1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Stauffer, M.E.
Skelton, N.J.
Fairbrother, W.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
NE
J.BIOMOL.NMR
JBNME9
0800
0925-2738
23
57
61
10.1023/A:1015346504499
12061718
Refinement of the Solution Structure of the Heparin-binding Domain of
Vascular Endothelial Growth Factor using Residual Dipolar Couplings
2002
UK
Structure
STRUE6
2005
0969-2126
6
637
648
10.1016/S0969-2126(98)00065-3
Solution Structure of the Heparin-binding Domain of Vascular endothelial Growth Factor
1998
10.2210/pdb1kmx/pdb
pdb_00001kmx
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
6496.479
vascular endothelial growth factor
heparin-binding domain
1
man
polymer
no
no
ARQENPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR
ARQENPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR
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
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-07-24
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
1VGH is the same protein but refined without using residual dipolar coupling restraints
2VGH is the minimized mean corresponding the the same protein refined without residual dipolar coupling restraints
RCSB
Y
RCSB
2001-12-17
REL
The structure was refined using 1H-15N dipolar coupling restraints
structures with the least restraint violations
100
20
DQF-COSY
2D NOESY
3D_15N-separated_NOESY
HNHA
DQF-COSY
2D NOESY
2D 15N IPAP-HSQC
2D 15N IPAP HSQC
25 mM sodium acetate; 50 mM sodium chloride
5.5
ambient
300
K
25 mM sodium acetate; 50 mM sodium chloride
5.5
ambient
300
K
25 mM sodium acetate; 50 mM sodium chloride
5.5
ambient
300
K
25 mM sodium acetate; 50 mM sodium chloride
5.5
ambient
300
K
The structures are based on 459 NOE-derived distance restraints, 28 H-bond restraints, 66 dihedral angle restraints, and 38 residual dipolar coupling restraints
torsion angle dynamics
1
fewest violations
2.0 mM VEGF heparin-binding domain; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide
90% H2O/10% D2O
2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide
90% H2O/10% D2O
2.0 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride, 0.02% sodium azide
99.9% D2O
0.6 mM VEGF heparin-binding domain U-15N; 25 mM sodium acetate; 50 mM sodium chloride; 0.02% sodium azide
4:1:0.2 ditridecanoyl-phosphatidylcholine/dihexanoyl-phosphatidylcholine/cetyltrimethylammonium bromide, 5% w/v total lipid in 90% H2O, 10% D2O
collection
UXNMR
collection
XwinNMR
processing
Felix
data analysis
Felix
structure solution
CNX
Molecular Simulations, Inc.
refinement
CNX
500
Bruker
AMX
500
Bruker
DRX
ALA
1
n
1
ALA
1
A
ARG
2
n
2
ARG
2
A
GLN
3
n
3
GLN
3
A
GLU
4
n
4
GLU
4
A
ASN
5
n
5
ASN
5
A
PRO
6
n
6
PRO
6
A
CYS
7
n
7
CYS
7
A
GLY
8
n
8
GLY
8
A
PRO
9
n
9
PRO
9
A
CYS
10
n
10
CYS
10
A
SER
11
n
11
SER
11
A
GLU
12
n
12
GLU
12
A
ARG
13
n
13
ARG
13
A
ARG
14
n
14
ARG
14
A
LYS
15
n
15
LYS
15
A
HIS
16
n
16
HIS
16
A
LEU
17
n
17
LEU
17
A
PHE
18
n
18
PHE
18
A
VAL
19
n
19
VAL
19
A
GLN
20
n
20
GLN
20
A
ASP
21
n
21
ASP
21
A
PRO
22
n
22
PRO
22
A
GLN
23
n
23
GLN
23
A
THR
24
n
24
THR
24
A
CYS
25
n
25
CYS
25
A
LYS
26
n
26
LYS
26
A
CYS
27
n
27
CYS
27
A
SER
28
n
28
SER
28
A
CYS
29
n
29
CYS
29
A
LYS
30
n
30
LYS
30
A
ASN
31
n
31
ASN
31
A
THR
32
n
32
THR
32
A
ASP
33
n
33
ASP
33
A
SER
34
n
34
SER
34
A
ARG
35
n
35
ARG
35
A
CYS
36
n
36
CYS
36
A
LYS
37
n
37
LYS
37
A
ALA
38
n
38
ALA
38
A
ARG
39
n
39
ARG
39
A
GLN
40
n
40
GLN
40
A
LEU
41
n
41
LEU
41
A
GLU
42
n
42
GLU
42
A
LEU
43
n
43
LEU
43
A
ASN
44
n
44
ASN
44
A
GLU
45
n
45
GLU
45
A
ARG
46
n
46
ARG
46
A
THR
47
n
47
THR
47
A
CYS
48
n
48
CYS
48
A
ARG
49
n
49
ARG
49
A
CYS
50
n
50
CYS
50
A
ASP
51
n
51
ASP
51
A
LYS
52
n
52
LYS
52
A
PRO
53
n
53
PRO
53
A
ARG
54
n
54
ARG
54
A
ARG
55
n
55
ARG
55
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
N
VAL
19
A
N
VAL
19
A
O
SER
28
A
O
SER
28
A
N
ASN
44
A
N
ASN
44
A
O
ARG
49
A
O
ARG
49
1
A
O
ARG
55
A
O
ARG
55
1
Y
2
A
O
ARG
55
A
O
ARG
55
1
Y
3
A
O
ARG
55
A
O
ARG
55
1
Y
4
A
O
ARG
55
A
O
ARG
55
1
Y
5
A
O
ARG
55
A
O
ARG
55
1
Y
6
A
O
ARG
55
A
O
ARG
55
1
Y
7
A
O
ARG
55
A
O
ARG
55
1
Y
8
A
O
ARG
55
A
O
ARG
55
1
Y
9
A
O
ARG
55
A
O
ARG
55
1
Y
10
A
O
ARG
55
A
O
ARG
55
1
Y
11
A
O
ARG
55
A
O
ARG
55
1
Y
12
A
O
ARG
55
A
O
ARG
55
1
Y
13
A
O
ARG
55
A
O
ARG
55
1
Y
14
A
O
ARG
55
A
O
ARG
55
1
Y
15
A
O
ARG
55
A
O
ARG
55
1
Y
16
A
O
ARG
55
A
O
ARG
55
1
Y
17
A
O
ARG
55
A
O
ARG
55
1
Y
18
A
O
ARG
55
A
O
ARG
55
1
Y
19
A
O
ARG
55
A
O
ARG
55
1
Y
20
A
O
ARG
55
A
O
ARG
55
1
Y
1
A
GLN
3
-160.20
-71.95
1
A
GLU
4
68.09
79.42
1
A
CYS
10
-91.73
-71.97
1
A
SER
11
-90.55
-159.16
1
A
GLU
12
-125.04
-70.82
1
A
ARG
14
-94.96
58.72
1
A
ARG
54
-163.65
-69.29
2
A
ARG
2
61.61
176.17
2
A
PRO
9
-45.43
172.32
2
A
CYS
10
-90.31
-82.83
2
A
ARG
13
-127.76
-59.40
2
A
ARG
14
-90.60
59.22
2
A
ARG
54
-159.83
-48.35
3
A
PRO
9
-56.61
174.85
3
A
CYS
10
-90.10
-79.70
3
A
ARG
13
-141.76
-71.49
3
A
ARG
14
-158.46
45.22
3
A
HIS
16
-161.16
-46.36
3
A
PRO
22
-89.68
39.40
3
A
GLN
23
-148.82
-49.24
3
A
PRO
53
-85.48
-75.09
3
A
ARG
54
-154.53
-140.42
4
A
ARG
2
60.72
-166.23
4
A
GLN
3
58.72
73.61
4
A
GLU
4
-141.21
33.98
4
A
ARG
14
-67.84
83.51
4
A
LYS
15
-41.52
176.55
4
A
HIS
16
-153.68
-48.14
4
A
ARG
54
-159.14
-92.12
5
A
ARG
2
-89.56
-159.57
5
A
GLU
4
64.98
112.39
5
A
ASN
5
-150.21
85.63
5
A
PRO
9
-47.97
178.84
5
A
CYS
10
-90.08
-93.65
5
A
GLU
12
-141.82
32.17
5
A
ARG
13
-150.49
-43.69
5
A
ARG
14
-152.61
60.58
5
A
LEU
17
-97.08
44.70
5
A
ARG
54
-139.16
-54.54
6
A
CYS
10
-90.37
-64.83
6
A
ARG
13
-138.71
-46.90
6
A
ARG
14
-93.47
59.07
6
A
ARG
54
-142.42
-69.51
7
A
ARG
2
-159.28
-45.58
7
A
PRO
6
-58.15
-156.45
7
A
PRO
9
-72.45
-169.45
7
A
CYS
10
-88.67
-76.16
7
A
SER
11
-88.48
-76.80
7
A
GLU
12
-156.97
-67.21
7
A
ARG
13
-142.36
-48.44
7
A
HIS
16
-165.04
-44.95
7
A
PRO
22
-91.21
32.52
7
A
GLN
23
-137.37
-48.93
7
A
ARG
54
-148.28
-63.96
8
A
ARG
2
-154.83
35.14
8
A
GLU
4
-99.08
43.02
8
A
CYS
10
-90.11
-75.02
8
A
SER
11
-89.96
-74.54
8
A
GLU
12
-162.77
-67.06
8
A
ARG
13
-144.37
-49.09
8
A
LYS
15
-38.48
137.13
8
A
HIS
16
-163.38
-44.44
8
A
PRO
22
-91.11
34.91
8
A
GLN
23
-142.52
-50.09
9
A
ARG
2
-92.82
-63.41
9
A
GLN
3
-66.74
-75.10
9
A
PRO
6
-61.26
-148.79
9
A
PRO
9
-51.43
-175.82
9
A
CYS
10
-89.98
-77.26
9
A
GLU
12
-158.54
-94.98
9
A
ARG
13
-150.56
68.34
9
A
ARG
14
178.43
-37.13
9
A
LYS
15
-60.77
62.63
9
A
ARG
54
-65.86
78.52
10
A
GLU
12
77.54
-53.61
10
A
LYS
15
-64.01
92.92
10
A
PRO
22
-84.02
38.79
10
A
GLN
23
-148.77
-48.70
11
A
GLN
3
62.08
-157.27
11
A
GLU
4
-173.50
16.32
11
A
CYS
10
-90.27
-61.64
11
A
SER
11
-89.76
-93.14
11
A
GLU
12
178.15
-40.39
11
A
ARG
13
-144.83
12.89
11
A
PRO
22
-89.58
36.91
11
A
GLN
23
-150.13
-49.21
12
A
SER
11
-59.45
-177.31
12
A
ARG
13
-129.33
-165.75
12
A
ARG
14
-62.37
85.08
12
A
LYS
15
-56.06
72.50
12
A
PRO
22
-88.95
40.85
12
A
GLN
23
-149.57
-47.71
12
A
PRO
53
-72.06
-168.46
13
A
ARG
2
-67.06
91.76
13
A
GLU
12
-141.59
36.69
13
A
ARG
13
-132.94
-75.01
14
A
GLU
4
-173.90
129.52
14
A
PRO
6
-58.29
-155.97
14
A
SER
11
-90.09
-75.36
14
A
GLU
12
-175.31
-85.09
14
A
ARG
13
-150.63
-59.17
14
A
LYS
15
-65.73
69.24
14
A
PRO
22
-89.50
32.81
14
A
GLN
23
-142.11
-49.93
15
A
ARG
2
-162.31
99.94
15
A
GLU
12
59.65
-168.18
15
A
LYS
15
-44.95
165.29
15
A
HIS
16
-168.26
-50.97
15
A
PRO
22
-89.91
38.69
15
A
GLN
23
-150.40
-48.77
15
A
ARG
54
-148.30
-49.64
16
A
ARG
2
-156.85
32.39
16
A
PRO
9
-50.41
173.35
16
A
CYS
10
-90.04
-87.67
16
A
GLU
12
-142.86
48.75
16
A
ARG
13
-146.94
-75.18
16
A
ARG
14
-141.28
37.73
16
A
HIS
16
-166.83
-44.64
16
A
PRO
22
-90.35
31.10
16
A
GLN
23
-135.29
-47.82
16
A
ARG
54
-161.08
91.50
17
A
ARG
2
60.88
157.08
17
A
GLN
3
-101.83
-61.34
17
A
GLU
4
-93.98
59.18
17
A
ASN
5
-150.19
87.22
17
A
PRO
6
-56.74
179.28
17
A
PRO
9
-45.15
153.33
17
A
GLU
12
-163.58
-164.46
17
A
LYS
15
-68.51
65.18
17
A
ARG
54
-98.86
-85.95
18
A
GLN
3
-65.51
-158.19
18
A
GLU
4
67.14
-152.27
18
A
SER
11
-91.41
37.53
18
A
GLU
12
67.86
-68.20
18
A
ARG
13
-146.26
-44.70
18
A
LYS
15
-37.14
133.45
18
A
HIS
16
-178.47
-43.82
18
A
PRO
22
-89.54
33.56
18
A
GLN
23
-146.86
-49.41
18
A
PRO
53
-79.97
-168.55
19
A
GLN
3
-170.50
-168.03
19
A
GLU
4
62.81
123.70
19
A
CYS
10
-90.56
-64.69
19
A
ARG
13
-150.15
-71.08
19
A
ARG
14
-158.82
34.48
19
A
HIS
16
-166.32
-45.41
19
A
ARG
54
-152.37
24.82
20
A
PRO
9
-68.02
-175.18
20
A
CYS
10
-90.59
-84.76
20
A
ARG
13
-150.00
-70.52
20
A
PRO
53
-87.25
-72.37
20
A
ARG
54
-155.62
-134.87
Heparin-binding Domain from Vascular Endothelial Growth Factor
1
N
N
A
THR
32
A
THR
32
HELX_P
A
ALA
38
A
ALA
38
1
1
7
disulf
2.033
A
CYS
7
A
SG
CYS
7
1_555
A
CYS
25
A
SG
CYS
25
1_555
disulf
2.026
A
CYS
10
A
SG
CYS
10
1_555
A
CYS
27
A
SG
CYS
27
1_555
disulf
2.029
A
CYS
29
A
SG
CYS
29
1_555
A
CYS
48
A
SG
CYS
48
1_555
disulf
2.030
A
CYS
36
A
SG
CYS
36
1_555
A
CYS
50
A
SG
CYS
50
1_555
HORMONE/GROWTH FACTOR
heparin-binding, angiogenesis, growth factor, HORMONE-GROWTH FACTOR COMPLEX
VEGFA_HUMAN
UNP
1
137
P15692
ARQENPCGPCSERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR
137
191
1KMX
1
55
P15692
A
1
1
55
2
2
anti-parallel
anti-parallel
A
PHE
18
A
PHE
18
A
GLN
20
A
GLN
20
A
CYS
27
A
CYS
27
A
CYS
29
A
CYS
29
A
GLU
42
A
GLU
42
A
ASN
44
A
ASN
44
A
ARG
49
A
ARG
49
A
ASP
51
A
ASP
51