0.027871
0.000000
0.000000
0.000000
0.023849
0.000000
0.000000
0.000000
0.006079
0.00000
0.00000
0.00000
Lamoureux, J.S.
Stuart, D.
Tsang, R.
Wu, C.
Glover, J.N.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
35.880
41.930
164.500
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
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
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
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
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
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
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
UK
Embo J.
EMJODG
0897
0261-4189
21
5721
5732
10.1093/emboj/cdf572
12411490
Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
2002
10.2210/pdb1mn4/pdb
pdb_00001mn4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
105
1
bent cylindrical Si-mirror (Rh coating)
CCD
2002-05-21
ADSC QUANTUM 4
Si(111) double-crystal
MAD
M
x-ray
1
0.9563
1.0
14-BM-D
APS
0.9563
SYNCHROTRON
APS BEAMLINE 14-BM-D
32385.701
NDT80 PROTEIN
DNA-binding core (Residues 59-340)
1
man
polymer
18.015
water
89
nat
water
no
no
STLQFKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRSYFTLVSTFETANCDLDTFLKSSFDLL
VEDSSVEGRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDS
TFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYD
ELALKNGSKGMFVYLQEMKTPPLIIRGRSPSNYASSQRITVR
STLQFKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRSYFTLVSTFETANCDLDTFLKSSFDLL
VEDSSVEGRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDS
TFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYD
ELALKNGSKGMFVYLQEMKTPPLIIRGRSPSNYASSQRITVR
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
NDT80
4932
Saccharomyces cerevisiae
511693
Escherichia coli BL21
BL21
PLASMID
pGEX-6P1
1
1.91
35.58
VAPOR DIFFUSION, HANGING DROP
7.0
PEG 4000, sodium acetate, magnesium chloride, spermine, 20mer DNA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
1
0
2002-11-06
1
1
2008-04-28
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2002-09-04
REL
REL
HOH
water
HOH
1
2
HOH
HOH
341
A
HOH
2
2
HOH
HOH
342
A
HOH
3
2
HOH
HOH
343
A
HOH
4
2
HOH
HOH
344
A
HOH
5
2
HOH
HOH
345
A
HOH
6
2
HOH
HOH
346
A
HOH
7
2
HOH
HOH
347
A
HOH
8
2
HOH
HOH
348
A
HOH
9
2
HOH
HOH
349
A
HOH
10
2
HOH
HOH
350
A
HOH
12
2
HOH
HOH
351
A
HOH
13
2
HOH
HOH
352
A
HOH
14
2
HOH
HOH
353
A
HOH
17
2
HOH
HOH
354
A
HOH
18
2
HOH
HOH
355
A
HOH
19
2
HOH
HOH
356
A
HOH
20
2
HOH
HOH
357
A
HOH
22
2
HOH
HOH
358
A
HOH
23
2
HOH
HOH
359
A
HOH
24
2
HOH
HOH
360
A
HOH
25
2
HOH
HOH
361
A
HOH
26
2
HOH
HOH
362
A
HOH
30
2
HOH
HOH
363
A
HOH
32
2
HOH
HOH
364
A
HOH
35
2
HOH
HOH
365
A
HOH
37
2
HOH
HOH
366
A
HOH
38
2
HOH
HOH
367
A
HOH
40
2
HOH
HOH
368
A
HOH
41
2
HOH
HOH
369
A
HOH
42
2
HOH
HOH
370
A
HOH
43
2
HOH
HOH
371
A
HOH
44
2
HOH
HOH
372
A
HOH
47
2
HOH
HOH
373
A
HOH
48
2
HOH
HOH
374
A
HOH
49
2
HOH
HOH
375
A
HOH
50
2
HOH
HOH
376
A
HOH
51
2
HOH
HOH
377
A
HOH
52
2
HOH
HOH
378
A
HOH
53
2
HOH
HOH
379
A
HOH
59
2
HOH
HOH
380
A
HOH
60
2
HOH
HOH
381
A
HOH
62
2
HOH
HOH
382
A
HOH
70
2
HOH
HOH
383
A
HOH
73
2
HOH
HOH
384
A
HOH
87
2
HOH
HOH
385
A
HOH
88
2
HOH
HOH
386
A
HOH
89
2
HOH
HOH
387
A
HOH
90
2
HOH
HOH
388
A
HOH
93
2
HOH
HOH
389
A
HOH
94
2
HOH
HOH
390
A
HOH
95
2
HOH
HOH
391
A
HOH
96
2
HOH
HOH
392
A
HOH
100
2
HOH
HOH
393
A
HOH
105
2
HOH
HOH
394
A
HOH
106
2
HOH
HOH
395
A
HOH
107
2
HOH
HOH
396
A
HOH
110
2
HOH
HOH
397
A
HOH
117
2
HOH
HOH
398
A
HOH
120
2
HOH
HOH
399
A
HOH
127
2
HOH
HOH
400
A
HOH
130
2
HOH
HOH
401
A
HOH
131
2
HOH
HOH
402
A
HOH
134
2
HOH
HOH
403
A
HOH
136
2
HOH
HOH
404
A
HOH
139
2
HOH
HOH
405
A
HOH
144
2
HOH
HOH
406
A
HOH
152
2
HOH
HOH
407
A
HOH
157
2
HOH
HOH
408
A
HOH
160
2
HOH
HOH
409
A
HOH
161
2
HOH
HOH
410
A
HOH
178
2
HOH
HOH
411
A
HOH
181
2
HOH
HOH
412
A
HOH
185
2
HOH
HOH
413
A
HOH
187
2
HOH
HOH
414
A
HOH
239
2
HOH
HOH
415
A
HOH
241
2
HOH
HOH
416
A
HOH
242
2
HOH
HOH
417
A
HOH
243
2
HOH
HOH
418
A
HOH
245
2
HOH
HOH
419
A
HOH
250
2
HOH
HOH
420
A
HOH
252
2
HOH
HOH
421
A
HOH
253
2
HOH
HOH
422
A
HOH
256
2
HOH
HOH
423
A
HOH
270
2
HOH
HOH
424
A
HOH
271
2
HOH
HOH
425
A
HOH
274
2
HOH
HOH
426
A
HOH
279
2
HOH
HOH
427
A
HOH
282
2
HOH
HOH
428
A
HOH
283
2
HOH
HOH
429
A
n
1
59
A
n
2
60
A
n
3
61
A
n
4
62
A
PHE
63
n
5
PHE
63
A
LYS
64
n
6
LYS
64
A
VAL
65
n
7
VAL
65
A
GLY
66
n
8
GLY
66
A
PRO
67
n
9
PRO
67
A
PRO
68
n
10
PRO
68
A
PHE
69
n
11
PHE
69
A
GLU
70
n
12
GLU
70
A
LEU
71
n
13
LEU
71
A
VAL
72
n
14
VAL
72
A
ARG
73
n
15
ARG
73
A
ASP
74
n
16
ASP
74
A
TYR
75
n
17
TYR
75
A
CYS
76
n
18
CYS
76
A
PRO
77
n
19
PRO
77
A
VAL
78
n
20
VAL
78
A
VAL
79
n
21
VAL
79
A
GLU
80
n
22
GLU
80
A
SER
81
n
23
SER
81
A
HIS
82
n
24
HIS
82
A
THR
83
n
25
THR
83
A
GLY
84
n
26
GLY
84
A
ARG
85
n
27
ARG
85
A
THR
86
n
28
THR
86
A
LEU
87
n
29
LEU
87
A
ASP
88
n
30
ASP
88
A
LEU
89
n
31
LEU
89
A
ARG
90
n
32
ARG
90
A
ILE
91
n
33
ILE
91
A
ILE
92
n
34
ILE
92
A
PRO
93
n
35
PRO
93
A
ARG
94
n
36
ARG
94
A
ILE
95
n
37
ILE
95
A
ASP
96
n
38
ASP
96
A
ARG
97
n
39
ARG
97
A
GLY
98
n
40
GLY
98
A
PHE
99
n
41
PHE
99
A
ASP
100
n
42
ASP
100
A
HIS
101
n
43
HIS
101
A
ILE
102
n
44
ILE
102
A
ASP
103
n
45
ASP
103
A
GLU
104
n
46
GLU
104
A
GLU
105
n
47
GLU
105
A
TRP
106
n
48
TRP
106
A
VAL
107
n
49
VAL
107
A
GLY
108
n
50
GLY
108
A
TYR
109
n
51
TYR
109
A
LYS
110
n
52
LYS
110
A
ARG
111
n
53
ARG
111
A
SER
112
n
54
SER
112
A
TYR
113
n
55
TYR
113
A
PHE
114
n
56
PHE
114
A
THR
115
n
57
THR
115
A
LEU
116
n
58
LEU
116
A
VAL
117
n
59
VAL
117
A
SER
118
n
60
SER
118
A
THR
119
n
61
THR
119
A
PHE
120
n
62
PHE
120
A
GLU
121
n
63
GLU
121
A
THR
122
n
64
THR
122
A
ALA
123
n
65
ALA
123
A
ASN
124
n
66
ASN
124
A
CYS
125
n
67
CYS
125
A
ASP
126
n
68
ASP
126
A
LEU
127
n
69
LEU
127
A
ASP
128
n
70
ASP
128
A
THR
129
n
71
THR
129
A
PHE
130
n
72
PHE
130
A
LEU
131
n
73
LEU
131
A
LYS
132
n
74
LYS
132
A
SER
133
n
75
SER
133
A
SER
134
n
76
SER
134
A
PHE
135
n
77
PHE
135
A
ASP
136
n
78
ASP
136
A
LEU
137
n
79
LEU
137
A
LEU
138
n
80
LEU
138
A
VAL
139
n
81
VAL
139
A
GLU
140
n
82
GLU
140
A
ASP
141
n
83
ASP
141
A
SER
142
n
84
SER
142
A
SER
143
n
85
SER
143
A
VAL
144
n
86
VAL
144
A
GLU
145
n
87
GLU
145
A
GLY
146
n
88
GLY
146
A
ARG
147
n
89
ARG
147
A
LEU
148
n
90
LEU
148
A
ARG
149
n
91
ARG
149
A
VAL
150
n
92
VAL
150
A
GLN
151
n
93
GLN
151
A
TYR
152
n
94
TYR
152
A
PHE
153
n
95
PHE
153
A
ALA
154
n
96
ALA
154
A
ILE
155
n
97
ILE
155
A
LYS
156
n
98
LYS
156
A
ILE
157
n
99
ILE
157
A
LYS
158
n
100
LYS
158
A
ALA
159
n
101
ALA
159
A
LYS
160
n
102
LYS
160
A
ASN
161
n
103
ASN
161
A
ASP
162
n
104
ASP
162
A
ASP
163
n
105
ASP
163
A
ASP
164
n
106
ASP
164
A
ASP
165
n
107
ASP
165
A
THR
166
n
108
THR
166
A
GLU
167
n
109
GLU
167
A
ILE
168
n
110
ILE
168
A
ASN
169
n
111
ASN
169
A
LEU
170
n
112
LEU
170
A
VAL
171
n
113
VAL
171
A
GLN
172
n
114
GLN
172
A
HIS
173
n
115
HIS
173
A
THR
174
n
116
THR
174
A
n
117
175
A
n
118
176
A
n
119
177
A
n
120
178
A
n
121
179
A
n
122
180
A
n
123
181
A
n
124
182
A
n
125
183
A
n
126
184
A
PRO
185
n
127
PRO
185
A
SER
186
n
128
SER
186
A
VAL
187
n
129
VAL
187
A
CYS
188
n
130
CYS
188
A
PRO
189
n
131
PRO
189
A
LEU
190
n
132
LEU
190
A
VAL
191
n
133
VAL
191
A
PRO
192
n
134
PRO
192
A
SER
193
n
135
SER
193
A
PRO
194
n
136
PRO
194
A
LEU
195
n
137
LEU
195
A
PRO
196
n
138
PRO
196
A
LYS
197
n
139
LYS
197
A
HIS
198
n
140
HIS
198
A
GLN
199
n
141
GLN
199
A
ILE
200
n
142
ILE
200
A
ILE
201
n
143
ILE
201
A
ARG
202
n
144
ARG
202
A
GLU
203
n
145
GLU
203
A
ALA
204
n
146
ALA
204
A
SER
205
n
147
SER
205
A
ASN
206
n
148
ASN
206
A
VAL
207
n
149
VAL
207
A
ARG
208
n
150
ARG
208
A
ASN
209
n
151
ASN
209
A
ILE
210
n
152
ILE
210
A
THR
211
n
153
THR
211
A
LYS
212
n
154
LYS
212
A
MET
213
n
155
MET
213
A
LYS
214
n
156
LYS
214
A
LYS
215
n
157
LYS
215
A
TYR
216
n
158
TYR
216
A
ASP
217
n
159
ASP
217
A
SER
218
n
160
SER
218
A
THR
219
n
161
THR
219
A
PHE
220
n
162
PHE
220
A
TYR
221
n
163
TYR
221
A
LEU
222
n
164
LEU
222
A
HIS
223
n
165
HIS
223
A
ARG
224
n
166
ARG
224
A
ASP
225
n
167
ASP
225
A
HIS
226
n
168
HIS
226
A
VAL
227
n
169
VAL
227
A
ASN
228
n
170
ASN
228
A
TYR
229
n
171
TYR
229
A
GLU
230
n
172
GLU
230
A
GLU
231
n
173
GLU
231
A
TYR
232
n
174
TYR
232
A
GLY
233
n
175
GLY
233
A
VAL
234
n
176
VAL
234
A
ASP
235
n
177
ASP
235
A
SER
236
n
178
SER
236
A
LEU
237
n
179
LEU
237
A
LEU
238
n
180
LEU
238
A
PHE
239
n
181
PHE
239
A
SER
240
n
182
SER
240
A
TYR
241
n
183
TYR
241
A
PRO
242
n
184
PRO
242
A
GLU
243
n
185
GLU
243
A
ASP
244
n
186
ASP
244
A
SER
245
n
187
SER
245
A
ILE
246
n
188
ILE
246
A
GLN
247
n
189
GLN
247
A
LYS
248
n
190
LYS
248
A
VAL
249
n
191
VAL
249
A
ALA
250
n
192
ALA
250
A
ARG
251
n
193
ARG
251
A
TYR
252
n
194
TYR
252
A
GLU
253
n
195
GLU
253
A
ARG
254
n
196
ARG
254
A
VAL
255
n
197
VAL
255
A
GLN
256
n
198
GLN
256
A
PHE
257
n
199
PHE
257
A
ALA
258
n
200
ALA
258
A
SER
259
n
201
SER
259
A
SER
260
n
202
SER
260
A
ILE
261
n
203
ILE
261
A
SER
262
n
204
SER
262
A
VAL
263
n
205
VAL
263
A
LYS
264
n
206
LYS
264
A
LYS
265
n
207
LYS
265
A
PRO
266
n
208
PRO
266
A
SER
267
n
209
SER
267
A
GLN
268
n
210
GLN
268
A
GLN
269
n
211
GLN
269
A
ASN
270
n
212
ASN
270
A
LYS
271
n
213
LYS
271
A
HIS
272
n
214
HIS
272
A
PHE
273
n
215
PHE
273
A
SER
274
n
216
SER
274
A
LEU
275
n
217
LEU
275
A
HIS
276
n
218
HIS
276
A
VAL
277
n
219
VAL
277
A
ILE
278
n
220
ILE
278
A
LEU
279
n
221
LEU
279
A
GLY
280
n
222
GLY
280
A
ALA
281
n
223
ALA
281
A
VAL
282
n
224
VAL
282
A
VAL
283
n
225
VAL
283
A
ASP
284
n
226
ASP
284
A
PRO
285
n
227
PRO
285
A
ASP
286
n
228
ASP
286
A
n
229
287
A
n
230
288
A
n
231
289
A
n
232
290
A
n
233
291
A
n
234
292
A
n
235
293
A
GLY
294
n
236
GLY
294
A
ILE
295
n
237
ILE
295
A
PRO
296
n
238
PRO
296
A
TYR
297
n
239
TYR
297
A
ASP
298
n
240
ASP
298
A
GLU
299
n
241
GLU
299
A
LEU
300
n
242
LEU
300
A
ALA
301
n
243
ALA
301
A
LEU
302
n
244
LEU
302
A
LYS
303
n
245
LYS
303
A
ASN
304
n
246
ASN
304
A
GLY
305
n
247
GLY
305
A
SER
306
n
248
SER
306
A
LYS
307
n
249
LYS
307
A
GLY
308
n
250
GLY
308
A
MET
309
n
251
MET
309
A
PHE
310
n
252
PHE
310
A
VAL
311
n
253
VAL
311
A
TYR
312
n
254
TYR
312
A
LEU
313
n
255
LEU
313
A
GLN
314
n
256
GLN
314
A
GLU
315
n
257
GLU
315
A
MET
316
n
258
MET
316
A
LYS
317
n
259
LYS
317
A
THR
318
n
260
THR
318
A
PRO
319
n
261
PRO
319
A
PRO
320
n
262
PRO
320
A
LEU
321
n
263
LEU
321
A
ILE
322
n
264
ILE
322
A
ILE
323
n
265
ILE
323
A
ARG
324
n
266
ARG
324
A
GLY
325
n
267
GLY
325
A
n
268
326
A
n
269
327
A
n
270
328
A
n
271
329
A
n
272
330
A
n
273
331
A
n
274
332
A
n
275
333
A
n
276
334
A
n
277
335
A
n
278
336
A
n
279
337
A
n
280
338
A
n
281
339
A
n
282
340
A
author_defined_assembly
1
monomeric
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
LEU
300
A
O
LEU
242
A
N
GLY
308
A
N
GLY
250
A
O
LYS
317
A
O
LYS
259
A
N
GLU
70
A
N
GLU
12
A
N
VAL
72
A
N
VAL
14
A
O
GLU
315
A
O
GLU
257
A
O
MET
316
A
O
MET
258
A
N
VAL
277
A
N
VAL
219
A
O
VAL
282
A
O
VAL
224
A
N
GLN
151
A
N
GLN
93
A
O
ILE
155
A
O
ILE
97
A
N
CYS
188
A
N
CYS
130
A
N
CYS
188
A
N
CYS
130
A
O
ILE
155
A
O
ILE
97
A
O
ALA
159
A
O
ALA
101
A
N
ILE
168
A
N
ILE
110
A
N
ILE
168
A
N
ILE
110
A
O
ALA
159
A
O
ALA
101
A
N
VAL
150
A
N
VAL
92
A
O
PHE
135
A
O
PHE
77
A
N
ASP
136
A
N
ASP
78
A
O
VAL
79
A
O
VAL
21
A
N
VAL
171
A
N
VAL
113
A
O
GLN
256
A
O
GLN
198
A
O
VAL
255
A
O
VAL
197
A
N
PHE
114
A
N
PHE
56
A
N
GLU
121
A
N
GLU
63
A
O
ARG
90
A
O
ARG
32
A
O
ASP
100
A
O
ASP
42
A
N
VAL
107
A
N
VAL
49
A
N
GLY
108
A
N
GLY
50
A
O
ILE
322
A
O
ILE
264
1
A
CG
GLU
104
A
CG
GLU
46
0
Y
1
A
CD
GLU
104
A
CD
GLU
46
0
Y
1
A
OE1
GLU
104
A
OE1
GLU
46
0
Y
1
A
OE2
GLU
104
A
OE2
GLU
46
0
Y
1
A
CG
ARG
208
A
CG
ARG
150
1
Y
1
A
CD
ARG
208
A
CD
ARG
150
1
Y
1
A
NE
ARG
208
A
NE
ARG
150
1
Y
1
A
CZ
ARG
208
A
CZ
ARG
150
1
Y
1
A
NH1
ARG
208
A
NH1
ARG
150
1
Y
1
A
NH2
ARG
208
A
NH2
ARG
150
1
Y
1
A
CG
ASP
286
A
CG
ASP
228
1
Y
1
A
OD1
ASP
286
A
OD1
ASP
228
1
Y
1
A
OD2
ASP
286
A
OD2
ASP
228
1
Y
1
A
SER
59
A
SER
1
1
Y
1
A
THR
60
A
THR
2
1
Y
1
A
LEU
61
A
LEU
3
1
Y
1
A
GLN
62
A
GLN
4
1
Y
1
A
ALA
175
A
ALA
117
1
Y
1
A
LYS
176
A
LYS
118
1
Y
1
A
ARG
177
A
ARG
119
1
Y
1
A
ASP
178
A
ASP
120
1
Y
1
A
LYS
179
A
LYS
121
1
Y
1
A
GLY
180
A
GLY
122
1
Y
1
A
PRO
181
A
PRO
123
1
Y
1
A
GLN
182
A
GLN
124
1
Y
1
A
PHE
183
A
PHE
125
1
Y
1
A
CYS
184
A
CYS
126
1
Y
1
A
THR
287
A
THR
229
1
Y
1
A
PHE
288
A
PHE
230
1
Y
1
A
HIS
289
A
HIS
231
1
Y
1
A
GLY
290
A
GLY
232
1
Y
1
A
GLU
291
A
GLU
233
1
Y
1
A
ASN
292
A
ASN
234
1
Y
1
A
PRO
293
A
PRO
235
1
Y
1
A
ARG
326
A
ARG
268
1
Y
1
A
SER
327
A
SER
269
1
Y
1
A
PRO
328
A
PRO
270
1
Y
1
A
SER
329
A
SER
271
1
Y
1
A
ASN
330
A
ASN
272
1
Y
1
A
TYR
331
A
TYR
273
1
Y
1
A
ALA
332
A
ALA
274
1
Y
1
A
SER
333
A
SER
275
1
Y
1
A
SER
334
A
SER
276
1
Y
1
A
GLN
335
A
GLN
277
1
Y
1
A
ARG
336
A
ARG
278
1
Y
1
A
ILE
337
A
ILE
279
1
Y
1
A
THR
338
A
THR
280
1
Y
1
A
VAL
339
A
VAL
281
1
Y
1
A
ARG
340
A
ARG
282
1
Y
1
A
TYR
75
-107.04
-116.24
1
A
ASP
103
28.81
79.43
1
A
ASP
141
59.39
-109.03
1
A
VAL
144
35.79
20.81
1
A
ASP
162
-58.62
-1.32
1
A
ASP
163
-102.96
-61.30
1
A
SER
193
-176.21
149.72
1
A
GLU
203
-48.80
-15.79
1
A
SER
205
-58.97
-112.34
1
A
ARG
208
-68.15
58.74
1
A
ASP
225
-69.29
0.20
1
A
ARG
254
51.62
75.52
1
A
LEU
302
-53.06
-159.07
protein_rep.param
protein.top
dna-rna_rep.param
dna-rna.top
water_rep.param
water.top
ion.param
ion.top
5.73
-1.32
-4.41
0
0
0
0.2680000
0.2260000
0.2290000
0.2290000
2.2
14.95
626
13291
13086
98.5
random
1
anisotropic
THROUGHOUT
0
0
MAD
Engh & Huber
0.27
5.0
0.21
2.2
14.95
89
2078
0
0
1989
0.006
1.3
1.837
1.5
2.290
2
3.177
2
3.524
2.5
14.3
2.2
14.95
1MN4
12530
13292
0
-3
0.0760000
1
20.9
11.7
98.1
2.20
2.25
7.9
0.2210000
5.4
100
data reduction
DENZO
data scaling
SCALEPACK
phasing
SHARP
refinement
CNS
1.0
Structure of Ndt80 (Residues 59-340) DNA-binding domain core
1
N
N
2
N
N
A
ASP
126
A
ASP
68
HELX_P
A
SER
133
A
SER
75
1
1
8
A
LYS
197
A
LYS
139
HELX_P
A
SER
205
A
SER
147
1
2
9
A
ASN
209
A
ASN
151
HELX_P
A
LYS
214
A
LYS
156
1
3
6
A
TYR
216
A
TYR
158
HELX_P
A
PHE
220
A
PHE
162
1
4
5
A
ASP
225
A
ASP
167
HELX_P
A
VAL
227
A
VAL
169
5
5
3
A
ASN
228
A
ASN
170
HELX_P
A
TYR
232
A
TYR
174
5
6
5
A
SER
236
A
SER
178
HELX_P
A
TYR
241
A
TYR
183
5
7
6
TRANSCRIPTION
IG FOLD, PROTEIN-DNA COMPLEX, TRANSCRIPTION
NDT80_YEAST
UNP
1
59
P38830
STLQFKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLL
VEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDS
TFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYD
ELALKNGSKGMFVYLQEMKTPPLIIRGRSPSNYASSQRITVR
59
340
1MN4
59
340
P38830
A
1
1
282
12
4
3
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
parallel
A
TYR
297
A
TYR
239
A
ALA
301
A
ALA
243
A
LYS
307
A
LYS
249
A
LYS
317
A
LYS
259
A
GLU
70
A
GLU
12
A
ASP
74
A
ASP
16
A
LYS
307
A
LYS
249
A
LYS
317
A
LYS
259
A
PHE
273
A
PHE
215
A
VAL
283
A
VAL
225
A
ARG
147
A
ARG
89
A
ASN
161
A
ASN
103
A
CYS
188
A
CYS
130
A
PRO
189
A
PRO
131
A
ARG
147
A
ARG
89
A
ASN
161
A
ASN
103
A
GLU
167
A
GLU
109
A
ILE
168
A
ILE
110
A
ARG
147
A
ARG
89
A
ASN
161
A
ASN
103
A
PHE
135
A
PHE
77
A
LEU
138
A
LEU
80
A
VAL
78
A
VAL
20
A
GLU
80
A
GLU
22
A
LEU
170
A
LEU
112
A
GLN
172
A
GLN
114
A
ALA
250
A
ALA
192
A
PHE
257
A
PHE
199
A
PHE
114
A
PHE
56
A
THR
122
A
THR
64
A
LEU
89
A
LEU
31
A
ARG
97
A
ARG
39
A
ASP
100
A
ASP
42
A
HIS
101
A
HIS
43
A
TRP
106
A
TRP
48
A
TYR
109
A
TYR
51
A
LEU
321
A
LEU
263
A
ARG
324
A
ARG
266
19
P 21 21 21