0.012387
0.000000
0.000000
0.000000
0.012387
0.000000
0.000000
0.000000
0.007014
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
80.732
80.732
142.581
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
C H2 O2
46.025
FORMIC ACID
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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 Se
196.106
n
SELENOMETHIONINE
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
To be published
0353
Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution
10.2210/pdb3mcp/pdb
pdb_00003mcp
100
1
Flat collimating mirror, toroid focusing mirror
CCD
2009-07-30
MARMOSAIC 325 mm CCD
Double crystal monochromator
MAD
M
x-ray
1
0.91162
1.0
0.97911
1.0
BL9-2
SSRL
0.91162,0.97911
SYNCHROTRON
SSRL BEAMLINE BL9-2
39298.441
Glucokinase
1
man
polymer
92.094
GLYCEROL
2
syn
non-polymer
46.025
FORMIC ACID
1
syn
non-polymer
18.015
water
13
nat
water
no
yes
G(MSE)(MSE)YTNDNRIV(MSE)TLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQAGLPEAPV
AISFAFPGPADYQAGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYK
NLLGVTLGTGFGAGVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAV(MSE)RVYAERSGDAGARTPKEIFEI
AEGIRPGNREAAIAAFEELGE(MSE)AGDALASAITLIDGLIVIGGGLSGASKYILPVLLKE(MSE)NAQTG(MSE)
(MSE)DGARFGRLQKEVYDLDEEKSFAGFARGEAVEVLVPGTNRKVGYDPCKRIGVTFSKQGANRSIA(MSE)GAYVFAL
NHLSK
GMMYTNDNRIVMTLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQAGLPEAPVAISFAFPGPADY
QAGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYKNLLGVTLGTGFG
AGVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAVMRVYAERSGDAGARTPKEIFEIAEGIRPGNREAAIAAF
EELGEMAGDALASAITLIDGLIVIGGGLSGASKYILPVLLKEMNAQTGMMDGARFGRLQKEVYDLDEEKSFAGFARGEAV
EVLVPGTNRKVGYDPCKRIGVTFSKQGANRSIAMGAYVFALNHLSK
A
400675
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
ATCC 8503 / DSM 20701 / NCTC 11152
sample
BDI_1628
435591
Parabacteroides distasonis
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.96
58.39
VAPOR DIFFUSION, SITTING DROP
7.3
10.0000% Glycerol, 3.6000M NaFormate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
software
struct_conn
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Refinement description
Data collection
Derived calculations
Refinement description
Database references
Derived calculations
1
0
2010-05-12
1
1
2011-07-13
1
2
2017-11-08
1
3
2019-07-17
1
4
2023-02-01
_software.classification
_software.name
_software.classification
_software.contact_author
_software.contact_author_email
_software.language
_software.location
_software.name
_software.type
_software.version
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2010-03-29
REL
REL
GOL
GLYCEROL
FMT
FORMIC ACID
HOH
water
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLYCINE AT POSITION 61 INSTEAD OF AN ASPARTATE AND A GLUTAMATE AT POSITION 306 INSTEAD OF AN ASPARTATE. THE GLYCINE AT POSITION 61 AND GLUTAMATE AT POSITION 306 ARE SUPPORTED BY THE ELECTRON DENSITY.
GOL
1
2
GOL
GOL
366
A
GOL
2
2
GOL
GOL
367
A
FMT
3
3
FMT
FMT
368
A
HOH
4
4
HOH
HOH
369
A
HOH
5
4
HOH
HOH
370
A
HOH
6
4
HOH
HOH
371
A
HOH
7
4
HOH
HOH
372
A
HOH
8
4
HOH
HOH
373
A
HOH
9
4
HOH
HOH
374
A
HOH
10
4
HOH
HOH
375
A
HOH
11
4
HOH
HOH
376
A
HOH
12
4
HOH
HOH
377
A
HOH
13
4
HOH
HOH
378
A
HOH
14
4
HOH
HOH
379
A
HOH
15
4
HOH
HOH
380
A
HOH
16
4
HOH
HOH
381
A
n
1
0
A
MSE
1
n
2
MSE
1
A
MSE
2
n
3
MSE
2
A
TYR
3
n
4
TYR
3
A
THR
4
n
5
THR
4
A
ASN
5
n
6
ASN
5
A
ASP
6
n
7
ASP
6
A
ASN
7
n
8
ASN
7
A
ARG
8
n
9
ARG
8
A
ILE
9
n
10
ILE
9
A
VAL
10
n
11
VAL
10
A
MSE
11
n
12
MSE
11
A
THR
12
n
13
THR
12
A
LEU
13
n
14
LEU
13
A
ASP
14
n
15
ASP
14
A
ALA
15
n
16
ALA
15
A
GLY
16
n
17
GLY
16
A
GLY
17
n
18
GLY
17
A
THR
18
n
19
THR
18
A
ASN
19
n
20
ASN
19
A
PHE
20
n
21
PHE
20
A
VAL
21
n
22
VAL
21
A
PHE
22
n
23
PHE
22
A
SER
23
n
24
SER
23
A
ALA
24
n
25
ALA
24
A
ILE
25
n
26
ILE
25
A
GLN
26
n
27
GLN
26
A
GLY
27
n
28
GLY
27
A
GLY
28
n
29
GLY
28
A
LYS
29
n
30
LYS
29
A
GLU
30
n
31
GLU
30
A
ILE
31
n
32
ILE
31
A
ALA
32
n
33
ALA
32
A
ASP
33
n
34
ASP
33
A
PRO
34
n
35
PRO
34
A
VAL
35
n
36
VAL
35
A
VAL
36
n
37
VAL
36
A
LEU
37
n
38
LEU
37
A
PRO
38
n
39
PRO
38
A
ALA
39
n
40
ALA
39
A
CYS
40
n
41
CYS
40
A
ALA
41
n
42
ALA
41
A
ASP
42
n
43
ASP
42
A
CYS
43
n
44
CYS
43
A
LEU
44
n
45
LEU
44
A
ASP
45
n
46
ASP
45
A
LYS
46
n
47
LYS
46
A
CYS
47
n
48
CYS
47
A
LEU
48
n
49
LEU
48
A
GLY
49
n
50
GLY
49
A
ASN
50
n
51
ASN
50
A
LEU
51
n
52
LEU
51
A
VAL
52
n
53
VAL
52
A
GLU
53
n
54
GLU
53
A
GLY
54
n
55
GLY
54
A
PHE
55
n
56
PHE
55
A
LYS
56
n
57
LYS
56
A
ALA
57
n
58
ALA
57
A
ILE
58
n
59
ILE
58
A
GLN
59
n
60
GLN
59
A
ALA
60
n
61
ALA
60
A
GLY
61
n
62
GLY
61
A
LEU
62
n
63
LEU
62
A
PRO
63
n
64
PRO
63
A
GLU
64
n
65
GLU
64
A
ALA
65
n
66
ALA
65
A
PRO
66
n
67
PRO
66
A
VAL
67
n
68
VAL
67
A
ALA
68
n
69
ALA
68
A
ILE
69
n
70
ILE
69
A
SER
70
n
71
SER
70
A
PHE
71
n
72
PHE
71
A
ALA
72
n
73
ALA
72
A
PHE
73
n
74
PHE
73
A
PRO
74
n
75
PRO
74
A
GLY
75
n
76
GLY
75
A
PRO
76
n
77
PRO
76
A
ALA
77
n
78
ALA
77
A
ASP
78
n
79
ASP
78
A
TYR
79
n
80
TYR
79
A
GLN
80
n
81
GLN
80
A
ALA
81
n
82
ALA
81
A
GLY
82
n
83
GLY
82
A
ILE
83
n
84
ILE
83
A
ILE
84
n
85
ILE
84
A
GLY
85
n
86
GLY
85
A
ASP
86
n
87
ASP
86
A
LEU
87
n
88
LEU
87
A
PRO
88
n
89
PRO
88
A
ASN
89
n
90
ASN
89
A
PHE
90
n
91
PHE
90
A
PRO
91
n
92
PRO
91
A
SER
92
n
93
SER
92
A
PHE
93
n
94
PHE
93
A
ARG
94
n
95
ARG
94
A
GLY
95
n
96
GLY
95
A
GLY
96
n
97
GLY
96
A
VAL
97
n
98
VAL
97
A
ALA
98
n
99
ALA
98
A
LEU
99
n
100
LEU
99
A
GLY
100
n
101
GLY
100
A
PRO
101
n
102
PRO
101
A
PHE
102
n
103
PHE
102
A
LEU
103
n
104
LEU
103
A
GLU
104
n
105
GLU
104
A
ASP
105
n
106
ASP
105
A
ILE
106
n
107
ILE
106
A
PHE
107
n
108
PHE
107
A
GLY
108
n
109
GLY
108
A
ILE
109
n
110
ILE
109
A
PRO
110
n
111
PRO
110
A
VAL
111
n
112
VAL
111
A
PHE
112
n
113
PHE
112
A
ILE
113
n
114
ILE
113
A
ASN
114
n
115
ASN
114
A
ASN
115
n
116
ASN
115
A
ASP
116
n
117
ASP
116
A
GLY
117
n
118
GLY
117
A
SER
118
n
119
SER
118
A
LEU
119
n
120
LEU
119
A
PHE
120
n
121
PHE
120
A
ALA
121
n
122
ALA
121
A
TYR
122
n
123
TYR
122
A
GLY
123
n
124
GLY
123
A
GLU
124
n
125
GLU
124
A
ALA
125
n
126
ALA
125
A
LEU
126
n
127
LEU
126
A
THR
127
n
128
THR
127
A
GLY
128
n
129
GLY
128
A
VAL
129
n
130
VAL
129
A
LEU
130
n
131
LEU
130
A
PRO
131
n
132
PRO
131
A
GLU
132
n
133
GLU
132
A
ILE
133
n
134
ILE
133
A
ASN
134
n
135
ASN
134
A
ARG
135
n
136
ARG
135
A
ARG
136
n
137
ARG
136
A
LEU
137
n
138
LEU
137
A
ARG
138
n
139
ARG
138
A
GLU
139
n
140
GLU
139
A
ALA
140
n
141
ALA
140
A
GLY
141
n
142
GLY
141
A
SER
142
n
143
SER
142
A
THR
143
n
144
THR
143
A
LYS
144
n
145
LYS
144
A
ARG
145
n
146
ARG
145
A
TYR
146
n
147
TYR
146
A
LYS
147
n
148
LYS
147
A
ASN
148
n
149
ASN
148
A
LEU
149
n
150
LEU
149
A
LEU
150
n
151
LEU
150
A
GLY
151
n
152
GLY
151
A
VAL
152
n
153
VAL
152
A
THR
153
n
154
THR
153
A
LEU
154
n
155
LEU
154
A
GLY
155
n
156
GLY
155
A
THR
156
n
157
THR
156
A
GLY
157
n
158
GLY
157
A
PHE
158
n
159
PHE
158
A
GLY
159
n
160
GLY
159
A
ALA
160
n
161
ALA
160
A
GLY
161
n
162
GLY
161
A
VAL
162
n
163
VAL
162
A
VAL
163
n
164
VAL
163
A
ILE
164
n
165
ILE
164
A
ASP
165
n
166
ASP
165
A
GLY
166
n
167
GLY
166
A
GLU
167
n
168
GLU
167
A
LEU
168
n
169
LEU
168
A
LEU
169
n
170
LEU
169
A
ARG
170
n
171
ARG
170
A
GLY
171
n
172
GLY
171
A
ASP
172
n
173
ASP
172
A
ASN
173
n
174
ASN
173
A
ALA
174
n
175
ALA
174
A
ALA
175
n
176
ALA
175
A
GLY
176
n
177
GLY
176
A
GLY
177
n
178
GLY
177
A
TYR
178
n
179
TYR
178
A
VAL
179
n
180
VAL
179
A
TRP
180
n
181
TRP
180
A
CYS
181
n
182
CYS
181
A
LEU
182
n
183
LEU
182
A
ARG
183
n
184
ARG
183
A
ASN
184
n
185
ASN
184
A
LYS
185
n
186
LYS
185
A
LYS
186
n
187
LYS
186
A
TYR
187
n
188
TYR
187
A
PRO
188
n
189
PRO
188
A
GLU
189
n
190
GLU
189
A
TYR
190
n
191
TYR
190
A
ILE
191
n
192
ILE
191
A
VAL
192
n
193
VAL
192
A
GLU
193
n
194
GLU
193
A
GLU
194
n
195
GLU
194
A
SER
195
n
196
SER
195
A
VAL
196
n
197
VAL
196
A
SER
197
n
198
SER
197
A
ILE
198
n
199
ILE
198
A
ARG
199
n
200
ARG
199
A
ALA
200
n
201
ALA
200
A
VAL
201
n
202
VAL
201
A
MSE
202
n
203
MSE
202
A
ARG
203
n
204
ARG
203
A
VAL
204
n
205
VAL
204
A
TYR
205
n
206
TYR
205
A
ALA
206
n
207
ALA
206
A
GLU
207
n
208
GLU
207
A
ARG
208
n
209
ARG
208
A
SER
209
n
210
SER
209
A
GLY
210
n
211
GLY
210
A
ASP
211
n
212
ASP
211
A
ALA
212
n
213
ALA
212
A
GLY
213
n
214
GLY
213
A
ALA
214
n
215
ALA
214
A
ARG
215
n
216
ARG
215
A
THR
216
n
217
THR
216
A
PRO
217
n
218
PRO
217
A
LYS
218
n
219
LYS
218
A
GLU
219
n
220
GLU
219
A
ILE
220
n
221
ILE
220
A
PHE
221
n
222
PHE
221
A
GLU
222
n
223
GLU
222
A
ILE
223
n
224
ILE
223
A
ALA
224
n
225
ALA
224
A
GLU
225
n
226
GLU
225
A
GLY
226
n
227
GLY
226
A
ILE
227
n
228
ILE
227
A
ARG
228
n
229
ARG
228
A
PRO
229
n
230
PRO
229
A
GLY
230
n
231
GLY
230
A
ASN
231
n
232
ASN
231
A
ARG
232
n
233
ARG
232
A
GLU
233
n
234
GLU
233
A
ALA
234
n
235
ALA
234
A
ALA
235
n
236
ALA
235
A
ILE
236
n
237
ILE
236
A
ALA
237
n
238
ALA
237
A
ALA
238
n
239
ALA
238
A
PHE
239
n
240
PHE
239
A
GLU
240
n
241
GLU
240
A
GLU
241
n
242
GLU
241
A
LEU
242
n
243
LEU
242
A
GLY
243
n
244
GLY
243
A
GLU
244
n
245
GLU
244
A
MSE
245
n
246
MSE
245
A
ALA
246
n
247
ALA
246
A
GLY
247
n
248
GLY
247
A
ASP
248
n
249
ASP
248
A
ALA
249
n
250
ALA
249
A
LEU
250
n
251
LEU
250
A
ALA
251
n
252
ALA
251
A
SER
252
n
253
SER
252
A
ALA
253
n
254
ALA
253
A
ILE
254
n
255
ILE
254
A
THR
255
n
256
THR
255
A
LEU
256
n
257
LEU
256
A
ILE
257
n
258
ILE
257
A
ASP
258
n
259
ASP
258
A
GLY
259
n
260
GLY
259
A
LEU
260
n
261
LEU
260
A
ILE
261
n
262
ILE
261
A
VAL
262
n
263
VAL
262
A
ILE
263
n
264
ILE
263
A
GLY
264
n
265
GLY
264
A
GLY
265
n
266
GLY
265
A
GLY
266
n
267
GLY
266
A
LEU
267
n
268
LEU
267
A
SER
268
n
269
SER
268
A
GLY
269
n
270
GLY
269
A
ALA
270
n
271
ALA
270
A
SER
271
n
272
SER
271
A
LYS
272
n
273
LYS
272
A
TYR
273
n
274
TYR
273
A
ILE
274
n
275
ILE
274
A
LEU
275
n
276
LEU
275
A
PRO
276
n
277
PRO
276
A
VAL
277
n
278
VAL
277
A
LEU
278
n
279
LEU
278
A
LEU
279
n
280
LEU
279
A
LYS
280
n
281
LYS
280
A
GLU
281
n
282
GLU
281
A
MSE
282
n
283
MSE
282
A
ASN
283
n
284
ASN
283
A
ALA
284
n
285
ALA
284
A
GLN
285
n
286
GLN
285
A
THR
286
n
287
THR
286
A
GLY
287
n
288
GLY
287
A
MSE
288
n
289
MSE
288
A
MSE
289
n
290
MSE
289
A
n
291
290
A
n
292
291
A
n
293
292
A
n
294
293
A
n
295
294
A
n
296
295
A
n
297
296
A
n
298
297
A
GLN
298
n
299
GLN
298
A
LYS
299
n
300
LYS
299
A
GLU
300
n
301
GLU
300
A
VAL
301
n
302
VAL
301
A
TYR
302
n
303
TYR
302
A
ASP
303
n
304
ASP
303
A
LEU
304
n
305
LEU
304
A
ASP
305
n
306
ASP
305
A
GLU
306
n
307
GLU
306
A
GLU
307
n
308
GLU
307
A
LYS
308
n
309
LYS
308
A
SER
309
n
310
SER
309
A
PHE
310
n
311
PHE
310
A
ALA
311
n
312
ALA
311
A
GLY
312
n
313
GLY
312
A
PHE
313
n
314
PHE
313
A
ALA
314
n
315
ALA
314
A
ARG
315
n
316
ARG
315
A
GLY
316
n
317
GLY
316
A
GLU
317
n
318
GLU
317
A
ALA
318
n
319
ALA
318
A
VAL
319
n
320
VAL
319
A
GLU
320
n
321
GLU
320
A
VAL
321
n
322
VAL
321
A
LEU
322
n
323
LEU
322
A
VAL
323
n
324
VAL
323
A
PRO
324
n
325
PRO
324
A
GLY
325
n
326
GLY
325
A
THR
326
n
327
THR
326
A
ASN
327
n
328
ASN
327
A
ARG
328
n
329
ARG
328
A
LYS
329
n
330
LYS
329
A
VAL
330
n
331
VAL
330
A
GLY
331
n
332
GLY
331
A
TYR
332
n
333
TYR
332
A
ASP
333
n
334
ASP
333
A
PRO
334
n
335
PRO
334
A
CYS
335
n
336
CYS
335
A
LYS
336
n
337
LYS
336
A
ARG
337
n
338
ARG
337
A
ILE
338
n
339
ILE
338
A
GLY
339
n
340
GLY
339
A
VAL
340
n
341
VAL
340
A
THR
341
n
342
THR
341
A
PHE
342
n
343
PHE
342
A
SER
343
n
344
SER
343
A
LYS
344
n
345
LYS
344
A
GLN
345
n
346
GLN
345
A
GLY
346
n
347
GLY
346
A
ALA
347
n
348
ALA
347
A
ASN
348
n
349
ASN
348
A
ARG
349
n
350
ARG
349
A
SER
350
n
351
SER
350
A
ILE
351
n
352
ILE
351
A
ALA
352
n
353
ALA
352
A
MSE
353
n
354
MSE
353
A
GLY
354
n
355
GLY
354
A
ALA
355
n
356
ALA
355
A
TYR
356
n
357
TYR
356
A
VAL
357
n
358
VAL
357
A
PHE
358
n
359
PHE
358
A
ALA
359
n
360
ALA
359
A
LEU
360
n
361
LEU
360
A
ASN
361
n
362
ASN
361
A
HIS
362
n
363
HIS
362
A
LEU
363
n
364
LEU
363
A
n
365
364
A
n
366
365
A
author_and_software_defined_assembly
PISA
2
dimeric
6220
-39
28200
A
MSE
1
SELENOMETHIONINE
A
MSE
2
MET
A
MSE
2
SELENOMETHIONINE
A
MSE
3
MET
A
MSE
11
SELENOMETHIONINE
A
MSE
12
MET
A
MSE
202
SELENOMETHIONINE
A
MSE
203
MET
A
MSE
245
SELENOMETHIONINE
A
MSE
246
MET
A
MSE
282
SELENOMETHIONINE
A
MSE
283
MET
A
MSE
288
SELENOMETHIONINE
A
MSE
289
MET
A
MSE
289
SELENOMETHIONINE
A
MSE
290
MET
A
MSE
353
SELENOMETHIONINE
A
MSE
354
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_556
y,x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
142.5810000000
A
O
LYS
29
A
O
LYS
30
A
N
GLN
26
A
N
GLN
27
A
N
PHE
22
A
N
PHE
23
A
O
VAL
35
A
O
VAL
36
A
O
LYS
29
A
O
LYS
30
A
N
GLN
26
A
N
GLN
27
A
O
ILE
25
A
O
ILE
26
A
N
VAL
10
A
N
VAL
11
A
N
MSE
11
A
N
MSE
12
A
O
ALA
68
A
O
ALA
69
A
N
ILE
69
A
N
ILE
70
A
O
PHE
112
A
O
PHE
113
A
N
ASP
78
A
N
ASP
79
A
O
ILE
83
A
O
ILE
84
A
O
GLU
167
A
O
GLU
168
A
N
ILE
164
A
N
ILE
165
A
O
GLY
161
A
O
GLY
162
A
N
GLY
151
A
N
GLY
152
A
N
LEU
154
A
N
LEU
155
A
O
GLY
264
A
O
GLY
265
A
N
ILE
261
A
N
ILE
262
A
O
GLY
339
A
O
GLY
340
A
O
ILE
338
A
O
ILE
339
A
N
GLU
300
A
N
GLU
301
A
N
VAL
321
A
N
VAL
322
A
O
VAL
330
A
O
VAL
331
1
A
CG
ASN
5
A
CG
ASN
6
1
Y
1
A
OD1
ASN
5
A
OD1
ASN
6
1
Y
1
A
ND2
ASN
5
A
ND2
ASN
6
1
Y
1
A
CG
ASN
7
A
CG
ASN
8
1
Y
1
A
OD1
ASN
7
A
OD1
ASN
8
1
Y
1
A
ND2
ASN
7
A
ND2
ASN
8
1
Y
1
A
CG
LYS
29
A
CG
LYS
30
1
Y
1
A
CD
LYS
29
A
CD
LYS
30
1
Y
1
A
CE
LYS
29
A
CE
LYS
30
1
Y
1
A
NZ
LYS
29
A
NZ
LYS
30
1
Y
1
A
CD
GLU
30
A
CD
GLU
31
1
Y
1
A
OE1
GLU
30
A
OE1
GLU
31
1
Y
1
A
OE2
GLU
30
A
OE2
GLU
31
1
Y
1
A
CG
LEU
44
A
CG
LEU
45
1
Y
1
A
CD1
LEU
44
A
CD1
LEU
45
1
Y
1
A
CD2
LEU
44
A
CD2
LEU
45
1
Y
1
A
CG
LYS
46
A
CG
LYS
47
1
Y
1
A
CD
LYS
46
A
CD
LYS
47
1
Y
1
A
CE
LYS
46
A
CE
LYS
47
1
Y
1
A
NZ
LYS
46
A
NZ
LYS
47
1
Y
1
A
CD
GLU
64
A
CD
GLU
65
1
Y
1
A
OE1
GLU
64
A
OE1
GLU
65
1
Y
1
A
OE2
GLU
64
A
OE2
GLU
65
1
Y
1
A
OG
SER
92
A
OG
SER
93
1
Y
1
A
NH1
ARG
94
A
NH1
ARG
95
1
Y
1
A
NH2
ARG
94
A
NH2
ARG
95
1
Y
1
A
CG
ARG
145
A
CG
ARG
146
1
Y
1
A
CD
ARG
145
A
CD
ARG
146
1
Y
1
A
NE
ARG
145
A
NE
ARG
146
1
Y
1
A
CZ
ARG
145
A
CZ
ARG
146
1
Y
1
A
NH1
ARG
145
A
NH1
ARG
146
1
Y
1
A
NH2
ARG
145
A
NH2
ARG
146
1
Y
1
A
NE
ARG
183
A
NE
ARG
184
1
Y
1
A
CZ
ARG
183
A
CZ
ARG
184
1
Y
1
A
NH1
ARG
183
A
NH1
ARG
184
1
Y
1
A
NH2
ARG
183
A
NH2
ARG
184
1
Y
1
A
CG
GLU
189
A
CG
GLU
190
1
Y
1
A
CD
GLU
189
A
CD
GLU
190
1
Y
1
A
OE1
GLU
189
A
OE1
GLU
190
1
Y
1
A
OE2
GLU
189
A
OE2
GLU
190
1
Y
1
A
CZ
ARG
215
A
CZ
ARG
216
1
Y
1
A
NH1
ARG
215
A
NH1
ARG
216
1
Y
1
A
NH2
ARG
215
A
NH2
ARG
216
1
Y
1
A
CD
LYS
218
A
CD
LYS
219
1
Y
1
A
CE
LYS
218
A
CE
LYS
219
1
Y
1
A
NZ
LYS
218
A
NZ
LYS
219
1
Y
1
A
NZ
LYS
280
A
NZ
LYS
281
1
Y
1
A
OE1
GLU
306
A
OE1
GLU
307
1
Y
1
A
OE2
GLU
306
A
OE2
GLU
307
1
Y
1
A
NZ
LYS
308
A
NZ
LYS
309
1
Y
1
A
OG1
THR
326
A
OG1
THR
327
1
Y
1
A
CG2
THR
326
A
CG2
THR
327
1
Y
1
A
CZ
ARG
328
A
CZ
ARG
329
1
Y
1
A
NH1
ARG
328
A
NH1
ARG
329
1
Y
1
A
NH2
ARG
328
A
NH2
ARG
329
1
Y
1
A
CD
LYS
329
A
CD
LYS
330
1
Y
1
A
CE
LYS
329
A
CE
LYS
330
1
Y
1
A
NZ
LYS
329
A
NZ
LYS
330
1
Y
1
A
CG1
VAL
330
A
CG1
VAL
331
1
Y
1
A
CG2
VAL
330
A
CG2
VAL
331
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
ASP
290
A
ASP
291
1
Y
1
A
GLY
291
A
GLY
292
1
Y
1
A
ALA
292
A
ALA
293
1
Y
1
A
ARG
293
A
ARG
294
1
Y
1
A
PHE
294
A
PHE
295
1
Y
1
A
GLY
295
A
GLY
296
1
Y
1
A
ARG
296
A
ARG
297
1
Y
1
A
LEU
297
A
LEU
298
1
Y
1
A
SER
364
A
SER
365
1
Y
1
A
LYS
365
A
LYS
366
1
Y
1
A
THR
18
83.92
-43.90
1
A
PRO
63
-64.15
-73.33
1
A
ALA
68
178.80
-178.07
1
A
ASP
165
37.91
57.95
1
A
TYR
187
-147.50
59.47
1
A
PRO
188
-38.22
-31.35
1
A
SER
197
179.20
173.35
1
A
ASP
258
60.26
61.09
1
A
PRO
324
-39.13
124.39
94.43
53.803
22.42
-1.800
0.000
0.000
-1.800
0.000
3.600
0.931
0.907
1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) AND FORMIC ACID FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
0.249
0.206
0.209
3.000
28.748
477
9970
4.800
99.810
1.00
0.75
18.642
0.336
RANDOM
1
THROUGHOUT
0.00
MAD
0.400
0.800
0.800
1.400
MAXIMUM LIKELIHOOD WITH PHASES
MASK
3.000
28.748
13
2618
15
0
2590
0.010
0.022
2650
0.001
0.020
1770
0.919
1.980
3584
0.682
3.000
4318
3.396
5.000
353
27.812
24.369
103
13.335
15.000
406
11.117
15.000
14
0.060
0.200
400
0.006
0.021
3023
0.001
0.020
533
0.839
2.000
1746
0.064
2.000
739
1.722
4.000
2757
2.578
6.000
904
4.437
8.000
827
0.343
0.297
3.078
30
680
710
20
99.720
70.492
3.00
28.748
3MCP
10015
0.130
0.130
1
14.800
7.000
99.900
0.716
3.00
3.08
1.1
5232
714
0.716
7.30
100.00
0.605
3.08
3.16
1.3
5022
697
0.605
7.20
100.00
0.478
3.16
3.25
1.6
4968
691
0.478
7.20
100.00
0.375
3.25
3.35
2.0
4790
663
0.375
7.20
100.00
0.322
3.35
3.46
2.3
4587
641
0.322
7.20
100.00
0.239
3.46
3.59
3.2
4500
628
0.239
7.20
100.00
0.190
3.59
3.72
3.9
4360
607
0.190
7.20
100.00
0.164
3.72
3.87
4.6
4139
581
0.164
7.10
100.00
0.141
3.87
4.05
5.2
4023
567
0.141
7.10
100.00
0.115
4.05
4.24
6.5
3890
546
0.115
7.10
100.00
0.100
4.24
4.47
6.9
3576
510
0.100
7.00
100.00
0.090
4.47
4.74
7.9
3475
495
0.090
7.00
100.00
0.080
4.74
5.07
9.1
3177
458
0.080
6.90
100.00
0.087
5.07
5.48
8.3
3066
442
0.087
6.90
100.00
0.091
5.48
6.00
8.0
2770
404
0.091
6.90
100.00
0.083
6.00
6.71
8.7
2586
380
0.083
6.80
100.00
0.058
6.71
7.75
11.7
2158
326
0.058
6.60
100.00
0.047
7.75
9.49
13.6
1886
293
0.047
6.40
100.00
0.040
9.49
13.42
15.2
1445
238
0.040
6.10
100.00
0.046
13.42
28.75
13.0
703
134
0.046
5.20
90.60
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0102
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data scaling
Phil R. Evans
pre@mrc-lmb.cam.ac.uk
5/04/2004
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.2.5
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.006
data reduction
MOSFLM
phasing
SHELXD
phasing
autoSHARP
Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
CYS
43
A
CYS
44
HELX_P
A
ALA
60
A
ALA
61
1
1
18
A
PHE
90
A
PHE
91
HELX_P
A
ARG
94
A
ARG
95
5
2
5
A
ALA
98
A
ALA
99
HELX_P
A
GLY
108
A
GLY
109
1
3
11
A
ASN
115
A
ASN
116
HELX_P
A
THR
127
A
THR
128
1
4
13
A
GLY
128
A
GLY
129
HELX_P
A
ALA
140
A
ALA
141
1
5
13
A
ILE
191
A
ILE
192
HELX_P
A
SER
195
A
SER
196
5
6
5
A
SER
197
A
SER
198
HELX_P
A
SER
209
A
SER
210
1
7
13
A
THR
216
A
THR
217
HELX_P
A
GLU
225
A
GLU
226
1
8
10
A
ASN
231
A
ASN
232
HELX_P
A
ASP
258
A
ASP
259
1
9
28
A
GLY
265
A
GLY
266
HELX_P
A
GLY
269
A
GLY
270
5
10
5
A
ALA
270
A
ALA
271
HELX_P
A
THR
286
A
THR
287
1
11
17
A
GLU
306
A
GLU
307
HELX_P
A
GLY
316
A
GLY
317
1
12
11
A
GLY
346
A
GLY
347
HELX_P
A
LEU
363
A
LEU
364
1
13
18
covale
1.331
both
A
MSE
1
A
C
MSE
2
1_555
A
MSE
2
A
N
MSE
3
1_555
covale
1.342
both
A
MSE
2
A
C
MSE
3
1_555
A
TYR
3
A
N
TYR
4
1_555
covale
1.329
both
A
VAL
10
A
C
VAL
11
1_555
A
MSE
11
A
N
MSE
12
1_555
covale
1.321
both
A
MSE
11
A
C
MSE
12
1_555
A
THR
12
A
N
THR
13
1_555
covale
1.328
both
A
VAL
201
A
C
VAL
202
1_555
A
MSE
202
A
N
MSE
203
1_555
covale
1.328
both
A
MSE
202
A
C
MSE
203
1_555
A
ARG
203
A
N
ARG
204
1_555
covale
1.336
both
A
GLU
244
A
C
GLU
245
1_555
A
MSE
245
A
N
MSE
246
1_555
covale
1.328
both
A
MSE
245
A
C
MSE
246
1_555
A
ALA
246
A
N
ALA
247
1_555
covale
1.324
both
A
GLU
281
A
C
GLU
282
1_555
A
MSE
282
A
N
MSE
283
1_555
covale
1.337
both
A
MSE
282
A
C
MSE
283
1_555
A
ASN
283
A
N
ASN
284
1_555
covale
1.337
both
A
GLY
287
A
C
GLY
288
1_555
A
MSE
288
A
N
MSE
289
1_555
covale
1.342
both
A
MSE
288
A
C
MSE
289
1_555
A
MSE
289
A
N
MSE
290
1_555
covale
1.333
both
A
ALA
352
A
C
ALA
353
1_555
A
MSE
353
A
N
MSE
354
1_555
covale
1.323
both
A
MSE
353
A
C
MSE
354
1_555
A
GLY
354
A
N
GLY
355
1_555
TRANSFERASE
Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, TRANSFERASE
A
GLY
75
A
GLY
76
1
A
PRO
76
A
PRO
77
6.06
A6LCG6_PARD8
UNP
1
1
A6LCG6
MMYTNDNRIVMTLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQADLPEAPVAISFAFPGPADYQ
AGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYKNLLGVTLGTGFGA
GVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAVMRVYAERSGDAGARTPKEIFEIAEGIRPGNREAAIAAFE
ELGEMAGDALASAITLIDGLIVIGGGLSGASKYILPVLLKEMNAQTGMMDGARFGRLQKEVYDLDDEKSFAGFARGEAVE
VLVPGTNRKVGYDPCKRIGVTFSKQGANRSIAMGAYVFALNHLSK
1
365
3MCP
1
365
A6LCG6
A
1
2
366
1
expression tag
GLY
0
3MCP
A
A6LCG6
UNP
1
1
ASP
see remark 999
GLY
61
3MCP
A
A6LCG6
UNP
61
62
1
ASP
see remark 999
GLU
306
3MCP
A
A6LCG6
UNP
306
307
3
5
2
6
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
parallel
anti-parallel
A
LYS
29
A
LYS
30
A
GLU
30
A
GLU
31
A
ASN
19
A
ASN
20
A
GLN
26
A
GLN
27
A
VAL
35
A
VAL
36
A
PRO
38
A
PRO
39
A
LYS
29
A
LYS
30
A
GLU
30
A
GLU
31
A
ASN
19
A
ASN
20
A
GLN
26
A
GLN
27
A
ILE
9
A
ILE
10
A
ASP
14
A
ASP
15
A
ALA
68
A
ALA
69
A
ALA
72
A
ALA
73
A
VAL
111
A
VAL
112
A
ASN
114
A
ASN
115
A
ALA
77
A
ALA
78
A
ASP
78
A
ASP
79
A
ILE
83
A
ILE
84
A
ILE
84
A
ILE
85
A
GLU
167
A
GLU
168
A
LEU
168
A
LEU
169
A
PHE
158
A
PHE
159
A
ILE
164
A
ILE
165
A
ASN
148
A
ASN
149
A
LEU
154
A
LEU
155
A
LEU
260
A
LEU
261
A
GLY
264
A
GLY
265
A
ARG
337
A
ARG
338
A
PHE
342
A
PHE
343
A
GLU
300
A
GLU
301
A
ASP
303
A
ASP
304
A
VAL
319
A
VAL
320
A
LEU
322
A
LEU
323
A
LYS
329
A
LYS
330
A
TYR
332
A
TYR
333
BINDING SITE FOR RESIDUE GOL A 366
A
GOL
366
Software
1
BINDING SITE FOR RESIDUE GOL A 367
A
GOL
367
Software
4
BINDING SITE FOR RESIDUE FMT A 368
A
FMT
368
Software
7
A
GLY
266
A
GLY
267
1
1_555
A
GLY
117
A
GLY
118
4
1_555
A
GLY
159
A
GLY
160
4
1_555
A
ALA
160
A
ALA
161
4
1_555
A
TYR
178
A
TYR
179
4
1_555
A
GLU
132
A
GLU
133
7
1_555
A
ILE
133
A
ILE
134
7
1_555
A
ARG
136
A
ARG
137
7
1_555
A
LEU
304
A
LEU
305
7
1_555
A
ASP
305
A
ASP
306
7
1_555
A
THR
341
A
THR
342
7
1_555
A
LYS
344
A
LYS
345
7
1_555
96
P 43 21 2