL
188
A
VAL
189
n
189
VAL
189
A
ASP
190
n
190
ASP
190
A
VAL
191
n
191
VAL
191
A
ILE
192
n
192
ILE
192
A
SER
193
n
193
SER
193
A
GLU
194
n
194
GLU
194
A
LYS
195
n
195
LYS
195
A
PHE
196
n
196
PHE
196
A
GLY
197
n
197
GLY
197
A
VAL
198
n
198
VAL
198
A
PRO
199
n
199
PRO
199
A
LYS
200
n
200
LYS
200
A
GLU
201
n
201
GLU
201
A
ARG
202
n
202
ARG
202
A
MSE
203
n
203
MSE
203
A
ALA
204
n
204
ALA
204
A
MSE
205
n
205
MSE
205
A
VAL
206
n
206
VAL
206
A
GLY
207
n
207
GLY
207
A
ASP
208
n
208
ASP
208
A
ARG
209
n
209
ARG
209
A
LEU
210
n
210
LEU
210
A
TYR
211
n
211
TYR
211
A
THR
212
n
212
THR
212
A
ASP
213
n
213
ASP
213
A
VAL
214
n
214
VAL
214
A
LYS
215
n
215
LYS
215
A
LEU
216
n
216
LEU
216
A
GLY
217
n
217
GLY
217
A
LYS
218
n
218
LYS
218
A
ASN
219
n
219
ASN
219
A
ALA
220
n
220
ALA
220
A
GLY
221
n
221
GLY
221
A
ILE
222
n
222
ILE
222
A
VAL
223
n
223
VAL
223
A
SER
224
n
224
SER
224
A
ILE
225
n
225
ILE
225
A
LEU
226
n
226
LEU
226
A
VAL
227
n
227
VAL
227
A
LEU
228
n
228
LEU
228
A
THR
229
n
229
THR
229
A
GLY
230
n
230
GLY
230
A
GLU
231
n
231
GLU
231
A
THR
232
n
232
THR
232
A
THR
233
n
233
THR
233
A
PRO
234
n
234
PRO
234
A
GLU
235
n
235
GLU
235
A
ASP
236
n
236
ASP
236
A
LEU
237
n
237
LEU
237
A
GLU
238
n
238
GLU
238
A
ARG
239
n
239
ARG
239
A
ALA
240
n
240
ALA
240
A
GLU
241
n
241
GLU
241
A
THR
242
n
242
THR
242
A
LYS
243
n
243
LYS
243
A
PRO
244
n
244
PRO
244
A
ASP
245
n
245
ASP
245
A
PHE
246
n
246
PHE
246
A
VAL
247
n
247
VAL
247
A
PHE
248
n
248
PHE
248
A
LYS
249
n
249
LYS
249
A
ASN
250
n
250
ASN
250
A
LEU
251
n
251
LEU
251
A
GLY
252
n
252
GLY
252
A
GLU
253
n
253
GLU
253
A
author_defined_assembly
1
monomeric
A
MSE
1
SELENOMETHIONINE
A
MSE
1
MET
A
MSE
12
SELENOMETHIONINE
A
MSE
12
MET
A
MSE
61
SELENOMETHIONINE
A
MSE
61
MET
A
MSE
81
SELENOMETHIONINE
A
MSE
81
MET
A
MSE
166
SELENOMETHIONINE
A
MSE
166
MET
A
MSE
203
SELENOMETHIONINE
A
MSE
203
MET
A
MSE
205
SELENOMETHIONINE
A
MSE
205
MET
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
O
VAL
71
A
O
VAL
71
A
N
THR
44
A
N
THR
44
A
O
ARG
39
A
O
ARG
39
A
N
PHE
8
A
N
PHE
8
A
N
LEU
7
A
N
LEU
7
A
O
ALA
204
A
O
ALA
204
A
N
MSE
205
A
N
MSE
205
A
O
ILE
225
A
O
ILE
225
A
N
LEU
226
A
N
LEU
226
A
O
GLU
241
A
O
GLU
241
A
N
LEU
18
A
N
LEU
18
A
O
SER
21
A
O
SER
21
A
O
VAL
108
A
O
VAL
108
A
N
ILE
90
A
N
ILE
90
A
N
LEU
93
A
N
LEU
93
A
O
VAL
118
A
O
VAL
118
A
N
LEU
119
A
N
LEU
119
A
O
ILE
144
A
O
ILE
144
A
N
ALA
145
A
N
ALA
145
A
O
LEU
179
A
O
LEU
179
A
N
CYS
152
A
N
CYS
152
A
O
VAL
159
A
O
VAL
159
1
9.57
1.50
119.30
128.87
A
A
A
C
N
CA
LYS
PRO
PRO
243
244
244
Y
1
A
LEU
2
55.02
174.37
1
A
ASP
3
80.78
-11.97
1
A
MSE
12
-111.23
-93.67
1
A
THR
15
-122.68
-54.26
1
A
LYS
36
-63.55
10.05
1
A
PRO
66
-57.15
173.86
1
A
PHE
85
-140.38
-24.78
1
A
GLU
112
-65.99
-76.75
1
A
ASP
149
-33.59
118.38
1
A
ASP
161
-128.33
-166.07
1
A
THR
233
-172.18
-60.91
1
A
ASP
236
-167.46
-150.82
1
A
LEU
237
46.11
-128.63
1
A
ARG
239
-122.70
-162.46
1
A
ALA
240
-168.85
-125.54
1
A
ASP
245
-155.53
-157.38
carbohydrate.param
protein.top
water_rep.param
carbohydrate.top
ion.param
water.top
ion.top
150.17
75.24
29.03
15.85
0.00
0.00
15.85
0.00
-31.71
The authors state there is extra electron density near/in the main chain between residues A239 and A242. It could be an extra amino acid (cloning artifact), or some sort of ligand or ligands. The authors are confident of the chain trace.
0.279
0.010
0.244
2.80
28.93
844
19675
16773
5.0
85.3
1.00
1.00
RANDOM
1
THROUGHOUT
CNS bulk solvent model used
54.6016
0.297685
0.49
0.43
5.00
0.71
0.73
2.80
2.80
28.93
88
2095
25
0
1982
0.008
1.4
24.0
0.93
0.472
0.060
0.446
2.93
61
1219
2397
1280
4.8
53.4
0.435
0.045
0.393
3.08
95
1659
2413
1754
5.4
72.7
0.337
0.035
0.32
3.27
95
1984
2418
2079
4.6
86.0
0.306
0.030
0.291
3.53
103
2083
2426
2186
4.7
90.1
0.279
0.027
0.249
3.88
106
2177
2435
2283
4.6
93.8
0.257
0.023
0.207
4.44
129
2222
2472
2351
5.5
95.1
0.23
0.020
0.187
5.59
128
2250
2478
2378
5.4
96.0
0.266
0.024
0.233
28.93
127
2335
2644
2462
5.2
93.1
70.6
2.80
28.93
1PW5
34
0
24
0
56
0
18344
18344
127621.03
0.200000
0.0
1
refinement
Axel T. Brunger
axel.brunger@yale.edu
1998
Fortran
CNS
package
1.1
data reduction
d*TREK
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
SOLVE
phasing
SHARP
PROTEIN
putative nagD protein
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
A
GLY
25
A
GLY
25
HELX_P
A
LYS
36
A
LYS
36
1
1
12
A
GLY
50
A
GLY
50
HELX_P
A
GLY
62
A
GLY
62
1
2
13
A
SER
73
A
SER
73
HELX_P
A
PHE
85
A
PHE
85
1
3
13
A
THR
95
A
THR
95
HELX_P
A
TYR
105
A
TYR
105
1
4
11
A
THR
126
A
THR
126
HELX_P
A
LYS
139
A
LYS
139
1
5
14
A
ASP
161
A
ASP
161
HELX_P
A
GLY
174
A
GLY
174
1
6
14
A
PRO
186
A
PRO
186
HELX_P
A
GLY
197
A
GLY
197
1
7
12
A
PRO
199
A
PRO
199
HELX_P
A
GLU
201
A
GLU
201
5
8
3
A
TYR
211
A
TYR
211
HELX_P
A
GLY
221
A
GLY
221
1
9
11
A
ASP
245
A
ASP
245
HELX_P
A
GLY
252
A
GLY
252
1
10
8
covale
1.333
both
A
MSE
1
A
C
MSE
1
1_555
A
LEU
2
A
N
LEU
2
1_555
covale
1.324
both
A
ASP
11
A
C
ASP
11
1_555
A
MSE
12
A
N
MSE
12
1_555
covale
1.326
both
A
MSE
12
A
C
MSE
12
1_555
A
ASP
13
A
N
ASP
13
1_555
covale
1.328
both
A
ASN
60
A
C
ASN
60
1_555
A
MSE
61
A
N
MSE
61
1_555
covale
1.326
both
A
MSE
61
A
C
MSE
61
1_555
A
GLY
62
A
N
GLY
62
1_555
covale
1.331
both
A
HIS
80
A
C
HIS
80
1_555
A
MSE
81
A
N
MSE
81
1_555
covale
1.333
both
A
MSE
81
A
C
MSE
81
1_555
A
LEU
82
A
N
LEU
82
1_555
covale
1.333
both
A
ILE
165
A
C
ILE
165
1_555
A
MSE
166
A
N
MSE
166
1_555
covale
1.319
both
A
MSE
166
A
C
MSE
166
1_555
A
ALA
167
A
N
ALA
167
1_555
covale
1.332
both
A
ARG
202
A
C
ARG
202
1_555
A
MSE
203
A
N
MSE
203
1_555
covale
1.328
both
A
MSE
203
A
C
MSE
203
1_555
A
ALA
204
A
N
ALA
204
1_555
covale
1.326
both
A
ALA
204
A
C
ALA
204
1_555
A
MSE
205
A
N
MSE
205
1_555
covale
1.325
both
A
MSE
205
A
C
MSE
205
1_555
A
VAL
206
A
N
VAL
206
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
nagD protein, T. maritima, structural genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION
A
LYS
183
A
LYS
183
1
A
PRO
184
A
PRO
184
0.46
Q9X264_THEMA
UNP
1
1
Q9X264
MLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSGEITAEH
MLKRFGRCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYERLKKACILLRKGKFYIATHPDINCPSKEGPVP
DAGSIMAAIEASTGRKPDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERA
ETKPDFVFKNLGE
1
253
1PW5
1
253
Q9X264
A
1
1
253
1
MET
modified residue
MSE
1
1PW5
A
Q9X264
UNP
1
1
1
MET
modified residue
MSE
12
1PW5
A
Q9X264
UNP
12
12
1
MET
modified residue
MSE
61
1PW5
A
Q9X264
UNP
61
61
1
MET
modified residue
MSE
81
1PW5
A
Q9X264
UNP
81
81
1
MET
modified residue
MSE
166
1PW5
A
Q9X264
UNP
166
166
1
MET
modified residue
MSE
203
1PW5
A
Q9X264
UNP
203
203
1
MET
modified residue
MSE
205
1PW5
A
Q9X264
UNP
205
205
6
2
5
2
parallel
parallel
parallel
parallel
parallel
anti-parallel
parallel
parallel
parallel
parallel
anti-parallel
A
VAL
70
A
VAL
70
A
THR
72
A
THR
72
A
ARG
39
A
ARG
39
A
THR
44
A
THR
44
A
LEU
7
A
LEU
7
A
LEU
10
A
LEU
10
A
MSE
203
A
MSE
203
A
GLY
207
A
GLY
207
A
VAL
223
A
VAL
223
A
VAL
227
A
VAL
227
A
GLU
241
A
GLU
241
A
LYS
243
A
LYS
243
A
TYR
17
A
TYR
17
A
LEU
18
A
LEU
18
A
SER
21
A
SER
21
A
LEU
22
A
LEU
22
A
VAL
108
A
VAL
108
A
ILE
109
A
ILE
109
A
ARG
89
A
ARG
89
A
LEU
93
A
LEU
93
A
PHE
116
A
PHE
116
A
LEU
119
A
LEU
119
A
PHE
142
A
PHE
142
A
ALA
145
A
ALA
145
A
LEU
179
A
LEU
179
A
ILE
180
A
ILE
180
A
ASN
151
A
ASN
151
A
CYS
152
A
CYS
152
A
VAL
159
A
VAL
159
A
PRO
160
A
PRO
160
92
P 41 21 2