0.007180
0.000000
0.000000
0.000000
0.007180
0.000000
0.000000
0.000000
0.007180
0.00000
0.00000
0.00000
Chapados, B.R.
Tainer, J.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
139.280
139.280
139.280
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
N
332
N
O
N
333
N
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
N
N
346
S
C
N
347
N
C
N
348
N
O
N
349
N
C
N
350
N
C
N
351
N
C
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
doub
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
35
1624
1637
10.1093/nar/gkm006
17308348
The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase.
2007
10.2210/pdb2od8/pdb
pdb_00002od8
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
1
Vertical focusing mirror
CCD
2002-06-02
ADSC QUANTUM 4
single crystal Si(311) bent (horizontal focusing)
SINGLE WAVELENGTH
M
x-ray
1
0.97900
1.0
BL9-1
SSRL
0.97900
SYNCHROTRON
SSRL BEAMLINE BL9-1
28944.051
Proliferating cell nuclear antigen
1
man
polymer
2456.945
DNA ligase I, mitochondrial precursor
6.5.1.1
Residues 32-53
1
syn
polymer
18.015
water
18
nat
water
PCNA
CDC9, Polydeoxyribonucleotide synthase
no
no
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILR
CGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINI
MITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILR
CGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINI
MITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE
A
polypeptide(L)
no
no
AGKKPKQATLARFFTSMKNKPT
AGKKPKQATLARFFTSMKNKPT
B
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
baker's yeast
Saccharomyces
Escherichia
Escherichia coli
sample
POL30
4932
Saccharomyces cerevisiae
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
pT7-PCNA
1
3.58
65.68
VAPOR DIFFUSION, HANGING DROP
5.6
1.6 M (NH4)2SO4, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
294
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Advisory
Version format compliance
Refinement description
Data collection
Database references
Refinement description
1
0
2007-05-01
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2023-08-30
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
SEQUENCE
CHAIN B IS THE PEPTIDE SYNTHESIZED BASED ON SEQUENCE OF
RESIDUES 32-53 OF CDC9 (UNP P04819) SHOWN IN DBREF.
RCSB
Y
RCSB
2006-12-21
REL
REL
HOH
water
Peptide synthesized based on Cdc9 sequence (UNP P04819), residues 32-53.
sample
1PLQ
PDB entry 1PLQ
PDB
experimental model
HOH
1
3
HOH
HOH
259
A
HOH
3
3
HOH
HOH
260
A
HOH
4
3
HOH
HOH
261
A
HOH
5
3
HOH
HOH
262
A
HOH
6
3
HOH
HOH
263
A
HOH
7
3
HOH
HOH
264
A
HOH
8
3
HOH
HOH
265
A
HOH
9
3
HOH
HOH
266
A
HOH
10
3
HOH
HOH
267
A
HOH
11
3
HOH
HOH
268
A
HOH
13
3
HOH
HOH
269
A
HOH
14
3
HOH
HOH
270
A
HOH
15
3
HOH
HOH
271
A
HOH
16
3
HOH
HOH
272
A
HOH
17
3
HOH
HOH
273
A
HOH
18
3
HOH
HOH
274
A
HOH
2
3
HOH
HOH
2
B
HOH
12
3
HOH
HOH
12
B
MET
1
n
1
MET
1
A
LEU
2
n
2
LEU
2
A
GLU
3
n
3
GLU
3
A
ALA
4
n
4
ALA
4
A
LYS
5
n
5
LYS
5
A
PHE
6
n
6
PHE
6
A
GLU
7
n
7
GLU
7
A
GLU
8
n
8
GLU
8
A
ALA
9
n
9
ALA
9
A
SER
10
n
10
SER
10
A
LEU
11
n
11
LEU
11
A
PHE
12
n
12
PHE
12
A
LYS
13
n
13
LYS
13
A
ARG
14
n
14
ARG
14
A
ILE
15
n
15
ILE
15
A
ILE
16
n
16
ILE
16
A
ASP
17
n
17
ASP
17
A
GLY
18
n
18
GLY
18
A
PHE
19
n
19
PHE
19
A
LYS
20
n
20
LYS
20
A
ASP
21
n
21
ASP
21
A
CYS
22
n
22
CYS
22
A
VAL
23
n
23
VAL
23
A
GLN
24
n
24
GLN
24
A
LEU
25
n
25
LEU
25
A
VAL
26
n
26
VAL
26
A
ASN
27
n
27
ASN
27
A
PHE
28
n
28
PHE
28
A
GLN
29
n
29
GLN
29
A
CYS
30
n
30
CYS
30
A
LYS
31
n
31
LYS
31
A
GLU
32
n
32
GLU
32
A
ASP
33
n
33
ASP
33
A
GLY
34
n
34
GLY
34
A
ILE
35
n
35
ILE
35
A
ILE
36
n
36
ILE
36
A
ALA
37
n
37
ALA
37
A
GLN
38
n
38
GLN
38
A
ALA
39
n
39
ALA
39
A
VAL
40
n
40
VAL
40
A
ASP
41
n
41
ASP
41
A
ASP
42
n
42
ASP
42
A
SER
43
n
43
SER
43
A
ARG
44
n
44
ARG
44
A
VAL
45
n
45
VAL
45
A
LEU
46
n
46
LEU
46
A
LEU
47
n
47
LEU
47
A
VAL
48
n
48
VAL
48
A
SER
49
n
49
SER
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ILE
52
n
52
ILE
52
A
GLY
53
n
53
GLY
53
A
VAL
54
n
54
VAL
54
A
GLU
55
n
55
GLU
55
A
ALA
56
n
56
ALA
56
A
PHE
57
n
57
PHE
57
A
GLN
58
n
58
GLN
58
A
GLU
59
n
59
GLU
59
A
TYR
60
n
60
TYR
60
A
ARG
61
n
61
ARG
61
A
CYS
62
n
62
CYS
62
A
ASP
63
n
63
ASP
63
A
HIS
64
n
64
HIS
64
A
PRO
65
n
65
PRO
65
A
VAL
66
n
66
VAL
66
A
THR
67
n
67
THR
67
A
LEU
68
n
68
LEU
68
A
GLY
69
n
69
GLY
69
A
MET
70
n
70
MET
70
A
ASP
71
n
71
ASP
71
A
LEU
72
n
72
LEU
72
A
THR
73
n
73
THR
73
A
SER
74
n
74
SER
74
A
LEU
75
n
75
LEU
75
A
SER
76
n
76
SER
76
A
LYS
77
n
77
LYS
77
A
ILE
78
n
78
ILE
78
A
LEU
79
n
79
LEU
79
A
ARG
80
n
80
ARG
80
A
CYS
81
n
81
CYS
81
A
GLY
82
n
82
GLY
82
A
ASN
83
n
83
ASN
83
A
ASN
84
n
84
ASN
84
A
THR
85
n
85
THR
85
A
ASP
86
n
86
ASP
86
A
THR
87
n
87
THR
87
A
LEU
88
n
88
LEU
88
A
THR
89
n
89
THR
89
A
LEU
90
n
90
LEU
90
A
ILE
91
n
91
ILE
91
A
ALA
92
n
92
ALA
92
A
ASP
93
n
93
ASP
93
A
ASN
94
n
94
ASN
94
A
THR
95
n
95
THR
95
A
PRO
96
n
96
PRO
96
A
ASP
97
n
97
ASP
97
A
SER
98
n
98
SER
98
A
ILE
99
n
99
ILE
99
A
ILE
100
n
100
ILE
100
A
LEU
101
n
101
LEU
101
A
LEU
102
n
102
LEU
102
A
PHE
103
n
103
PHE
103
A
GLU
104
n
104
GLU
104
A
ASP
105
n
105
ASP
105
A
THR
106
n
106
THR
106
A
LYS
107
n
107
LYS
107
A
LYS
108
n
108
LYS
108
A
ASP
109
n
109
ASP
109
A
ARG
110
n
110
ARG
110
A
ILE
111
n
111
ILE
111
A
ALA
112
n
112
ALA
112
A
GLU
113
n
113
GLU
113
A
TYR
114
n
114
TYR
114
A
SER
115
n
115
SER
115
A
LEU
116
n
116
LEU
116
A
LYS
117
n
117
LYS
117
A
LEU
118
n
118
LEU
118
A
MET
119
n
119
MET
119
A
ASP
120
n
120
ASP
120
A
ILE
121
n
121
ILE
121
A
ASP
122
n
122
ASP
122
A
ALA
123
n
123
ALA
123
A
ASP
124
n
124
ASP
124
A
PHE
125
n
125
PHE
125
A
LEU
126
n
126
LEU
126
A
LYS
127
n
127
LYS
127
A
ILE
128
n
128
ILE
128
A
GLU
129
n
129
GLU
129
A
GLU
130
n
130
GLU
130
A
LEU
131
n
131
LEU
131
A
GLN
132
n
132
GLN
132
A
TYR
133
n
133
TYR
133
A
ASP
134
n
134
ASP
134
A
SER
135
n
135
SER
135
A
THR
136
n
136
THR
136
A
LEU
137
n
137
LEU
137
A
SER
138
n
138
SER
138
A
LEU
139
n
139
LEU
139
A
PRO
140
n
140
PRO
140
A
SER
141
n
141
SER
141
A
SER
142
n
142
SER
142
A
GLU
143
n
143
GLU
143
A
PHE
144
n
144
PHE
144
A
SER
145
n
145
SER
145
A
LYS
146
n
146
LYS
146
A
ILE
147
n
147
ILE
147
A
VAL
148
n
148
VAL
148
A
ARG
149
n
149
ARG
149
A
ASP
150
n
150
ASP
150
A
LEU
151
n
151
LEU
151
A
SER
152
n
152
SER
152
A
GLN
153
n
153
GLN
153
A
LEU
154
n
154
LEU
154
A
SER
155
n
155
SER
155
A
ASP
156
n
156
ASP
156
A
SER
157
n
157
SER
157
A
ILE
158
n
158
ILE
158
A
ASN
159
n
159
ASN
159
A
ILE
160
n
160
ILE
160
A
MET
161
n
161
MET
161
A
ILE
162
n
162
ILE
162
A
THR
163
n
163
THR
163
A
LYS
164
n
164
LYS
164
A
GLU
165
n
165
GLU
165
A
THR
166
n
166
THR
166
A
ILE
167
n
167
ILE
167
A
LYS
168
n
168
LYS
168
A
PHE
169
n
169
PHE
169
A
VAL
170
n
170
VAL
170
A
ALA
171
n
171
ALA
171
A
ASP
172
n
172
ASP
172
A
GLY
173
n
173
GLY
173
A
ASP
174
n
174
ASP
174
A
ILE
175
n
175
ILE
175
A
GLY
176
n
176
GLY
176
A
SER
177
n
177
SER
177
A
GLY
178
n
178
GLY
178
A
SER
179
n
179
SER
179
A
VAL
180
n
180
VAL
180
A
ILE
181
n
181
ILE
181
A
ILE
182
n
182
ILE
182
A
LYS
183
n
183
LYS
183
A
PRO
184
n
184
PRO
184
A
PHE
185
n
185
PHE
185
A
VAL
186
n
186
VAL
186
A
ASP
187
n
187
ASP
187
A
MET
188
n
188
MET
188
A
GLU
189
n
189
GLU
189
A
HIS
190
n
190
HIS
190
A
PRO
191
n
191
PRO
191
A
GLU
192
n
192
GLU
192
A
THR
193
n
193
THR
193
A
SER
194
n
194
SER
194
A
ILE
195
n
195
ILE
195
A
LYS
196
n
196
LYS
196
A
LEU
197
n
197
LEU
197
A
GLU
198
n
198
GLU
198
A
MET
199
n
199
MET
199
A
ASP
200
n
200
ASP
200
A
GLN
201
n
201
GLN
201
A
PRO
202
n
202
PRO
202
A
VAL
203
n
203
VAL
203
A
ASP
204
n
204
ASP
204
A
LEU
205
n
205
LEU
205
A
THR
206
n
206
THR
206
A
PHE
207
n
207
PHE
207
A
GLY
208
n
208
GLY
208
A
ALA
209
n
209
ALA
209
A
LYS
210
n
210
LYS
210
A
TYR
211
n
211
TYR
211
A
LEU
212
n
212
LEU
212
A
LEU
213
n
213
LEU
213
A
ASP
214
n
214
ASP
214
A
ILE
215
n
215
ILE
215
A
ILE
216
n
216
ILE
216
A
LYS
217
n
217
LYS
217
A
GLY
218
n
218
GLY
218
A
SER
219
n
219
SER
219
A
SER
220
n
220
SER
220
A
LEU
221
n
221
LEU
221
A
SER
222
n
222
SER
222
A
ASP
223
n
223
ASP
223
A
ARG
224
n
224
ARG
224
A
VAL
225
n
225
VAL
225
A
GLY
226
n
226
GLY
226
A
ILE
227
n
227
ILE
227
A
ARG
228
n
228
ARG
228
A
LEU
229
n
229
LEU
229
A
SER
230
n
230
SER
230
A
SER
231
n
231
SER
231
A
GLU
232
n
232
GLU
232
A
ALA
233
n
233
ALA
233
A
PRO
234
n
234
PRO
234
A
ALA
235
n
235
ALA
235
A
LEU
236
n
236
LEU
236
A
PHE
237
n
237
PHE
237
A
GLN
238
n
238
GLN
238
A
PHE
239
n
239
PHE
239
A
ASP
240
n
240
ASP
240
A
LEU
241
n
241
LEU
241
A
LYS
242
n
242
LYS
242
A
SER
243
n
243
SER
243
A
GLY
244
n
244
GLY
244
A
PHE
245
n
245
PHE
245
A
LEU
246
n
246
LEU
246
A
GLN
247
n
247
GLN
247
A
PHE
248
n
248
PHE
248
A
PHE
249
n
249
PHE
249
A
LEU
250
n
250
LEU
250
A
ALA
251
n
251
ALA
251
A
PRO
252
n
252
PRO
252
A
LYS
253
n
253
LYS
253
A
PHE
254
n
254
PHE
254
A
ASN
255
n
255
ASN
255
A
n
256
256
A
n
257
257
A
n
258
258
A
n
1
32
B
n
2
33
B
n
3
34
B
LYS
35
n
4
LYS
35
B
PRO
36
n
5
PRO
36
B
LYS
37
n
6
LYS
37
B
GLN
38
n
7
GLN
38
B
ALA
39
n
8
ALA
39
B
THR
40
n
9
THR
40
B
LEU
41
n
10
LEU
41
B
ALA
42
n
11
ALA
42
B
ARG
43
n
12
ARG
43
B
PHE
44
n
13
PHE
44
B
PHE
45
n
14
PHE
45
B
n
15
46
B
n
16
47
B
n
17
48
B
n
18
49
B
n
19
50
B
n
20
51
B
n
21
52
B
n
22
53
B
11.4663
-4.1276
13.9890
14.7756
1.2566
20.0460
1.2736
-0.5391
-1.3595
0.9956
-0.8022
-2.6504
-1.1780
2.0207
-0.4714
1.1783
0.3405
0.0515
1.0623
0.0162
1.1730
refined
140.5880
18.2650
47.4900
X-RAY DIFFRACTION
4.1147
4.8737
-0.8938
7.7453
0.6118
1.6087
0.1806
-0.2079
-0.0507
1.0719
0.1373
-0.1509
0.7841
0.1530
-0.3179
0.9884
0.1721
-0.2015
0.5305
0.0537
0.4796
refined
119.4550
21.1500
51.0470
X-RAY DIFFRACTION
B
35
B
4
B
45
B
14
X-RAY DIFFRACTION
1
A
1
A
1
A
255
A
255
X-RAY DIFFRACTION
2
author_defined_assembly
6
hexameric
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
0.0000000000
-1.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
7_665
-z+1,-x+1,y
crystal symmetry operation
139.2800000000
139.2800000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
-1.0000000000
0.0000000000
0.0000000000
10_656
-y+1,z,-x+1
crystal symmetry operation
139.2800000000
0.0000000000
139.2800000000
A
O
ARG
61
A
O
ARG
61
A
N
GLU
3
A
N
GLU
3
A
N
PHE
6
A
N
PHE
6
A
O
LEU
88
A
O
LEU
88
A
N
ILE
91
A
N
ILE
91
A
O
ILE
100
A
O
ILE
100
A
N
PHE
103
A
N
PHE
103
A
O
ALA
112
A
O
ALA
112
A
O
VAL
66
A
O
VAL
66
A
N
CYS
30
A
N
CYS
30
A
N
GLN
29
A
N
GLN
29
A
O
ILE
36
A
O
ILE
36
A
N
ALA
39
A
N
ALA
39
A
O
VAL
48
A
O
VAL
48
A
N
SER
49
A
N
SER
49
A
O
GLN
247
A
O
GLN
247
A
O
PHE
248
A
O
PHE
248
A
N
PHE
237
A
N
PHE
237
A
O
GLN
238
A
O
GLN
238
A
N
GLY
226
A
N
GLY
226
A
O
ILE
227
A
O
ILE
227
A
N
LEU
137
A
N
LEU
137
A
N
SER
138
A
N
SER
138
A
O
LYS
196
A
O
LYS
196
A
O
VAL
180
A
O
VAL
180
A
N
PHE
169
A
N
PHE
169
A
O
VAL
170
A
O
VAL
170
A
N
ASN
159
A
N
ASN
159
A
N
ILE
158
A
N
ILE
158
A
O
PHE
207
A
O
PHE
207
A
N
PHE
254
A
N
PHE
254
B
O
LYS
37
B
O
LYS
6
1
A
ASP
256
A
ASP
256
1
Y
1
A
GLU
257
A
GLU
257
1
Y
1
A
GLU
258
A
GLU
258
1
Y
1
B
ALA
32
B
ALA
1
1
Y
1
B
GLY
33
B
GLY
2
1
Y
1
B
LYS
34
B
LYS
3
1
Y
1
B
THR
46
B
THR
15
1
Y
1
B
SER
47
B
SER
16
1
Y
1
B
MET
48
B
MET
17
1
Y
1
B
LYS
49
B
LYS
18
1
Y
1
B
ASN
50
B
ASN
19
1
Y
1
B
LYS
51
B
LYS
20
1
Y
1
B
PRO
52
B
PRO
21
1
Y
1
B
THR
53
B
THR
22
1
Y
1
A
GLN
24
-101.61
-61.74
1
A
LYS
31
-116.39
-152.65
1
A
ASN
83
-68.94
87.73
1
A
ARG
110
-146.43
54.41
1
A
ASP
122
75.15
47.35
1
A
ALA
123
-122.20
-161.13
1
A
THR
163
-112.18
-164.41
27.318
0.935
0.921
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.28527
0.24681
0.24865
2.80
29.70
537
11219
10682
4.8
99.75
43.060
0.371
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.0
0.0
MOLECULAR REPLACEMENT
0.684
0.361
0.80
0.80
1.20
PDB entry 1PLQ
MAXIMUM LIKELIHOOD
MASK
2.80
29.70
18
2113
0
0
2095
0.007
0.022
2127
1.081
1.991
2866
6.097
5.000
264
35.102
25.376
93
16.997
15.000
404
19.664
15.000
9
0.071
0.200
337
0.003
0.020
1550
0.160
0.300
877
0.313
0.500
1423
0.172
0.500
111
0.125
0.300
31
0.168
0.500
6
0.338
1.500
1362
0.607
2.000
2148
0.525
3.000
837
0.879
4.500
718
0.3
0.393
2.872
39
786
20
99.16
94
2.8
40
2OD8
11287
11287
0.0
0.0
0.039
0.039
1
5.0
4.4
99.2
0.418
2.8
2.9
2.0
1104
0.418
1
3.1
99.2
refinement
REFMAC
5.2.0019
data collection
Blu-Ice
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
phasing
AMoRE
Structure of a peptide derived from Cdc9 bound to PCNA
1
N
N
2
N
N
3
N
N
3
N
N
The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, z, -x and -z, -x, y
A
GLU
8
A
GLU
8
HELX_P
A
GLY
18
A
GLY
18
1
1
11
A
LEU
72
A
LEU
72
HELX_P
A
ARG
80
A
ARG
80
1
2
9
A
SER
141
A
SER
141
HELX_P
A
SER
152
A
SER
152
1
3
12
A
HIS
190
A
HIS
190
HELX_P
A
SER
194
A
SER
194
5
4
5
A
ALA
209
A
ALA
209
HELX_P
A
ILE
216
A
ILE
216
1
5
8
A
LYS
217
A
LYS
217
HELX_P
A
LEU
221
A
LEU
221
5
6
5
B
THR
40
B
THR
9
HELX_P
B
PHE
45
B
PHE
14
5
7
6
PROTEIN BINDING
homotrimer, PCNA-peptide complex, PCNA, PROTEIN BINDING
A
ILE
52
A
ILE
52
1
A
GLY
53
A
GLY
53
9.56
A
ASN
84
A
ASN
84
1
A
THR
85
A
THR
85
3.31
A
LYS
108
A
LYS
108
1
A
ASP
109
A
ASP
109
5.36
A
ILE
121
A
ILE
121
1
A
ASP
122
A
ASP
122
22.80
A
GLU
129
A
GLU
129
1
A
GLU
130
A
GLU
130
-19.59
A
LYS
242
A
LYS
242
1
A
SER
243
A
SER
243
3.64
PCNA_YEAST
UNP
1
1
P15873
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILR
CGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINI
MITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE
DNLI_YEAST
UNP
2
32
P04819
AGKKPKQATLARFFTSMKNKPT
1
258
2OD8
1
258
P15873
A
1
1
258
32
53
2OD8
32
53
P04819
B
2
1
22
5
9
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
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
PHE
57
A
PHE
57
A
CYS
62
A
CYS
62
A
LEU
2
A
LEU
2
A
PHE
6
A
PHE
6
A
THR
87
A
THR
87
A
ALA
92
A
ALA
92
A
SER
98
A
SER
98
A
GLU
104
A
GLU
104
A
ALA
112
A
ALA
112
A
LYS
117
A
LYS
117
A
VAL
66
A
VAL
66
A
ASP
71
A
ASP
71
A
LEU
25
A
LEU
25
A
CYS
30
A
CYS
30
A
ILE
35
A
ILE
35
A
VAL
40
A
VAL
40
A
LEU
46
A
LEU
46
A
ILE
52
A
ILE
52
A
GLY
244
A
GLY
244
A
LEU
250
A
LEU
250
A
ALA
235
A
ALA
235
A
LEU
241
A
LEU
241
A
ARG
224
A
ARG
224
A
LEU
229
A
LEU
229
A
SER
135
A
SER
135
A
PRO
140
A
PRO
140
A
LYS
196
A
LYS
196
A
MET
199
A
MET
199
A
SER
177
A
SER
177
A
ILE
182
A
ILE
182
A
THR
166
A
THR
166
A
ASP
172
A
ASP
172
A
SER
157
A
SER
157
A
THR
163
A
THR
163
A
VAL
203
A
VAL
203
A
GLY
208
A
GLY
208
A
LYS
253
A
LYS
253
A
PHE
254
A
PHE
254
B
LYS
37
B
LYS
6
B
GLN
38
B
GLN
7
197
I 2 3