0.008961
0.000000
0.000000
0.000000
0.022075
0.000000
0.000000
0.000000
0.009058
0.00000
0.00000
0.00000
Landry, R.C.
Klimowicz, A.C.
Lavictoire, S.J.
Borisova, S.
Kottachchi, D.T.
Lorimer, I.A.
Evans, S.V.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
111.600
45.300
110.400
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
308
883
893
10.1006/jmbi.2001.4628
11352579
Antibody recognition of a conformational epitope in a peptide antigen: Fv-peptide complex of an antibody fragment specific for the mutant EGF receptor, EGFRvIII.
2001
10.2210/pdb1i8i/pdb
pdb_00001i8i
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
1
AREA DETECTOR
2000-04-21
MARRESEARCH
Supper focussing mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
11745.038
EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV LIGHT CHAIN
D100C
1
man
polymer
13712.354
EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV HEAVY CHAIN
R344C
1
man
polymer
1421.531
EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN
N-TERMINAL FRAGMENT
1
syn
polymer
18.015
water
85
nat
water
DSFV MR1 VARIABLE DOMAIN LIGHT CHAIN
DSFV MR1 VARIABLE DOMAIN HEAVY CHAIN
EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN
no
no
DIELTQSPASLSVATGEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISEGNTLRPGVPSRFSSSGTGTDFVFTIENTLS
EDVGDYYCLQSFNVPLTFGCGTKLEIK
DIELTQSPASLSVATGEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISEGNTLRPGVPSRFSSSGTGTDFVFTIENTLS
EDVGDYYCLQSFNVPLTFGCGTKLEIK
A
polypeptide(L)
no
no
QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKCLEWVASISTGGYNTYYSDNVKGRFTISRENAKNTLY
LQMSSLKSEDTALYYCTRGYSSTSYAMDYWGQGTTVTVSGIEGR
QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKCLEWVASISTGGYNTYYSDNVKGRFTISRENAKNTLY
LQMSSLKSEDTALYYCTRGYSSTSYAMDYWGQGTTVTVSGIEGR
B
polypeptide(L)
no
no
EEKKGNYVVTDH
EEKKGNYVVTDH
C
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
house mouse
Mus
Escherichia
sample
10090
Mus musculus
562
Escherichia coli
TG1
M13KO7 HELPER PHAGE
house mouse
Mus
Escherichia
sample
10090
Mus musculus
562
Escherichia coli
TG1
M13KO7 HELPER PHAGE
1
2.60
52.61
VAPOR DIFFUSION, HANGING DROP
7.0
sodium chloride, MPD, PEG 10K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
1
0
2002-03-14
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
same protein, at liquid nitrogen temperature
SEQUENCE
Residues 100 of chain A and 344 of chain B have
been mutated to Cys residues to introduce a
disulfide bridge between chains A and B.
There is no sequence database match for chain C
because the sequence of EGFRvIII has not yet
been deposited in any database. The DNA
sequence of the normal EGF receptor has been
deposited (NM_005228).
RCSB
Y
RCSB
2001-03-14
REL
REL
HOH
water
The peptide sequence is from the N-terminus of the mutant epidermal growth factor receptor, EGFRvIII.
sample
WAT
601
4
HOH
HOH
601
A
WAT
602
4
HOH
HOH
602
A
WAT
604
4
HOH
HOH
604
A
WAT
607
4
HOH
HOH
607
A
WAT
613
4
HOH
HOH
613
A
WAT
618
4
HOH
HOH
618
A
WAT
625
4
HOH
HOH
625
A
WAT
631
4
HOH
HOH
631
A
WAT
633
4
HOH
HOH
633
A
WAT
634
4
HOH
HOH
634
A
WAT
635
4
HOH
HOH
635
A
WAT
637
4
HOH
HOH
637
A
WAT
641
4
HOH
HOH
641
A
WAT
649
4
HOH
HOH
649
A
WAT
651
4
HOH
HOH
651
A
WAT
653
4
HOH
HOH
653
A
WAT
654
4
HOH
HOH
654
A
WAT
655
4
HOH
HOH
655
A
WAT
656
4
HOH
HOH
656
A
WAT
657
4
HOH
HOH
657
A
WAT
658
4
HOH
HOH
658
A
WAT
659
4
HOH
HOH
659
A
WAT
660
4
HOH
HOH
660
A
WAT
664
4
HOH
HOH
664
A
WAT
666
4
HOH
HOH
666
A
WAT
668
4
HOH
HOH
668
A
WAT
673
4
HOH
HOH
673
A
WAT
674
4
HOH
HOH
674
A
WAT
684
4
HOH
HOH
684
A
WAT
600
4
HOH
HOH
600
B
WAT
603
4
HOH
HOH
603
B
WAT
605
4
HOH
HOH
605
B
WAT
606
4
HOH
HOH
606
B
WAT
608
4
HOH
HOH
608
B
WAT
609
4
HOH
HOH
609
B
WAT
610
4
HOH
HOH
610
B
WAT
612
4
HOH
HOH
612
B
WAT
614
4
HOH
HOH
614
B
WAT
615
4
HOH
HOH
615
B
WAT
616
4
HOH
HOH
616
B
WAT
617
4
HOH
HOH
617
B
WAT
619
4
HOH
HOH
619
B
WAT
620
4
HOH
HOH
620
B
WAT
621
4
HOH
HOH
621
B
WAT
622
4
HOH
HOH
622
B
WAT
623
4
HOH
HOH
623
B
WAT
624
4
HOH
HOH
624
B
WAT
626
4
HOH
HOH
626
B
WAT
627
4
HOH
HOH
627
B
WAT
628
4
HOH
HOH
628
B
WAT
629
4
HOH
HOH
629
B
WAT
630
4
HOH
HOH
630
B
WAT
632
4
HOH
HOH
632
B
WAT
636
4
HOH
HOH
636
B
WAT
638
4
HOH
HOH
638
B
WAT
640
4
HOH
HOH
640
B
WAT
642
4
HOH
HOH
642
B
WAT
643
4
HOH
HOH
643
B
WAT
644
4
HOH
HOH
644
B
WAT
645
4
HOH
HOH
645
B
WAT
646
4
HOH
HOH
646
B
WAT
647
4
HOH
HOH
647
B
WAT
648
4
HOH
HOH
648
B
WAT
650
4
HOH
HOH
650
B
WAT
652
4
HOH
HOH
652
B
WAT
661
4
HOH
HOH
661
B
WAT
663
4
HOH
HOH
663
B
WAT
665
4
HOH
HOH
665
B
WAT
667
4
HOH
HOH
667
B
WAT
669
4
HOH
HOH
669
B
WAT
670
4
HOH
HOH
670
B
WAT
671
4
HOH
HOH
671
B
WAT
672
4
HOH
HOH
672
B
WAT
675
4
HOH
HOH
675
B
WAT
676
4
HOH
HOH
676
B
WAT
677
4
HOH
HOH
677
B
WAT
678
4
HOH
HOH
678
B
WAT
679
4
HOH
HOH
679
B
WAT
680
4
HOH
HOH
680
B
WAT
681
4
HOH
HOH
681
B
WAT
682
4
HOH
HOH
682
B
WAT
683
4
HOH
HOH
683
B
WAT
611
4
HOH
HOH
611
C
WAT
639
4
HOH
HOH
639
C
WAT
662
4
HOH
HOH
662
C
ASP
1
n
1
ASP
1
A
ILE
2
n
2
ILE
2
A
GLU
3
n
3
GLU
3
A
LEU
4
n
4
LEU
4
A
THR
5
n
5
THR
5
A
GLN
6
n
6
GLN
6
A
SER
7
n
7
SER
7
A
PRO
8
n
8
PRO
8
A
ALA
9
n
9
ALA
9
A
SER
10
n
10
SER
10
A
LEU
11
n
11
LEU
11
A
SER
12
n
12
SER
12
A
VAL
13
n
13
VAL
13
A
ALA
14
n
14
ALA
14
A
THR
15
n
15
THR
15
A
GLY
16
n
16
GLY
16
A
GLU
17
n
17
GLU
17
A
LYS
18
n
18
LYS
18
A
VAL
19
n
19
VAL
19
A
THR
20
n
20
THR
20
A
ILE
21
n
21
ILE
21
A
ARG
22
n
22
ARG
22
A
CYS
23
n
23
CYS
23
A
MET
24
n
24
MET
24
A
THR
25
n
25
THR
25
A
SER
26
n
26
SER
26
A
THR
27
n
27
THR
27
A
ASP
28
n
28
ASP
28
A
ILE
29
n
29
ILE
29
A
ASP
30
n
30
ASP
30
A
ASP
31
n
31
ASP
31
A
ASP
32
n
32
ASP
32
A
MET
33
n
33
MET
33
A
ASN
34
n
34
ASN
34
A
TRP
35
n
35
TRP
35
A
TYR
36
n
36
TYR
36
A
GLN
37
n
37
GLN
37
A
GLN
38
n
38
GLN
38
A
LYS
39
n
39
LYS
39
A
PRO
40
n
40
PRO
40
A
GLY
41
n
41
GLY
41
A
GLU
42
n
42
GLU
42
A
PRO
43
n
43
PRO
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
PHE
46
n
46
PHE
46
A
LEU
47
n
47
LEU
47
A
ILE
48
n
48
ILE
48
A
SER
49
n
49
SER
49
A
GLU
50
n
50
GLU
50
A
GLY
51
n
51
GLY
51
A
ASN
52
n
52
ASN
52
A
THR
53
n
53
THR
53
A
LEU
54
n
54
LEU
54
A
ARG
55
n
55
ARG
55
A
PRO
56
n
56
PRO
56
A
GLY
57
n
57
GLY
57
A
VAL
58
n
58
VAL
58
A
PRO
59
n
59
PRO
59
A
SER
60
n
60
SER
60
A
ARG
61
n
61
ARG
61
A
PHE
62
n
62
PHE
62
A
SER
63
n
63
SER
63
A
SER
64
n
64
SER
64
A
SER
65
n
65
SER
65
A
GLY
66
n
66
GLY
66
A
THR
67
n
67
THR
67
A
GLY
68
n
68
GLY
68
A
THR
69
n
69
THR
69
A
ASP
70
n
70
ASP
70
A
PHE
71
n
71
PHE
71
A
VAL
72
n
72
VAL
72
A
PHE
73
n
73
PHE
73
A
THR
74
n
74
THR
74
A
ILE
75
n
75
ILE
75
A
GLU
76
n
76
GLU
76
A
ASN
77
n
77
ASN
77
A
THR
78
n
78
THR
78
A
LEU
79
n
79
LEU
79
A
SER
80
n
80
SER
80
A
GLU
81
n
81
GLU
81
A
ASP
82
n
82
ASP
82
A
VAL
83
n
83
VAL
83
A
GLY
84
n
84
GLY
84
A
ASP
85
n
85
ASP
85
A
TYR
86
n
86
TYR
86
A
TYR
87
n
87
TYR
87
A
CYS
88
n
88
CYS
88
A
LEU
89
n
89
LEU
89
A
GLN
90
n
90
GLN
90
A
SER
91
n
91
SER
91
A
PHE
92
n
92
PHE
92
A
ASN
93
n
93
ASN
93
A
VAL
94
n
94
VAL
94
A
PRO
95
n
95
PRO
95
A
LEU
96
n
96
LEU
96
A
THR
97
n
97
THR
97
A
PHE
98
n
98
PHE
98
A
GLY
99
n
99
GLY
99
A
CYS
100
n
100
CYS
100
A
GLY
101
n
101
GLY
101
A
THR
102
n
102
THR
102
A
LYS
103
n
103
LYS
103
A
LEU
104
n
104
LEU
104
A
GLU
105
n
105
GLU
105
A
ILE
106
n
106
ILE
106
A
n
107
107
A
GLN
301
n
1
GLN
301
B
VAL
302
n
2
VAL
302
B
LYS
303
n
3
LYS
303
B
LEU
304
n
4
LEU
304
B
GLN
305
n
5
GLN
305
B
GLN
306
n
6
GLN
306
B
SER
307
n
7
SER
307
B
GLY
308
n
8
GLY
308
B
GLY
309
n
9
GLY
309
B
GLY
310
n
10
GLY
310
B
LEU
311
n
11
LEU
311
B
VAL
312
n
12
VAL
312
B
LYS
313
n
13
LYS
313
B
PRO
314
n
14
PRO
314
B
GLY
315
n
15
GLY
315
B
ALA
316
n
16
ALA
316
B
SER
317
n
17
SER
317
B
LEU
318
n
18
LEU
318
B
LYS
319
n
19
LYS
319
B
LEU
320
n
20
LEU
320
B
SER
321
n
21
SER
321
B
CYS
322
n
22
CYS
322
B
VAL
323
n
23
VAL
323
B
THR
324
n
24
THR
324
B
SER
325
n
25
SER
325
B
GLY
326
n
26
GLY
326
B
PHE
327
n
27
PHE
327
B
THR
328
n
28
THR
328
B
PHE
329
n
29
PHE
329
B
ARG
330
n
30
ARG
330
B
LYS
331
n
31
LYS
331
B
PHE
332
n
32
PHE
332
B
GLY
333
n
33
GLY
333
B
MET
334
n
34
MET
334
B
SER
335
n
35
SER
335
B
TRP
336
n
36
TRP
336
B
VAL
337
n
37
VAL
337
B
ARG
338
n
38
ARG
338
B
GLN
339
n
39
GLN
339
B
THR
340
n
40
THR
340
B
SER
341
n
41
SER
341
B
ASP
342
n
42
ASP
342
B
LYS
343
n
43
LYS
343
B
CYS
344
n
44
CYS
344
B
LEU
345
n
45
LEU
345
B
GLU
346
n
46
GLU
346
B
TRP
347
n
47
TRP
347
B
VAL
348
n
48
VAL
348
B
ALA
349
n
49
ALA
349
B
SER
350
n
50
SER
350
B
ILE
351
n
51
ILE
351
B
SER
354
n
52
SER
352
B
THR
355
n
53
THR
353
B
GLY
356
n
54
GLY
354
B
GLY
357
n
55
GLY
355
B
TYR
358
n
56
TYR
356
B
ASN
359
n
57
ASN
357
B
THR
360
n
58
THR
358
B
TYR
361
n
59
TYR
359
B
TYR
362
n
60
TYR
360
B
SER
363
n
61
SER
361
B
ASP
364
n
62
ASP
362
B
ASN
365
n
63
ASN
363
B
VAL
366
n
64
VAL
364
B
LYS
367
n
65
LYS
365
B
GLY
368
n
66
GLY
366
B
ARG
369
n
67
ARG
367
B
PHE
370
n
68
PHE
368
B
THR
371
n
69
THR
369
B
ILE
372
n
70
ILE
370
B
SER
373
n
71
SER
371
B
ARG
374
n
72
ARG
372
B
GLU
375
n
73
GLU
373
B
ASN
376
n
74
ASN
374
B
ALA
377
n
75
ALA
375
B
LYS
378
n
76
LYS
376
B
ASN
379
n
77
ASN
377
B
THR
380
n
78
THR
378
B
LEU
381
n
79
LEU
379
B
TYR
382
n
80
TYR
380
B
LEU
383
n
81
LEU
381
B
GLN
384
n
82
GLN
382
B
MET
385
n
83
MET
383
B
SER
386
n
84
SER
384
B
SER
387
n
85
SER
385
B
LEU
388
n
86
LEU
386
B
LYS
389
n
87
LYS
387
B
SER
390
n
88
SER
388
B
GLU
391
n
89
GLU
389
B
ASP
392
n
90
ASP
390
B
THR
393
n
91
THR
391
B
ALA
394
n
92
ALA
392
B
LEU
395
n
93
LEU
393
B
TYR
396
n
94
TYR
394
B
TYR
397
n
95
TYR
395
B
CYS
398
n
96
CYS
396
B
THR
399
n
97
THR
397
B
ARG
400
n
98
ARG
398
B
GLY
401
n
99
GLY
399
B
TYR
402
n
100
TYR
400
B
SER
403
n
101
SER
401
B
SER
404
n
102
SER
402
B
THR
405
n
103
THR
403
B
SER
406
n
104
SER
404
B
TYR
407
n
105
TYR
405
B
ALA
408
n
106
ALA
406
B
MET
409
n
107
MET
407
B
ASP
410
n
108
ASP
408
B
TYR
411
n
109
TYR
409
B
TRP
412
n
110
TRP
410
B
GLY
413
n
111
GLY
411
B
GLN
414
n
112
GLN
412
B
GLY
415
n
113
GLY
413
B
THR
416
n
114
THR
414
B
THR
417
n
115
THR
415
B
VAL
418
n
116
VAL
416
B
THR
419
n
117
THR
417
B
VAL
420
n
118
VAL
418
B
SER
421
n
119
SER
419
B
n
120
420
B
n
121
421
B
n
122
422
B
n
123
423
B
n
124
424
B
n
1
499
C
n
2
500
C
n
3
501
C
LYS
502
n
4
LYS
502
C
GLY
503
n
5
GLY
503
C
ASN
504
n
6
ASN
504
C
TYR
505
n
7
TYR
505
C
VAL
506
n
8
VAL
506
C
VAL
507
n
9
VAL
507
C
THR
508
n
10
THR
508
C
ASP
509
n
11
ASP
509
C
HIS
510
n
12
HIS
510
C
author_and_software_defined_assembly
PISA
3
trimeric
2850
-17
10130
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
SER
7
A
O
SER
7
A
N
ARG
22
A
N
ARG
22
A
O
CYS
23
A
O
CYS
23
A
N
PHE
71
A
N
PHE
71
A
N
THR
74
A
N
THR
74
A
O
SER
63
A
O
SER
63
A
O
THR
53
A
O
THR
53
A
N
SER
49
A
N
SER
49
A
N
LEU
47
A
N
LEU
47
A
O
TRP
35
A
O
TRP
35
A
N
GLN
38
A
N
GLN
38
A
O
ASP
85
A
O
ASP
85
A
N
GLN
90
A
N
GLN
90
A
O
THR
97
A
O
THR
97
A
O
THR
53
A
O
THR
53
A
N
SER
49
A
N
SER
49
A
N
LEU
47
A
N
LEU
47
A
O
TRP
35
A
O
TRP
35
A
N
GLN
38
A
N
GLN
38
A
O
ASP
85
A
O
ASP
85
A
N
TYR
86
A
N
TYR
86
A
O
THR
102
A
O
THR
102
A
O
LYS
103
A
O
LYS
103
A
N
LEU
11
A
N
LEU
11
B
O
SER
307
B
O
SER
7
B
N
SER
321
B
N
SER
21
B
O
CYS
322
B
O
CYS
22
B
N
LEU
379
B
N
LEU
79
B
N
GLN
382
B
N
GLN
82
B
O
THR
369
B
O
THR
69
B
O
TYR
409
B
O
TYR
109
B
N
ARG
398
B
N
ARG
98
B
N
THR
397
B
N
THR
97
B
O
SER
335
B
O
SER
35
B
O
ARG
338
B
O
ARG
38
B
N
GLU
346
B
N
GLU
46
B
O
SER
350
B
O
SER
50
B
N
TYR
359
B
N
TYR
59
B
O
TYR
409
B
O
TYR
109
B
N
ARG
398
B
N
ARG
98
B
N
TYR
394
B
N
TYR
94
B
O
THR
414
B
O
THR
114
B
N
THR
417
B
N
THR
117
B
O
GLY
310
B
O
GLY
10
1
A
LYS
107
A
LYS
107
1
Y
1
B
GLY
420
B
GLY
120
1
Y
1
B
ILE
421
B
ILE
121
1
Y
1
B
GLU
422
B
GLU
122
1
Y
1
B
GLY
423
B
GLY
123
1
Y
1
B
ARG
424
B
ARG
124
1
Y
1
C
GLU
499
C
GLU
1
1
Y
1
C
GLU
500
C
GLU
2
1
Y
1
C
LYS
501
C
LYS
3
1
Y
1
C
TYR
505
0.084
SIDE CHAIN
1
-16.34
2.70
111.00
94.66
A
A
A
N
CA
C
ASP
ASP
ASP
1
1
1
N
1
6.82
0.80
106.30
113.12
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
35
35
35
N
1
-5.97
0.80
107.30
101.33
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
35
35
35
N
1
-4.04
0.60
121.00
116.96
A
A
A
CB
CG
CD1
TYR
TYR
TYR
36
36
36
N
1
-3.92
0.60
121.00
117.08
A
A
A
CB
CG
CD1
TYR
TYR
TYR
86
86
86
N
1
13.72
2.20
113.40
127.12
A
A
A
CA
CB
CG
LYS
LYS
LYS
103
103
103
N
1
14.57
2.30
115.30
129.87
A
A
A
CA
CB
CG
LEU
LEU
LEU
104
104
104
N
1
5.33
0.80
106.30
111.63
B
B
B
CD1
CG
CD2
TRP
TRP
TRP
336
336
336
N
1
-5.38
0.80
107.30
101.92
B
B
B
CE2
CD2
CG
TRP
TRP
TRP
336
336
336
N
1
-4.95
0.50
120.30
115.35
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
338
338
338
N
1
7.02
1.10
114.20
121.22
B
B
B
CA
CB
SG
CYS
CYS
CYS
344
344
344
N
1
6.87
0.80
106.30
113.17
B
B
B
CD1
CG
CD2
TRP
TRP
TRP
347
347
347
N
1
-6.47
1.00
110.10
103.63
B
B
B
CG
CD1
NE1
TRP
TRP
TRP
347
347
347
N
1
-4.93
0.80
107.30
102.37
B
B
B
CE2
CD2
CG
TRP
TRP
TRP
347
347
347
N
1
5.56
0.50
120.30
125.86
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
372
372
372
N
1
-5.80
0.50
120.30
114.50
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
372
372
372
N
1
-11.70
1.90
110.30
98.60
B
B
B
N
CA
CB
THR
THR
THR
397
397
397
N
1
5.07
0.50
120.30
125.37
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
398
398
398
N
1
-3.17
0.50
120.30
117.13
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
398
398
398
N
1
18.71
2.70
111.00
129.71
B
B
B
N
CA
C
SER
SER
SER
402
402
402
N
1
-12.16
1.90
110.30
98.14
B
B
B
N
CA
CB
THR
THR
THR
403
403
403
N
1
6.41
0.80
106.30
112.71
B
B
B
CD1
CG
CD2
TRP
TRP
TRP
410
410
410
N
1
-5.57
0.80
107.30
101.73
B
B
B
CE2
CD2
CG
TRP
TRP
TRP
410
410
410
N
1
9.79
1.60
110.90
120.69
B
B
B
CG1
CB
CG2
VAL
VAL
VAL
416
416
416
N
1
A
GLU
50
-36.75
129.86
1
A
GLU
105
45.09
79.31
1
B
ALA
316
-68.49
-179.67
1
B
ASP
342
-95.56
33.79
1
B
LYS
343
48.44
3.69
1
B
SER
401
-173.50
129.91
1
B
SER
402
21.23
-31.32
1
C
ASN
504
26.57
84.00
26
0.262
0.156
0.176
0.173
2.4
6.0
997
9686
9119
RANDOM
1
3
3
MOLECULAR REPLACEMENT
CHARMm
2.4
6.0
85
1896
0
0
1811
3.2
0.017
0.344
0.245
2.50
83
678
8170
65.3
40.12
2.4
6.0
1I8I
9686
9119
3
3
0.06
1
16.2
2.6
91.9
0.115
2.4
2.48
2.46
62.3
data reduction
DENZO
data scaling
SCALEPACK
phasing
MERLOT
refinement
X-PLOR
CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII, AT ROOM TEMPERATURE
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
LEU
79
A
LEU
79
HELX_P
A
VAL
83
A
VAL
83
5
1
5
B
THR
328
B
THR
28
HELX_P
B
PHE
332
B
PHE
32
5
2
5
B
LYS
387
B
LYS
87
HELX_P
B
THR
391
B
THR
91
5
3
5
disulf
2.001
A
CYS
23
A
SG
CYS
23
1_555
A
CYS
88
A
SG
CYS
88
1_555
disulf
1.985
A
CYS
100
A
SG
CYS
100
1_555
B
CYS
344
B
SG
CYS
44
1_555
disulf
1.988
B
CYS
322
B
SG
CYS
22
1_555
B
CYS
396
B
SG
CYS
96
1_555
IMMUNE SYSTEM
antibody-peptide complex, immunoglobulin fold, peptide antigen, type II' beta turn, IMMUNE SYSTEM
A
SER
7
A
SER
7
1
A
PRO
8
A
PRO
8
-1.76
A
VAL
94
A
VAL
94
1
A
PRO
95
A
PRO
95
-3.90
Q8R028
UNP
1
136
Q8R028
DIELTQSPASLSVATGEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISEGNTLRPGVPSRFSSSGTGTDFVFTIENTLS
EDVGDYYCLQSFNVPLTFGDGTKLEIK
HV58_MOUSE
UNP
2
1
P18529
QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKRLEWVASISTGGYNTYYSDNVKGRFTISRENAKNTLY
LQMSSLKSEDTALYYCTRGYSSTSYAMDYWGQGTTVTVSGIEGR
1I8I
PDB
3
1I8I
136
242
1I8I
1
107
Q8R028
A
1
1
107
1
124
1I8I
301
424
P18529
B
2
1
124
499
510
1I8I
499
510
1I8I
C
3
1
12
1
ASP
engineered mutation
CYS
100
1I8I
A
Q8R028
UNP
235
100
2
ARG
engineered mutation
CYS
344
1I8I
B
P18529
UNP
44
44
2
SER
conflict
GLY
420
1I8I
B
P18529
UNP
120
120
2
SER
conflict
ILE
421
1I8I
B
P18529
UNP
121
121
2
GLY
conflict
GLU
422
1I8I
B
P18529
UNP
122
122
2
GLY
conflict
ARG
424
1I8I
B
P18529
UNP
124
124
4
5
6
4
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
A
LEU
4
A
LEU
4
A
SER
7
A
SER
7
A
VAL
19
A
VAL
19
A
THR
25
A
THR
25
A
ASP
70
A
ASP
70
A
ILE
75
A
ILE
75
A
PHE
62
A
PHE
62
A
THR
67
A
THR
67
A
THR
53
A
THR
53
A
LEU
54
A
LEU
54
A
LYS
45
A
LYS
45
A
SER
49
A
SER
49
A
MET
33
A
MET
33
A
GLN
38
A
GLN
38
A
GLY
84
A
GLY
84
A
GLN
90
A
GLN
90
A
THR
97
A
THR
97
A
PHE
98
A
PHE
98
A
THR
53
A
THR
53
A
LEU
54
A
LEU
54
A
LYS
45
A
LYS
45
A
SER
49
A
SER
49
A
MET
33
A
MET
33
A
GLN
38
A
GLN
38
A
GLY
84
A
GLY
84
A
GLN
90
A
GLN
90
A
THR
102
A
THR
102
A
LEU
104
A
LEU
104
A
SER
10
A
SER
10
A
LEU
11
A
LEU
11
B
LYS
303
B
LYS
3
B
SER
307
B
SER
7
B
LEU
318
B
LEU
18
B
SER
325
B
SER
25
B
THR
378
B
THR
78
B
MET
383
B
MET
83
B
PHE
368
B
PHE
68
B
GLU
373
B
GLU
73
B
SER
404
B
SER
104
B
TRP
410
B
TRP
110
B
ALA
392
B
ALA
92
B
SER
401
B
SER
101
B
MET
334
B
MET
34
B
GLN
339
B
GLN
39
B
LEU
345
B
LEU
45
B
ILE
351
B
ILE
51
B
THR
358
B
THR
58
B
TYR
360
B
TYR
60
B
SER
404
B
SER
104
B
TRP
410
B
TRP
110
B
ALA
392
B
ALA
92
B
SER
401
B
SER
101
B
THR
414
B
THR
114
B
VAL
418
B
VAL
118
B
GLY
310
B
GLY
10
B
VAL
312
B
VAL
12
20
C 2 2 21