0.018325
0.000000
0.000000
0.000000
0.018325
0.000000
0.000000
0.000000
0.027894
0.00000
0.00000
0.00000
Luo, J.
Obmolova, O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
54.570
54.570
35.850
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
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
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
C4 H10 O3
106.120
DI(HYDROXYETHYL)ETHER
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
US
Science
SCIEAS
0038
1095-9203
362
598
602
10.1126/science.aaq0620
30385580
Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
2018
0000-0002-7512-2649
0000-0002-5766-8912
0000-0002-1192-4116
0000-0002-4822-7445
0000-0002-1045-7114
0000-0003-4282-4588
0000-0001-8234-201X
0000-0002-3270-1587
0000-0002-9778-1776
0000-0002-9630-3131
0000-0002-5025-3802
0000-0002-9621-3646
0000-0002-6469-2419
100
1
PIXEL
2015-07-20
DECTRIS PILATUS 6M-F
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
17-ID
APS
1.0
SYNCHROTRON
APS BEAMLINE 17-ID
12564.941
humanized antibody SD84h
1
man
polymer
59.044
ACETATE ION
3
syn
non-polymer
106.120
DI(HYDROXYETHYL)ETHER
4
syn
non-polymer
18.015
water
122
nat
water
no
no
EVQLVESGGGLVQPGGSLRLSCAASGFTFSTSWMYWLRQAPGKGLEWVSVINTDGGTYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKDWGGPEPTRGQGTLVTVSS
EVQLVESGGGLVQPGGSLRLSCAASGFTFSTSWMYWLRQAPGKGLEWVSVINTDGGTYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKDWGGPEPTRGQGTLVTVSS
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
sample
1
116
37965
hybrid
HEK293Fexpi
9606
Homo sapiens
Biological sequence
1
2.12
42.09
VAPOR DIFFUSION, SITTING DROP
4.5
2.4 M (NH4)2SO4, 0.1 M sodium acetate, 5% PEG 400
295
repository
Initial release
1
0
2018-11-14
N
RCSB
Y
RCSB
2018-03-09
REL
REL
ACT
ACETATE ION
PEG
DI(HYDROXYETHYL)ETHER
HOH
water
ACT
1
2
ACT
ACT
201
A
ACT
2
2
ACT
ACT
202
A
ACT
3
2
ACT
ACT
203
A
PEG
1
3
PEG
PEG
204
A
PEG
2
3
PEG
PEG
205
A
PEG
3
3
PEG
PEG
206
A
PEG
4
3
PEG
PEG
207
A
HOH
89
4
HOH
HOH
301
A
HOH
53
4
HOH
HOH
302
A
HOH
107
4
HOH
HOH
303
A
HOH
100
4
HOH
HOH
304
A
HOH
48
4
HOH
HOH
305
A
HOH
56
4
HOH
HOH
306
A
HOH
93
4
HOH
HOH
307
A
HOH
46
4
HOH
HOH
308
A
HOH
39
4
HOH
HOH
309
A
HOH
68
4
HOH
HOH
310
A
HOH
58
4
HOH
HOH
311
A
HOH
73
4
HOH
HOH
312
A
HOH
38
4
HOH
HOH
313
A
HOH
101
4
HOH
HOH
314
A
HOH
117
4
HOH
HOH
315
A
HOH
54
4
HOH
HOH
316
A
HOH
4
4
HOH
HOH
317
A
HOH
40
4
HOH
HOH
318
A
HOH
74
4
HOH
HOH
319
A
HOH
60
4
HOH
HOH
320
A
HOH
67
4
HOH
HOH
321
A
HOH
72
4
HOH
HOH
322
A
HOH
12
4
HOH
HOH
323
A
HOH
52
4
HOH
HOH
324
A
HOH
15
4
HOH
HOH
325
A
HOH
16
4
HOH
HOH
326
A
HOH
97
4
HOH
HOH
327
A
HOH
63
4
HOH
HOH
328
A
HOH
45
4
HOH
HOH
329
A
HOH
28
4
HOH
HOH
330
A
HOH
51
4
HOH
HOH
331
A
HOH
75
4
HOH
HOH
332
A
HOH
30
4
HOH
HOH
333
A
HOH
41
4
HOH
HOH
334
A
HOH
78
4
HOH
HOH
335
A
HOH
112
4
HOH
HOH
336
A
HOH
6
4
HOH
HOH
337
A
HOH
11
4
HOH
HOH
338
A
HOH
3
4
HOH
HOH
339
A
HOH
21
4
HOH
HOH
340
A
HOH
24
4
HOH
HOH
341
A
HOH
1
4
HOH
HOH
342
A
HOH
65
4
HOH
HOH
343
A
HOH
2
4
HOH
HOH
344
A
HOH
64
4
HOH
HOH
345
A
HOH
90
4
HOH
HOH
346
A
HOH
26
4
HOH
HOH
347
A
HOH
84
4
HOH
HOH
348
A
HOH
122
4
HOH
HOH
349
A
HOH
13
4
HOH
HOH
350
A
HOH
10
4
HOH
HOH
351
A
HOH
80
4
HOH
HOH
352
A
HOH
88
4
HOH
HOH
353
A
HOH
76
4
HOH
HOH
354
A
HOH
98
4
HOH
HOH
355
A
HOH
14
4
HOH
HOH
356
A
HOH
31
4
HOH
HOH
357
A
HOH
8
4
HOH
HOH
358
A
HOH
7
4
HOH
HOH
359
A
HOH
5
4
HOH
HOH
360
A
HOH
34
4
HOH
HOH
361
A
HOH
49
4
HOH
HOH
362
A
HOH
27
4
HOH
HOH
363
A
HOH
79
4
HOH
HOH
364
A
HOH
35
4
HOH
HOH
365
A
HOH
25
4
HOH
HOH
366
A
HOH
102
4
HOH
HOH
367
A
HOH
43
4
HOH
HOH
368
A
HOH
20
4
HOH
HOH
369
A
HOH
37
4
HOH
HOH
370
A
HOH
18
4
HOH
HOH
371
A
HOH
109
4
HOH
HOH
372
A
HOH
77
4
HOH
HOH
373
A
HOH
47
4
HOH
HOH
374
A
HOH
104
4
HOH
HOH
375
A
HOH
42
4
HOH
HOH
376
A
HOH
32
4
HOH
HOH
377
A
HOH
119
4
HOH
HOH
378
A
HOH
59
4
HOH
HOH
379
A
HOH
69
4
HOH
HOH
380
A
HOH
23
4
HOH
HOH
381
A
HOH
17
4
HOH
HOH
382
A
HOH
62
4
HOH
HOH
383
A
HOH
99
4
HOH
HOH
384
A
HOH
86
4
HOH
HOH
385
A
HOH
70
4
HOH
HOH
386
A
HOH
9
4
HOH
HOH
387
A
HOH
103
4
HOH
HOH
388
A
HOH
29
4
HOH
HOH
389
A
HOH
85
4
HOH
HOH
390
A
HOH
33
4
HOH
HOH
391
A
HOH
71
4
HOH
HOH
392
A
HOH
91
4
HOH
HOH
393
A
HOH
36
4
HOH
HOH
394
A
HOH
66
4
HOH
HOH
395
A
HOH
121
4
HOH
HOH
396
A
HOH
95
4
HOH
HOH
397
A
HOH
55
4
HOH
HOH
398
A
HOH
19
4
HOH
HOH
399
A
HOH
57
4
HOH
HOH
400
A
HOH
115
4
HOH
HOH
401
A
HOH
82
4
HOH
HOH
402
A
HOH
114
4
HOH
HOH
403
A
HOH
111
4
HOH
HOH
404
A
HOH
94
4
HOH
HOH
405
A
HOH
118
4
HOH
HOH
406
A
HOH
96
4
HOH
HOH
407
A
HOH
50
4
HOH
HOH
408
A
HOH
110
4
HOH
HOH
409
A
HOH
108
4
HOH
HOH
410
A
HOH
83
4
HOH
HOH
411
A
HOH
22
4
HOH
HOH
412
A
HOH
116
4
HOH
HOH
413
A
HOH
44
4
HOH
HOH
414
A
HOH
92
4
HOH
HOH
415
A
HOH
120
4
HOH
HOH
416
A
HOH
81
4
HOH
HOH
417
A
HOH
61
4
HOH
HOH
418
A
HOH
105
4
HOH
HOH
419
A
HOH
106
4
HOH
HOH
420
A
HOH
113
4
HOH
HOH
421
A
HOH
87
4
HOH
HOH
422
A
GLU
1
n
1
GLU
1
A
VAL
2
n
2
VAL
2
A
GLN
3
n
3
GLN
3
A
LEU
4
n
4
LEU
4
A
VAL
5
n
5
VAL
5
A
GLU
6
n
6
GLU
6
A
SER
7
n
7
SER
7
A
GLY
8
n
8
GLY
8
A
GLY
9
n
9
GLY
9
A
GLY
10
n
10
GLY
10
A
LEU
11
n
11
LEU
11
A
VAL
12
n
12
VAL
12
A
GLN
13
n
13
GLN
13
A
PRO
14
n
14
PRO
14
A
GLY
15
n
15
GLY
15
A
GLY
16
n
16
GLY
16
A
SER
17
n
17
SER
17
A
LEU
18
n
18
LEU
18
A
ARG
19
n
19
ARG
19
A
LEU
20
n
20
LEU
20
A
SER
21
n
21
SER
21
A
CYS
22
n
22
CYS
22
A
ALA
23
n
23
ALA
23
A
ALA
24
n
24
ALA
24
A
SER
25
n
25
SER
25
A
GLY
26
n
26
GLY
26
A
PHE
27
n
27
PHE
27
A
THR
28
n
28
THR
28
A
PHE
29
n
29
PHE
29
A
SER
30
n
30
SER
30
A
THR
31
n
31
THR
31
A
SER
32
n
32
SER
32
A
TRP
33
n
33
TRP
33
A
MET
34
n
34
MET
34
A
TYR
35
n
35
TYR
35
A
TRP
36
n
36
TRP
36
A
LEU
37
n
37
LEU
37
A
ARG
38
n
38
ARG
38
A
GLN
39
n
39
GLN
39
A
ALA
40
n
40
ALA
40
A
PRO
41
n
41
PRO
41
A
GLY
42
n
42
GLY
42
A
LYS
43
n
43
LYS
43
A
GLY
44
n
44
GLY
44
A
LEU
45
n
45
LEU
45
A
GLU
46
n
46
GLU
46
A
TRP
47
n
47
TRP
47
A
VAL
48
n
48
VAL
48
A
SER
49
n
49
SER
49
A
VAL
50
n
50
VAL
50
A
ILE
51
n
51
ILE
51
A
ASN
52
n
52
ASN
52
A
THR
53
n
53
THR
53
A
ASP
54
n
54
ASP
54
A
GLY
55
n
55
GLY
55
A
GLY
56
n
56
GLY
56
A
THR
57
n
57
THR
57
A
TYR
58
n
58
TYR
58
A
TYR
59
n
59
TYR
59
A
ALA
60
n
60
ALA
60
A
ASP
61
n
61
ASP
61
A
SER
62
n
62
SER
62
A
VAL
63
n
63
VAL
63
A
LYS
64
n
64
LYS
64
A
GLY
65
n
65
GLY
65
A
ARG
66
n
66
ARG
66
A
PHE
67
n
67
PHE
67
A
THR
68
n
68
THR
68
A
ILE
69
n
69
ILE
69
A
SER
70
n
70
SER
70
A
ARG
71
n
71
ARG
71
A
ASP
72
n
72
ASP
72
A
ASN
73
n
73
ASN
73
A
SER
74
n
74
SER
74
A
LYS
75
n
75
LYS
75
A
ASN
76
n
76
ASN
76
A
THR
77
n
77
THR
77
A
LEU
78
n
78
LEU
78
A
TYR
79
n
79
TYR
79
A
LEU
80
n
80
LEU
80
A
GLN
81
n
81
GLN
81
A
MET
82
n
82
MET
82
A
ASN
83
n
83
ASN
83
A
SER
84
n
84
SER
84
A
LEU
85
n
85
LEU
85
A
ARG
86
n
86
ARG
86
A
ALA
87
n
87
ALA
87
A
GLU
88
n
88
GLU
88
A
ASP
89
n
89
ASP
89
A
THR
90
n
90
THR
90
A
ALA
91
n
91
ALA
91
A
VAL
92
n
92
VAL
92
A
TYR
93
n
93
TYR
93
A
TYR
94
n
94
TYR
94
A
CYS
95
n
95
CYS
95
A
ALA
96
n
96
ALA
96
A
LYS
97
n
97
LYS
97
A
ASP
98
n
98
ASP
98
A
TRP
99
n
99
TRP
99
A
GLY
100
n
100
GLY
100
A
GLY
101
n
101
GLY
101
A
PRO
102
n
102
PRO
102
A
GLU
103
n
103
GLU
103
A
PRO
104
n
104
PRO
104
A
THR
105
n
105
THR
105
A
ARG
106
n
106
ARG
106
A
GLY
107
n
107
GLY
107
A
GLN
108
n
108
GLN
108
A
GLY
109
n
109
GLY
109
A
THR
110
n
110
THR
110
A
LEU
111
n
111
LEU
111
A
VAL
112
n
112
VAL
112
A
THR
113
n
113
THR
113
A
VAL
114
n
114
VAL
114
A
SER
115
n
115
SER
115
A
SER
116
n
116
SER
116
A
author_defined_assembly
1
monomeric
gel filtration
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
N
GLN
3
A
N
GLN
3
A
O
SER
25
A
O
SER
25
A
N
LEU
18
A
N
LEU
18
A
O
MET
82
A
O
MET
82
A
O
TYR
79
A
O
TYR
79
A
N
SER
70
A
N
SER
70
A
N
VAL
12
A
N
VAL
12
A
O
THR
113
A
O
THR
113
A
O
THR
110
A
O
THR
110
A
N
TYR
93
A
N
TYR
93
A
O
TYR
94
A
O
TYR
94
A
N
LEU
37
A
N
LEU
37
A
N
TRP
36
A
N
TRP
36
A
O
VAL
48
A
O
VAL
48
A
N
VAL
50
A
N
VAL
50
A
O
TYR
58
A
O
TYR
58
A
N
VAL
12
A
N
VAL
12
A
O
THR
113
A
O
THR
113
A
O
THR
110
A
O
THR
110
A
N
TYR
93
A
N
TYR
93
A
N
LYS
97
A
N
LYS
97
A
O
THR
105
A
O
THR
105
1
A
C1
PEG
207
H
C1
PEG
1
1
N
1
A
O1
PEG
207
H
O1
PEG
1
1
N
1
A
A
O
O
HOH
HOH
312
363
1.98
1
A
A
O
O
HOH
HOH
304
313
2.12
1
A
A
O
O
HOH
HOH
409
410
1.99
1_555
2_545
0.1394
0.1257
0.1263
0.920
24.404
3179
63552
5.00
86.91
0.04
1
FREE R-VALUE
1.37
MOLECULAR REPLACEMENT
12.26
0.90
1.11
0.920
24.404
122
1043
38
0
883
0.006
966
1.009
1304
22.263
347
0.088
138
0.006
166
0.1944
0.2873
0.9338
27
502
17.00
0.2233
0.2374
0.9484
47
891
30.00
0.2266
0.2039
0.9640
67
1271
42.00
0.1960
0.1759
0.9806
88
1672
56.00
0.1545
0.1501
0.9984
110
2088
70.00
0.1503
0.1298
1.0176
145
2763
91.00
0.1137
0.1171
1.0384
157
2982
100.00
0.1238
0.1065
1.0610
160
3023
100.00
0.1267
0.0998
1.0856
158
3016
100.00
0.1166
0.0936
1.1128
158
3005
100.00
0.1146
0.0919
1.1429
158
2986
100.00
0.1052
0.0936
1.1765
157
2990
100.00
0.1083
0.0968
1.2145
159
3030
100.00
0.1117
0.0974
1.2579
158
3001
100.00
0.0972
0.1032
1.3082
158
3004
99.00
0.1257
0.1122
1.3678
160
3025
100.00
0.1363
0.1138
1.4399
158
2999
100.00
0.1351
0.1132
1.5301
157
2984
99.00
0.1410
0.1215
1.6482
159
3029
99.00
0.1338
0.1294
1.8140
158
2993
99.00
0.1301
0.1278
2.0764
157
2997
99.00
0.1419
0.1334
2.6156
160
3026
99.00
0.1732
0.1479
24.4130
163
3096
99.00
0.92
26.27
6CNW
63610
1.00
1
20.39
5.76
86.2
0.92
0.97
2.17
3146
0.78
1
2.46
29.3
refinement
PHENIX
(1.10_2155: ???)
data reduction
XDS
data scaling
XSCALE
phasing
PHASER
N
SD84h
STRUCTURE OF HUMANIZED SINGLE DOMAIN ANTIBODY SD84
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
A
THR
28
A
THR
28
HELX_P
A
SER
32
A
SER
32
5
AA1
5
A
ASP
61
A
ASP
61
HELX_P
A
LYS
64
A
LYS
64
5
AA2
4
A
ASN
73
A
ASN
73
HELX_P
A
LYS
75
A
LYS
75
5
AA3
3
A
ARG
86
A
ARG
86
HELX_P
A
THR
90
A
THR
90
5
AA4
5
disulf
2.057
A
A
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
95
A
SG
CYS
95
1_555
disulf
2.052
B
B
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
95
A
SG
CYS
95
1_555
IMMUNE SYSTEM
single domain antibody, humanization, influenza, hemagglutinin, IMMUNE SYSTEM
A
GLY
101
A
GLY
101
1
A
PRO
102
A
PRO
102
-0.30
6CNW
PDB
1
1
6CNW
1
116
6CNW
1
116
6CNW
A
1
1
116
4
6
4
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
3
A
GLN
3
A
SER
7
A
SER
7
A
LEU
18
A
LEU
18
A
SER
25
A
SER
25
A
THR
77
A
THR
77
A
MET
82
A
MET
82
A
PHE
67
A
PHE
67
A
ASP
72
A
ASP
72
A
LEU
11
A
LEU
11
A
VAL
12
A
VAL
12
A
THR
110
A
THR
110
A
VAL
114
A
VAL
114
A
ALA
91
A
ALA
91
A
LYS
97
A
LYS
97
A
MET
34
A
MET
34
A
GLN
39
A
GLN
39
A
LEU
45
A
LEU
45
A
ILE
51
A
ILE
51
A
THR
57
A
THR
57
A
TYR
59
A
TYR
59
A
LEU
11
A
LEU
11
A
VAL
12
A
VAL
12
A
THR
110
A
THR
110
A
VAL
114
A
VAL
114
A
ALA
91
A
ALA
91
A
LYS
97
A
LYS
97
A
THR
105
A
THR
105
A
ARG
106
A
ARG
106
binding site for residue ACT A 201
A
ACT
201
Software
3
binding site for residue ACT A 202
A
ACT
202
Software
5
binding site for residue ACT A 203
A
ACT
203
Software
6
binding site for residue PEG A 204
A
PEG
204
Software
8
binding site for residue PEG A 205
A
PEG
205
Software
5
binding site for residue PEG A 206
A
PEG
206
Software
4
binding site for residue PEG A 207
A
PEG
207
Software
3
A
PHE
27
A
PHE
27
3
1_555
A
THR
28
A
THR
28
3
1_555
A
HOH
347
I
HOH
3
1_555
A
THR
57
A
THR
57
5
1_555
A
TYR
59
A
TYR
59
5
1_555
A
HOH
325
I
HOH
5
1_555
A
HOH
329
I
HOH
5
1_555
A
HOH
359
I
HOH
5
1_555
A
ASP
72
A
ASP
72
6
1_555
A
ASN
73
A
ASN
73
6
1_555
A
SER
74
A
SER
74
6
1_555
A
PEG
204
E
PEG
6
3_545
A
HOH
303
I
HOH
6
1_555
A
HOH
399
I
HOH
6
1_555
A
ASN
52
A
ASN
52
8
1_555
A
GLY
56
A
GLY
56
8
1_555
A
THR
57
A
THR
57
8
1_555
A
ACT
203
D
ACT
8
4_654
A
PEG
207
H
PEG
8
1_555
A
HOH
302
I
HOH
8
1_555
A
HOH
315
I
HOH
8
1_555
A
HOH
396
I
HOH
8
1_555
A
ASN
83
A
ASN
83
5
4_554
A
SER
115
A
SER
115
5
1_555
A
SER
116
A
SER
116
5
1_555
A
HOH
332
I
HOH
5
1_555
A
HOH
388
I
HOH
5
1_555
A
THR
31
A
THR
31
4
4_654
A
VAL
50
A
VAL
50
4
1_555
A
TYR
58
A
TYR
58
4
1_555
A
HOH
306
I
HOH
4
1_555
A
THR
53
A
THR
53
3
4_654
A
PEG
204
E
PEG
3
1_555
A
HOH
349
I
HOH
3
1_555
76
P 41