0.014176
0.000000
0.001038
0.000000
0.022909
0.000000
0.000000
0.000000
0.018876
0.00000
0.00000
0.00000
Andersen, J.F.
Weichsel, A.
Champagne, D.E.
Balfour, C.A.
Montfort, W.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
94.19
90.00
70.540
43.650
53.120
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
C34 H32 Fe N4 O4
616.487
PROTOPORPHYRIN IX CONTAINING FE
HEME
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 S
149.211
y
METHIONINE
L-peptide linking
H3 N
17.031
AMMONIA
non-polymer
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
C
N
138
N
C
N
139
N
C
N
140
N
C
Y
141
N
C
Y
142
N
C
Y
143
N
C
Y
144
N
C
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
O
N
150
N
O
N
151
N
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
C
Y
158
N
C
Y
159
N
C
Y
160
N
C
Y
161
N
C
N
162
N
C
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
O
Y
175
N
N
N
176
N
N
Y
177
N
N
N
178
N
N
N
179
N
FE
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
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
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
N
N
213
S
C
N
214
N
C
N
215
N
O
N
216
N
C
Y
217
N
C
Y
218
N
N
Y
219
N
C
Y
220
N
C
Y
221
N
N
N
222
N
O
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
H
N
231
N
H
N
232
N
H
N
233
N
O
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
S
C
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
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
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
C
N
288
N
N
N
289
N
O
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
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
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
C
N
311
N
S
N
312
N
C
N
313
N
O
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
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
N
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
N
N
330
S
C
N
331
N
C
N
332
N
O
N
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
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
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
N
N
353
S
C
N
354
N
C
N
355
N
O
N
356
N
C
N
357
N
C
N
358
N
C
N
359
N
O
N
360
N
H
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
N
N
370
S
C
N
371
N
C
N
372
N
O
N
373
N
C
N
374
N
O
N
375
N
O
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
R
C
N
388
N
O
N
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
N
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
Y
413
N
C
N
414
N
O
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
N
N
428
S
C
N
429
N
C
N
430
N
O
N
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
N
438
N
O
N
439
N
O
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
N
N
452
S
C
N
453
N
C
N
454
N
O
N
455
N
C
N
456
N
C
N
457
N
C
N
458
N
O
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
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
doub
N
131
N
sing
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
Y
141
N
doub
Y
142
N
sing
Y
143
N
sing
N
144
N
sing
Y
145
N
doub
N
146
N
sing
Y
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
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
doub
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
Y
173
N
sing
Y
174
N
sing
Y
175
N
doub
N
176
N
sing
Y
177
N
sing
N
178
N
sing
Y
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
doub
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
doub
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
doub
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
Y
222
N
sing
Y
223
N
doub
Y
224
N
doub
N
225
N
sing
Y
226
N
sing
N
227
N
sing
Y
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
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
doub
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
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
doub
N
283
N
sing
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
sing
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
doub
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
doub
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
doub
N
340
N
sing
Y
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
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
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
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
doub
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
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
doub
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
Y
402
N
doub
Y
403
N
sing
Y
404
N
sing
N
405
N
sing
Y
406
N
doub
Y
407
N
sing
Y
408
N
sing
N
409
N
sing
Y
410
N
sing
Y
411
N
doub
N
412
N
sing
Y
413
N
doub
N
414
N
sing
Y
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
doub
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
Y
430
N
doub
Y
431
N
sing
Y
432
N
sing
N
433
N
sing
Y
434
N
doub
N
435
N
sing
Y
436
N
doub
N
437
N
sing
Y
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
doub
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
UK
Structure
STRUE6
2005
0969-2126
6
1315
1327
10.1016/S0969-2126(98)00131-2
9782054
The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein.
1998
10.2210/pdb1np4/pdb
pdb_00001np4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293.0
1
COLLIMATOR
AREA DETECTOR
1997-10-22
ENRAF-NONIUS
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS FR571
20292.664
PROTEIN (NITROPHORIN 4)
1
man
polymer
616.487
PROTOPORPHYRIN IX CONTAINING FE
1
syn
non-polymer
17.031
AMMONIA
1
syn
non-polymer
18.015
water
76
nat
water
NP4
no
no
ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLG
KYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEF
SKFISTKENNCAYDNDSLKSLLTK
ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLG
KYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEF
SKFISTKENNCAYDNDSLKSLLTK
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
Rhodnius
Escherichia
Escherichia coli
sample
13249
SALIVARY GLAND
Rhodnius prolixus
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PET17B
PET17B-NP4
1
2.01
38.79
5.6
2.8 M AMMONIUM PHOSPHATE, 0.1 M NA CACODYLATE, PH 5.6 (FINAL PH 7.5), ROOM TEMPERATURE
room temp
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
1998-08-05
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2023-08-16
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
RCSB
1998-07-29
REL
HEM
PROTOPORPHYRIN IX CONTAINING FE
NH3
AMMONIA
HOH
water
1NP1
PDB ENTRY 1NP1
PDB
experimental model
HEM
185
2
HEM
HEM
185
A
NH3
262
3
NH3
NH3
262
A
HOH
186
4
HOH
HOH
186
A
HOH
187
4
HOH
HOH
187
A
HOH
188
4
HOH
HOH
188
A
HOH
189
4
HOH
HOH
189
A
HOH
190
4
HOH
HOH
190
A
HOH
191
4
HOH
HOH
191
A
HOH
192
4
HOH
HOH
192
A
HOH
193
4
HOH
HOH
193
A
HOH
194
4
HOH
HOH
194
A
HOH
195
4
HOH
HOH
195
A
HOH
196
4
HOH
HOH
196
A
HOH
197
4
HOH
HOH
197
A
HOH
198
4
HOH
HOH
198
A
HOH
199
4
HOH
HOH
199
A
HOH
200
4
HOH
HOH
200
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
207
4
HOH
HOH
207
A
HOH
208
4
HOH
HOH
208
A
HOH
209
4
HOH
HOH
209
A
HOH
210
4
HOH
HOH
210
A
HOH
211
4
HOH
HOH
211
A
HOH
212
4
HOH
HOH
212
A
HOH
213
4
HOH
HOH
213
A
HOH
214
4
HOH
HOH
214
A
HOH
215
4
HOH
HOH
215
A
HOH
216
4
HOH
HOH
216
A
HOH
217
4
HOH
HOH
217
A
HOH
218
4
HOH
HOH
218
A
HOH
219
4
HOH
HOH
219
A
HOH
220
4
HOH
HOH
220
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
242
4
HOH
HOH
242
A
HOH
243
4
HOH
HOH
243
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
HOH
246
4
HOH
HOH
246
A
HOH
247
4
HOH
HOH
247
A
HOH
248
4
HOH
HOH
248
A
HOH
249
4
HOH
HOH
249
A
HOH
250
4
HOH
HOH
250
A
HOH
251
4
HOH
HOH
251
A
HOH
252
4
HOH
HOH
252
A
HOH
253
4
HOH
HOH
253
A
HOH
254
4
HOH
HOH
254
A
HOH
255
4
HOH
HOH
255
A
HOH
256
4
HOH
HOH
256
A
HOH
257
4
HOH
HOH
257
A
HOH
258
4
HOH
HOH
258
A
HOH
259
4
HOH
HOH
259
A
HOH
260
4
HOH
HOH
260
A
HOH
261
4
HOH
HOH
261
A
ALA
1
n
1
ALA
1
A
CYS
2
n
2
CYS
2
A
THR
3
n
3
THR
3
A
LYS
4
n
4
LYS
4
A
ASN
5
n
5
ASN
5
A
ALA
6
n
6
ALA
6
A
ILE
7
n
7
ILE
7
A
ALA
8
n
8
ALA
8
A
GLN
9
n
9
GLN
9
A
THR
10
n
10
THR
10
A
GLY
11
n
11
GLY
11
A
PHE
12
n
12
PHE
12
A
ASN
13
n
13
ASN
13
A
LYS
14
n
14
LYS
14
A
ASP
15
n
15
ASP
15
A
LYS
16
n
16
LYS
16
A
TYR
17
n
17
TYR
17
A
PHE
18
n
18
PHE
18
A
ASN
19
n
19
ASN
19
A
GLY
20
n
20
GLY
20
A
ASP
21
n
21
ASP
21
A
VAL
22
n
22
VAL
22
A
TRP
23
n
23
TRP
23
A
TYR
24
n
24
TYR
24
A
VAL
25
n
25
VAL
25
A
THR
26
n
26
THR
26
A
ASP
27
n
27
ASP
27
A
TYR
28
n
28
TYR
28
A
LEU
29
n
29
LEU
29
A
ASP
30
n
30
ASP
30
A
LEU
31
n
31
LEU
31
A
GLU
32
n
32
GLU
32
A
PRO
33
n
33
PRO
33
A
ASP
34
n
34
ASP
34
A
ASP
35
n
35
ASP
35
A
VAL
36
n
36
VAL
36
A
PRO
37
n
37
PRO
37
A
LYS
38
n
38
LYS
38
A
ARG
39
n
39
ARG
39
A
TYR
40
n
40
TYR
40
A
CYS
41
n
41
CYS
41
A
ALA
42
n
42
ALA
42
A
ALA
43
n
43
ALA
43
A
LEU
44
n
44
LEU
44
A
ALA
45
n
45
ALA
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
THR
48
n
48
THR
48
A
ALA
49
n
49
ALA
49
A
SER
50
n
50
SER
50
A
GLY
51
n
51
GLY
51
A
LYS
52
n
52
LYS
52
A
LEU
53
n
53
LEU
53
A
LYS
54
n
54
LYS
54
A
GLU
55
n
55
GLU
55
A
ALA
56
n
56
ALA
56
A
LEU
57
n
57
LEU
57
A
TYR
58
n
58
TYR
58
A
HIS
59
n
59
HIS
59
A
TYR
60
n
60
TYR
60
A
ASP
61
n
61
ASP
61
A
PRO
62
n
62
PRO
62
A
LYS
63
n
63
LYS
63
A
THR
64
n
64
THR
64
A
GLN
65
n
65
GLN
65
A
ASP
66
n
66
ASP
66
A
THR
67
n
67
THR
67
A
PHE
68
n
68
PHE
68
A
TYR
69
n
69
TYR
69
A
ASP
70
n
70
ASP
70
A
VAL
71
n
71
VAL
71
A
SER
72
n
72
SER
72
A
GLU
73
n
73
GLU
73
A
LEU
74
n
74
LEU
74
A
GLN
75
n
75
GLN
75
A
VAL
76
n
76
VAL
76
A
GLU
77
n
77
GLU
77
A
SER
78
n
78
SER
78
A
LEU
79
n
79
LEU
79
A
GLY
80
n
80
GLY
80
A
LYS
81
n
81
LYS
81
A
TYR
82
n
82
TYR
82
A
THR
83
n
83
THR
83
A
ALA
84
n
84
ALA
84
A
ASN
85
n
85
ASN
85
A
PHE
86
n
86
PHE
86
A
LYS
87
n
87
LYS
87
A
LYS
88
n
88
LYS
88
A
VAL
89
n
89
VAL
89
A
ASP
90
n
90
ASP
90
A
LYS
91
n
91
LYS
91
A
ASN
92
n
92
ASN
92
A
GLY
93
n
93
GLY
93
A
ASN
94
n
94
ASN
94
A
VAL
95
n
95
VAL
95
A
LYS
96
n
96
LYS
96
A
VAL
97
n
97
VAL
97
A
ALA
98
n
98
ALA
98
A
VAL
99
n
99
VAL
99
A
THR
100
n
100
THR
100
A
ALA
101
n
101
ALA
101
A
GLY
102
n
102
GLY
102
A
ASN
103
n
103
ASN
103
A
TYR
104
n
104
TYR
104
A
TYR
105
n
105
TYR
105
A
THR
106
n
106
THR
106
A
PHE
107
n
107
PHE
107
A
THR
108
n
108
THR
108
A
VAL
109
n
109
VAL
109
A
MET
110
n
110
MET
110
A
TYR
111
n
111
TYR
111
A
ALA
112
n
112
ALA
112
A
ASP
113
n
113
ASP
113
A
ASP
114
n
114
ASP
114
A
SER
115
n
115
SER
115
A
SER
116
n
116
SER
116
A
ALA
117
n
117
ALA
117
A
LEU
118
n
118
LEU
118
A
ILE
119
n
119
ILE
119
A
HIS
120
n
120
HIS
120
A
THR
121
n
121
THR
121
A
CYS
122
n
122
CYS
122
A
LEU
123
n
123
LEU
123
A
HIS
124
n
124
HIS
124
A
LYS
125
n
125
LYS
125
A
GLY
126
n
126
GLY
126
A
ASN
127
n
127
ASN
127
A
LYS
128
n
128
LYS
128
A
ASP
129
n
129
ASP
129
A
LEU
130
n
130
LEU
130
A
GLY
131
n
131
GLY
131
A
ASP
132
n
132
ASP
132
A
LEU
133
n
133
LEU
133
A
TYR
134
n
134
TYR
134
A
ALA
135
n
135
ALA
135
A
VAL
136
n
136
VAL
136
A
LEU
137
n
137
LEU
137
A
ASN
138
n
138
ASN
138
A
ARG
139
n
139
ARG
139
A
ASN
140
n
140
ASN
140
A
LYS
141
n
141
LYS
141
A
ASP
142
n
142
ASP
142
A
ALA
143
n
143
ALA
143
A
ALA
144
n
144
ALA
144
A
ALA
145
n
145
ALA
145
A
GLY
146
n
146
GLY
146
A
ASP
147
n
147
ASP
147
A
LYS
148
n
148
LYS
148
A
VAL
149
n
149
VAL
149
A
LYS
150
n
150
LYS
150
A
SER
151
n
151
SER
151
A
ALA
152
n
152
ALA
152
A
VAL
153
n
153
VAL
153
A
SER
154
n
154
SER
154
A
ALA
155
n
155
ALA
155
A
ALA
156
n
156
ALA
156
A
THR
157
n
157
THR
157
A
LEU
158
n
158
LEU
158
A
GLU
159
n
159
GLU
159
A
PHE
160
n
160
PHE
160
A
SER
161
n
161
SER
161
A
LYS
162
n
162
LYS
162
A
PHE
163
n
163
PHE
163
A
ILE
164
n
164
ILE
164
A
SER
165
n
165
SER
165
A
THR
166
n
166
THR
166
A
LYS
167
n
167
LYS
167
A
GLU
168
n
168
GLU
168
A
ASN
169
n
169
ASN
169
A
ASN
170
n
170
ASN
170
A
CYS
171
n
171
CYS
171
A
ALA
172
n
172
ALA
172
A
TYR
173
n
173
TYR
173
A
ASP
174
n
174
ASP
174
A
ASN
175
n
175
ASN
175
A
ASP
176
n
176
ASP
176
A
SER
177
n
177
SER
177
A
LEU
178
n
178
LEU
178
A
LYS
179
n
179
LYS
179
A
SER
180
n
180
SER
180
A
LEU
181
n
181
LEU
181
A
LEU
182
n
182
LEU
182
A
THR
183
n
183
THR
183
A
LYS
184
n
184
LYS
184
A
author_defined_assembly
1
monomeric
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NA
HEM
1_555
89.4
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NB
HEM
1_555
90.0
A
HEM
185
B
NA
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NB
HEM
1_555
89.9
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NC
HEM
1_555
90.3
A
HEM
185
B
NA
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NC
HEM
1_555
179.3
A
HEM
185
B
NB
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
NC
HEM
1_555
90.7
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
ND
HEM
1_555
91.3
A
HEM
185
B
NA
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
ND
HEM
1_555
89.0
A
HEM
185
B
NB
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
ND
HEM
1_555
178.3
A
HEM
185
B
NC
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
HEM
185
B
ND
HEM
1_555
90.3
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
175.1
A
HEM
185
B
NA
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
88.9
A
HEM
185
B
NB
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
94.5
A
HEM
185
B
NC
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
91.4
A
HEM
185
B
ND
HEM
1_555
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
84.1
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
TRP
23
A
O
TRP
23
A
N
LEU
44
A
N
LEU
44
A
O
CYS
41
A
O
CYS
41
A
N
TYR
60
A
N
TYR
60
A
O
GLU
55
A
O
GLU
55
A
N
SER
72
A
N
SER
72
A
O
TYR
69
A
O
TYR
69
A
N
VAL
89
A
N
VAL
89
A
O
TYR
82
A
O
TYR
82
A
N
PHE
107
A
N
PHE
107
A
O
TYR
104
A
O
TYR
104
A
N
HIS
124
A
N
HIS
124
A
O
ALA
117
A
O
ALA
117
A
N
LEU
137
A
N
LEU
137
A
O
TYR
134
A
O
TYR
134
A
N
LEU
29
A
N
LEU
29
1
A
HOH
193
D
HOH
1
A
HOH
194
D
HOH
1
A
HOH
195
D
HOH
1
A
HOH
196
D
HOH
PROTEIN_REP.PARAM
TOPHCSDX.PRO
PARAM19X.HEME
TOPH19X.HEME
PARAM19.SOL
TOPH19.SOL
22.53
0.262
0.012
0.204
0.204
1.50
21.0
2253
22822
10.000
82.0
RANDOM
10000000.000
0.0010
1
THROUGHOUT
0
MOLECULAR REPLACEMENT
PDB ENTRY 1NP1
0.23
0.19
5.00
1.50
21.0
76
1548
44
0
1428
0.006
1.35
0.275
0.02
0.28
1.57
218
2112
8
10.00
18.66
1.50
22.0
1NP4
23988
0.000
0.039
1
9.2000
2.100
91.1
1.50
1.55
5.300
0.135
1.40
74.1
data collection
MADNESS
data reduction
ROTAVATA
model building
CCP4
refinement
X-PLOR
3.851
data reduction
MADNESS
data scaling
CCP4
(AGROVATA
data scaling
ROTAVATA
phasing
CCP4
CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS
1
N
N
2
N
N
3
N
N
4
N
N
A
LYS
14
A
LYS
14
HELX_P
A
TYR
17
A
TYR
17
1
1
4
A
ASP
147
A
ASP
147
HELX_P
A
ALA
156
A
ALA
156
1
2
10
A
PHE
160
A
PHE
160
HELX_P
A
LYS
162
A
LYS
162
5
3
3
A
LYS
167
A
LYS
167
HELX_P
A
ASN
169
A
ASN
169
5
4
3
A
ASN
175
A
ASN
175
HELX_P
A
LEU
182
A
LEU
182
1
5
8
disulf
2.024
A
CYS
2
A
SG
CYS
2
1_555
A
CYS
122
A
SG
CYS
122
1_555
disulf
2.028
A
CYS
41
A
SG
CYS
41
1_555
A
CYS
171
A
SG
CYS
171
1_555
metalc
2.022
A
HIS
59
A
NE2
HIS
59
1_555
A
HEM
185
B
FE
HEM
1_555
metalc
2.175
A
HEM
185
B
FE
HEM
1_555
A
NH3
262
C
N
NH3
1_555
TRANSPORT PROTEIN
NITRIC OXIDE TRANSPORT, FERRIC HEME, ANTIHISTAMINE, VASODILATOR, LIPOCALIN, BILIN BINDING PROTEIN, TRANSPORT PROTEIN
NP4_RHOPR
UNP
1
Q94734
22
205
1NP4
1
184
Q94734
A
1
1
184
9
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
22
A
VAL
22
A
TYR
24
A
TYR
24
A
CYS
41
A
CYS
41
A
ALA
49
A
ALA
49
A
LYS
52
A
LYS
52
A
TYR
60
A
TYR
60
A
THR
67
A
THR
67
A
SER
78
A
SER
78
A
LYS
81
A
LYS
81
A
VAL
89
A
VAL
89
A
TYR
104
A
TYR
104
A
ALA
112
A
ALA
112
A
SER
116
A
SER
116
A
HIS
124
A
HIS
124
A
ASP
132
A
ASP
132
A
ASN
138
A
ASN
138
A
TYR
24
A
TYR
24
A
ASP
30
A
ASP
30
BINDING SITE FOR RESIDUE HEM A 185
A
HEM
185
Software
15
BINDING SITE FOR RESIDUE NH3 A 262
A
NH3
262
Software
2
A
VAL
25
A
VAL
25
15
1_555
A
TYR
40
A
TYR
40
15
1_555
A
LEU
57
A
LEU
57
15
1_555
A
HIS
59
A
HIS
59
15
1_555
A
PHE
68
A
PHE
68
15
1_555
A
ASP
70
A
ASP
70
15
1_555
A
PHE
86
A
PHE
86
15
1_555
A
LYS
88
A
LYS
88
15
1_555
A
TYR
105
A
TYR
105
15
1_555
A
LEU
123
A
LEU
123
15
1_555
A
LYS
125
A
LYS
125
15
1_555
A
LEU
133
A
LEU
133
15
1_555
A
HOH
203
D
HOH
15
1_555
A
HOH
242
D
HOH
15
1_555
A
NH3
262
C
NH3
15
1_555
A
HEM
185
B
HEM
2
1_555
A
HOH
226
D
HOH
2
1_555
5
C 1 2 1