0.007500
0.004330
0.000000
0.000000
0.008660
0.000000
0.000000
0.000000
0.020437
0.00000
0.00000
0.00000
Leppanen, V.-M.
Tvorogov, D.
Kisko, K.
Prota, A.E.
Jeltsch, M.
Anisimov, A.
Markovic-Mueller, S.
Stuttfeld, E.
Goldie, K.N.
Ballmer-Hofer, K.
Alitalo, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
133.340
133.340
48.930
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
D-saccharide, beta 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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
110
12960
10.1073/PNAS.1301415110
23878260
Structural and Mechanistic Insights Into Vegfr-3 Ligand Binding and Activation
2013
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
PIXEL
2011-04-09
DECTRIS PILATUS 6M
SI(111) MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.00
1.0
X06SA
SLS
1.00
SYNCHROTRON
SLS BEAMLINE X06SA
26521.211
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
2.7.10.1
EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553
1
man
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
2
man
non-polymer
18.015
water
21
nat
water
VEGFR-3, FMS-LIKE TYROSINE KINASE 4, FLT-4, TYROSINE-PROTEIN KINASE RECEPTOR FLT4, VEGFR-3
no
no
DHNPFISVEWLKGPILEATAGDELVKLPVKLAAYPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAG
LRRNISLELVVNVPPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQDLMPQCR
DWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKVGQDERLIYFYVTTHHHHHH
DHNPFISVEWLKGPILEATAGDELVKLPVKLAAYPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAG
LRRNISLELVVNVPPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQDLMPQCR
DWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKVGQDERLIYFYVTTHHHHHH
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
HUMAN
FALL ARMYWORM
sample
9606
HOMO SAPIENS
Sf21
7108
SPODOPTERA FRUGIPERDA
BACULOVIRUS
PFASTBAC1
1
4.74
74.1
NONE
VAPOR DIFFUSION, SITTING DROP
8
VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%.
298
atom_site
pdbx_nonpoly_scheme
pdbx_struct_sheet_hbond
pdbx_struct_special_symmetry
struct_conf
struct_conn
struct_sheet
struct_sheet_order
struct_sheet_range
struct_site
database_PDB_rev
database_PDB_rev_record
exptl_crystal_grow
struct_biol
entity_src_gen
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_database_status
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Database references
Atomic model
Data collection
Derived calculations
Data collection
Experimental preparation
Data collection
Source and taxonomy
Data collection
Derived calculations
Other
Structure summary
1
0
2013-07-31
1
1
2013-08-21
2
0
2018-04-11
2
1
2019-01-30
2
2
2019-04-24
2
3
2020-07-29
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_seq_id
_atom_site.occupancy
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_struct_special_symmetry.auth_seq_id
_struct_conf.pdbx_PDB_helix_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr2_auth_seq_id
_struct_site.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_exptl_crystal_grow.method
_exptl_crystal_grow.temp
_entity_src_gen.pdbx_host_org_cell_line
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_database_status.status_code_sf
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_role
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH VEGFR-3 DOMAINS D1-2
PDBE
Y
PDBE
2013-06-10
REL
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
HOH
water
N-ACETYL GLUCOSAMINE (NAG): THE NAG MOIETIES ARE COVALENTLY
LINKED TO ASN411 AND ASN515.
ASP 328 AND HIS329 ARE A CLONING ARTEFACT AND HIS554 IS
PART OF THE HIS-TAG. RESIDUES 470-483 WERE OMITTED FROM
THE MODEL DUE TO LACK OF ELECTRON DENSITY.
NAG
601
2
NAG
NAG
601
A
NAG
701
2
NAG
NAG
602
A
HOH
2002
3
HOH
HOH
701
A
HOH
2004
3
HOH
HOH
702
A
HOH
2015
3
HOH
HOH
703
A
HOH
2009
3
HOH
HOH
704
A
HOH
2018
3
HOH
HOH
705
A
HOH
2003
3
HOH
HOH
706
A
HOH
2019
3
HOH
HOH
707
A
HOH
2001
3
HOH
HOH
708
A
HOH
2008
3
HOH
HOH
709
A
HOH
2014
3
HOH
HOH
710
A
HOH
2007
3
HOH
HOH
711
A
HOH
2005
3
HOH
HOH
712
A
HOH
2006
3
HOH
HOH
713
A
HOH
2012
3
HOH
HOH
714
A
HOH
2021
3
HOH
HOH
715
A
HOH
2010
3
HOH
HOH
716
A
HOH
2020
3
HOH
HOH
717
A
HOH
2011
3
HOH
HOH
718
A
HOH
2013
3
HOH
HOH
719
A
HOH
2017
3
HOH
HOH
720
A
HOH
2016
3
HOH
HOH
721
A
ASP
328
n
1
ASP
328
A
HIS
329
n
2
HIS
329
A
ASN
330
n
3
ASN
330
A
PRO
331
n
4
PRO
331
A
PHE
332
n
5
PHE
332
A
ILE
333
n
6
ILE
333
A
SER
334
n
7
SER
334
A
VAL
335
n
8
VAL
335
A
GLU
336
n
9
GLU
336
A
TRP
337
n
10
TRP
337
A
LEU
338
n
11
LEU
338
A
LYS
339
n
12
LYS
339
A
GLY
340
n
13
GLY
340
A
PRO
341
n
14
PRO
341
A
ILE
342
n
15
ILE
342
A
LEU
343
n
16
LEU
343
A
GLU
344
n
17
GLU
344
A
ALA
345
n
18
ALA
345
A
THR
346
n
19
THR
346
A
ALA
347
n
20
ALA
347
A
GLY
348
n
21
GLY
348
A
ASP
349
n
22
ASP
349
A
GLU
350
n
23
GLU
350
A
LEU
351
n
24
LEU
351
A
VAL
352
n
25
VAL
352
A
LYS
353
n
26
LYS
353
A
LEU
354
n
27
LEU
354
A
PRO
355
n
28
PRO
355
A
VAL
356
n
29
VAL
356
A
LYS
357
n
30
LYS
357
A
LEU
358
n
31
LEU
358
A
ALA
359
n
32
ALA
359
A
ALA
360
n
33
ALA
360
A
TYR
361
n
34
TYR
361
A
PRO
362
n
35
PRO
362
A
PRO
363
n
36
PRO
363
A
PRO
364
n
37
PRO
364
A
GLU
365
n
38
GLU
365
A
PHE
366
n
39
PHE
366
A
GLN
367
n
40
GLN
367
A
TRP
368
n
41
TRP
368
A
TYR
369
n
42
TYR
369
A
LYS
370
n
43
LYS
370
A
ASP
371
n
44
ASP
371
A
GLY
372
n
45
GLY
372
A
LYS
373
n
46
LYS
373
A
ALA
374
n
47
ALA
374
A
LEU
375
n
48
LEU
375
A
SER
376
n
49
SER
376
A
GLY
377
n
50
GLY
377
A
ARG
378
n
51
ARG
378
A
HIS
379
n
52
HIS
379
A
SER
380
n
53
SER
380
A
PRO
381
n
54
PRO
381
A
HIS
382
n
55
HIS
382
A
ALA
383
n
56
ALA
383
A
LEU
384
n
57
LEU
384
A
VAL
385
n
58
VAL
385
A
LEU
386
n
59
LEU
386
A
LYS
387
n
60
LYS
387
A
GLU
388
n
61
GLU
388
A
VAL
389
n
62
VAL
389
A
THR
390
n
63
THR
390
A
GLU
391
n
64
GLU
391
A
ALA
392
n
65
ALA
392
A
SER
393
n
66
SER
393
A
THR
394
n
67
THR
394
A
GLY
395
n
68
GLY
395
A
THR
396
n
69
THR
396
A
TYR
397
n
70
TYR
397
A
THR
398
n
71
THR
398
A
LEU
399
n
72
LEU
399
A
ALA
400
n
73
ALA
400
A
LEU
401
n
74
LEU
401
A
TRP
402
n
75
TRP
402
A
ASN
403
n
76
ASN
403
A
SER
404
n
77
SER
404
A
ALA
405
n
78
ALA
405
A
ALA
406
n
79
ALA
406
A
GLY
407
n
80
GLY
407
A
LEU
408
n
81
LEU
408
A
ARG
409
n
82
ARG
409
A
ARG
410
n
83
ARG
410
A
ASN
411
n
84
ASN
411
A
ILE
412
n
85
ILE
412
A
SER
413
n
86
SER
413
A
LEU
414
n
87
LEU
414
A
GLU
415
n
88
GLU
415
A
LEU
416
n
89
LEU
416
A
VAL
417
n
90
VAL
417
A
VAL
418
n
91
VAL
418
A
ASN
419
n
92
ASN
419
A
VAL
420
n
93
VAL
420
A
PRO
421
n
94
PRO
421
A
PRO
422
n
95
PRO
422
A
GLN
423
n
96
GLN
423
A
ILE
424
n
97
ILE
424
A
HIS
425
n
98
HIS
425
A
GLU
426
n
99
GLU
426
A
LYS
427
n
100
LYS
427
A
GLU
428
n
101
GLU
428
A
ALA
429
n
102
ALA
429
A
SER
430
n
103
SER
430
A
SER
431
n
104
SER
431
A
PRO
432
n
105
PRO
432
A
SER
433
n
106
SER
433
A
ILE
434
n
107
ILE
434
A
TYR
435
n
108
TYR
435
A
SER
436
n
109
SER
436
A
ARG
437
n
110
ARG
437
A
HIS
438
n
111
HIS
438
A
SER
439
n
112
SER
439
A
ARG
440
n
113
ARG
440
A
GLN
441
n
114
GLN
441
A
ALA
442
n
115
ALA
442
A
LEU
443
n
116
LEU
443
A
THR
444
n
117
THR
444
A
CYS
445
n
118
CYS
445
A
THR
446
n
119
THR
446
A
ALA
447
n
120
ALA
447
A
TYR
448
n
121
TYR
448
A
GLY
449
n
122
GLY
449
A
VAL
450
n
123
VAL
450
A
PRO
451
n
124
PRO
451
A
LEU
452
n
125
LEU
452
A
PRO
453
n
126
PRO
453
A
LEU
454
n
127
LEU
454
A
SER
455
n
128
SER
455
A
ILE
456
n
129
ILE
456
A
GLN
457
n
130
GLN
457
A
TRP
458
n
131
TRP
458
A
HIS
459
n
132
HIS
459
A
TRP
460
n
133
TRP
460
A
ARG
461
n
134
ARG
461
A
PRO
462
n
135
PRO
462
A
TRP
463
n
136
TRP
463
A
THR
464
n
137
THR
464
A
PRO
465
n
138
PRO
465
A
CYS
466
n
139
CYS
466
A
LYS
467
n
140
LYS
467
A
MET
468
n
141
MET
468
A
PHE
469
n
142
PHE
469
A
n
143
470
A
n
144
471
A
n
145
472
A
n
146
473
A
n
147
474
A
n
148
475
A
n
149
476
A
n
150
477
A
n
151
478
A
n
152
479
A
n
153
480
A
n
154
481
A
n
155
482
A
n
156
483
A
PRO
484
n
157
PRO
484
A
GLN
485
n
158
GLN
485
A
CYS
486
n
159
CYS
486
A
ARG
487
n
160
ARG
487
A
ASP
488
n
161
ASP
488
A
TRP
489
n
162
TRP
489
A
ARG
490
n
163
ARG
490
A
ALA
491
n
164
ALA
491
A
VAL
492
n
165
VAL
492
A
THR
493
n
166
THR
493
A
THR
494
n
167
THR
494
A
GLN
495
n
168
GLN
495
A
ASP
496
n
169
ASP
496
A
ALA
497
n
170
ALA
497
A
VAL
498
n
171
VAL
498
A
ASN
499
n
172
ASN
499
A
PRO
500
n
173
PRO
500
A
ILE
501
n
174
ILE
501
A
GLU
502
n
175
GLU
502
A
SER
503
n
176
SER
503
A
LEU
504
n
177
LEU
504
A
ASP
505
n
178
ASP
505
A
THR
506
n
179
THR
506
A
TRP
507
n
180
TRP
507
A
THR
508
n
181
THR
508
A
GLU
509
n
182
GLU
509
A
PHE
510
n
183
PHE
510
A
VAL
511
n
184
VAL
511
A
GLU
512
n
185
GLU
512
A
GLY
513
n
186
GLY
513
A
LYS
514
n
187
LYS
514
A
ASN
515
n
188
ASN
515
A
LYS
516
n
189
LYS
516
A
THR
517
n
190
THR
517
A
VAL
518
n
191
VAL
518
A
SER
519
n
192
SER
519
A
LYS
520
n
193
LYS
520
A
LEU
521
n
194
LEU
521
A
VAL
522
n
195
VAL
522
A
ILE
523
n
196
ILE
523
A
GLN
524
n
197
GLN
524
A
ASN
525
n
198
ASN
525
A
ALA
526
n
199
ALA
526
A
ASN
527
n
200
ASN
527
A
VAL
528
n
201
VAL
528
A
SER
529
n
202
SER
529
A
ALA
530
n
203
ALA
530
A
MET
531
n
204
MET
531
A
TYR
532
n
205
TYR
532
A
LYS
533
n
206
LYS
533
A
CYS
534
n
207
CYS
534
A
VAL
535
n
208
VAL
535
A
VAL
536
n
209
VAL
536
A
SER
537
n
210
SER
537
A
ASN
538
n
211
ASN
538
A
LYS
539
n
212
LYS
539
A
VAL
540
n
213
VAL
540
A
GLY
541
n
214
GLY
541
A
GLN
542
n
215
GLN
542
A
ASP
543
n
216
ASP
543
A
GLU
544
n
217
GLU
544
A
ARG
545
n
218
ARG
545
A
LEU
546
n
219
LEU
546
A
ILE
547
n
220
ILE
547
A
TYR
548
n
221
TYR
548
A
PHE
549
n
222
PHE
549
A
TYR
550
n
223
TYR
550
A
VAL
551
n
224
VAL
551
A
THR
552
n
225
THR
552
A
THR
553
n
226
THR
553
A
HIS
554
n
227
HIS
554
A
n
228
555
A
n
229
556
A
n
230
557
A
n
231
558
A
n
232
559
A
author_defined_assembly
2
dimeric
software_defined_assembly
PISA
1
monomeric
A
ASN
411
GLYCOSYLATION SITE
A
ASN
84
ASN
A
ASN
515
GLYCOSYLATION SITE
A
ASN
188
ASN
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
-0.5000000000
0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLU
336
A
N
GLU
9
A
O
LYS
357
A
O
LYS
30
A
N
VAL
352
A
N
VAL
25
A
O
LEU
386
A
O
LEU
59
A
N
LEU
343
A
N
LEU
16
A
O
GLU
415
A
O
GLU
88
A
O
LEU
414
A
O
LEU
87
A
N
TYR
397
A
N
TYR
70
A
O
ALA
400
A
O
ALA
73
A
N
GLN
367
A
N
GLN
40
A
N
LYS
370
A
N
LYS
43
A
O
LYS
373
A
O
LYS
46
A
N
LEU
343
A
N
LEU
16
A
O
GLU
415
A
O
GLU
88
A
N
VAL
420
A
N
VAL
93
A
O
VAL
450
A
O
VAL
123
A
N
ALA
447
A
N
ALA
120
A
O
THR
517
A
O
THR
190
A
O
LYS
514
A
O
LYS
187
A
N
VAL
511
A
N
VAL
184
A
N
TYR
435
A
N
TYR
108
A
O
THR
552
A
O
THR
225
A
O
ARG
490
A
O
ARG
163
A
N
TRP
460
A
N
TRP
133
A
N
ARG
461
A
N
ARG
134
A
O
MET
531
A
O
MET
204
A
N
TYR
532
A
N
TYR
205
A
O
ILE
547
A
O
ILE
220
1
A
HOH
712
D
HOH
1
A
HOH
721
D
HOH
1
A
CG
ASP
328
A
CG
ASP
1
1
Y
1
A
OD1
ASP
328
A
OD1
ASP
1
1
Y
1
A
OD2
ASP
328
A
OD2
ASP
1
1
Y
1
A
CG
HIS
329
A
CG
HIS
2
1
Y
1
A
ND1
HIS
329
A
ND1
HIS
2
1
Y
1
A
CD2
HIS
329
A
CD2
HIS
2
1
Y
1
A
CE1
HIS
329
A
CE1
HIS
2
1
Y
1
A
NE2
HIS
329
A
NE2
HIS
2
1
Y
1
A
CG
PHE
469
A
CG
PHE
142
1
Y
1
A
CD1
PHE
469
A
CD1
PHE
142
1
Y
1
A
CD2
PHE
469
A
CD2
PHE
142
1
Y
1
A
CE1
PHE
469
A
CE1
PHE
142
1
Y
1
A
CE2
PHE
469
A
CE2
PHE
142
1
Y
1
A
CZ
PHE
469
A
CZ
PHE
142
1
Y
1
A
CG
GLN
485
A
CG
GLN
158
1
Y
1
A
CD
GLN
485
A
CD
GLN
158
1
Y
1
A
OE1
GLN
485
A
OE1
GLN
158
1
Y
1
A
NE2
GLN
485
A
NE2
GLN
158
1
Y
1
A
CG
ARG
487
A
CG
ARG
160
1
Y
1
A
CD
ARG
487
A
CD
ARG
160
1
Y
1
A
NE
ARG
487
A
NE
ARG
160
1
Y
1
A
CZ
ARG
487
A
CZ
ARG
160
1
Y
1
A
NH1
ARG
487
A
NH1
ARG
160
1
Y
1
A
NH2
ARG
487
A
NH2
ARG
160
1
Y
1
A
ALA
470
A
ALA
143
1
Y
1
A
GLN
471
A
GLN
144
1
Y
1
A
ARG
472
A
ARG
145
1
Y
1
A
SER
473
A
SER
146
1
Y
1
A
LEU
474
A
LEU
147
1
Y
1
A
ARG
475
A
ARG
148
1
Y
1
A
ARG
476
A
ARG
149
1
Y
1
A
ARG
477
A
ARG
150
1
Y
1
A
GLN
478
A
GLN
151
1
Y
1
A
GLN
479
A
GLN
152
1
Y
1
A
GLN
480
A
GLN
153
1
Y
1
A
ASP
481
A
ASP
154
1
Y
1
A
LEU
482
A
LEU
155
1
Y
1
A
MET
483
A
MET
156
1
Y
1
A
HIS
555
A
HIS
228
1
Y
1
A
HIS
556
A
HIS
229
1
Y
1
A
HIS
557
A
HIS
230
1
Y
1
A
HIS
558
A
HIS
231
1
Y
1
A
HIS
559
A
HIS
232
1
Y
1
A
LYS
339
-135.39
-56.80
1
A
HIS
438
71.59
-12.30
1
A
ASN
538
-125.62
-167.60
61.2
AN INITIAL MODEL WAS BUILT WITH ARPWARP AND REFINED WITH REFMAC. RESIDUES 470-483 AND SIDECHAINS OF RESIDUES 328, 329, 469, 485 AND 487 ARE DISORDERED AND WERE OMITTED FROM THE FINAL MODEL.
0.2533
0.2098
0.2118
2.500
38.492
878
17525
5.0
99.82
0.33
1
1.99
SIRAS
28.74
0.90
1.11
NONE
ML
FLAT BULK SOLVENT MODEL
2.500
38.492
21
1722
28
0
1673
0.006
1753
1.021
2396
13.566
633
0.066
274
0.004
297
0.3380
0.3115
2.6567
142
2746
100.00
0.3072
0.2964
2.8617
135
2746
100.00
0.3149
0.2642
3.1496
155
2746
100.00
0.2623
0.2291
3.6050
172
2738
100.00
0.2190
0.1925
4.5408
140
2790
100.00
0.2421
0.1825
38.4965
134
2881
100.00
73.0
2.50
50.00
4BSJ
17532
0.0
0.05
1
28.10
9.9
99.8
1.32
2.50
2.65
2.20
1
10.3
99.7
refinement
PHENIX
(PHENIX.REFINE)
data reduction
XDS
data scaling
XDS
phasing
autoSHARP
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 (E.C.2.7.10.1)
Crystal structure of VEGFR-3 extracellular domains D4-5
1
N
N
2
N
N
2
N
N
3
N
N
A
THR
390
A
THR
63
HELX_P
A
THR
394
A
THR
67
5
AA1
5
A
GLU
426
A
GLU
99
HELX_P
A
ALA
429
A
ALA
102
5
AA2
4
disulf
2.032
A
CYS
445
A
SG
CYS
118
1_555
A
CYS
534
A
SG
CYS
207
1_555
disulf
2.036
A
CYS
466
A
SG
CYS
139
1_555
A
CYS
486
A
SG
CYS
159
1_555
covale
1.445
one
N-Glycosylation
A
ASN
411
A
ND2
ASN
84
1_555
A
NAG
601
B
C1
NAG
1_555
covale
1.444
one
N-Glycosylation
A
ASN
515
A
ND2
ASN
188
1_555
A
NAG
602
C
C1
NAG
1_555
TRANSFERASE
TRANSFERASE, LYMPHANGIOGENESIS, ANGIOGENESIS, VASCULAR, IG DOMAIN, GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, DIMERIZATION
A
GLY
340
A
GLY
13
1
A
PRO
341
A
PRO
14
-7.80
A
TYR
361
A
TYR
34
1
A
PRO
362
A
PRO
35
-5.77
A
VAL
450
A
VAL
123
1
A
PRO
451
A
PRO
124
-1.25
VGFR3_HUMAN
UNP
1
P35916
330
553
4BSJ
330
553
P35916
A
1
3
226
1
cloning artifact
ASP
328
4BSJ
A
P35916
UNP
1
1
cloning artifact
HIS
329
4BSJ
A
P35916
UNP
2
1
expression tag
HIS
554
4BSJ
A
P35916
UNP
227
1
expression tag
HIS
555
4BSJ
A
P35916
UNP
228
1
expression tag
HIS
556
4BSJ
A
P35916
UNP
229
1
expression tag
HIS
557
4BSJ
A
P35916
UNP
230
1
expression tag
HIS
558
4BSJ
A
P35916
UNP
231
1
expression tag
HIS
559
4BSJ
A
P35916
UNP
232
3
5
5
2
4
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
PHE
332
A
PHE
5
A
TRP
337
A
TRP
10
A
GLU
350
A
GLU
23
A
TYR
361
A
TYR
34
A
ALA
383
A
ALA
56
A
GLU
388
A
GLU
61
A
ILE
342
A
ILE
15
A
THR
346
A
THR
19
A
LEU
408
A
LEU
81
A
ILE
424
A
ILE
97
A
GLY
395
A
GLY
68
A
ASN
403
A
ASN
76
A
GLU
365
A
GLU
38
A
LYS
370
A
LYS
43
A
LYS
373
A
LYS
46
A
ALA
374
A
ALA
47
A
ILE
342
A
ILE
15
A
THR
346
A
THR
19
A
LEU
408
A
LEU
81
A
ILE
424
A
ILE
97
A
GLN
441
A
GLN
114
A
VAL
450
A
VAL
123
A
LYS
514
A
LYS
187
A
ILE
523
A
ILE
196
A
ILE
501
A
ILE
174
A
VAL
511
A
VAL
184
A
TYR
435
A
TYR
108
A
SER
436
A
SER
109
A
VAL
551
A
VAL
224
A
THR
552
A
THR
225
A
ARG
490
A
ARG
163
A
ALA
491
A
ALA
164
A
GLN
457
A
GLN
130
A
PRO
462
A
PRO
135
A
ALA
530
A
ALA
203
A
ASN
538
A
ASN
211
A
GLY
541
A
GLY
214
A
PHE
549
A
PHE
222
152
P 31 2 1