1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sato, M.
Tochio, N.
Koshiba, S.
Inoue, M.
Kigawa, T.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
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
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
To be Published
0353
Solution structures of the fn3 domain of human ephrin type-B receptor 1
10.2210/pdb2djs/pdb
pdb_00002djs
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11804.199
Ephrin type-B receptor 1
2.7.1.112
Fibronectin type III domain
1
man
polymer
Tyrosine-protein kinase receptor EPH-2, NET, HEK6, ELK
no
no
GSSGSSGPSTVPIMHQVSATMRSITLSWPQPEQPNGIILDYEIRYYEKEHNEFNSSMARSQTNTARIDGLRPGMVYVVQV
RARTVAGYGKFSGKMCFQTLTDSGPSSG
GSSGSSGPSTVPIMHQVSATMRSITLSWPQPEQPNGIILDYEIRYYEKEHNEFNSSMARSQTNTARIDGLRPGMVYVVQV
RARTVAGYGKFSGKMCFQTLTDSGPSSG
A
hso002001071.1
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
human
Homo
sample
Cell-free protein synthesis
EPHB1
9606
Homo sapiens
Cell free synthesis
PLASMID
P050912-11
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-10-05
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
Y
PDBJ
Y
PDBJ
2006-04-05
REL
REL
target function, structures with the least restraint violations
100
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
120mM
7.0
ambient
296
K
torsion angle dynamics
1
lowest energy
1mM fn3 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.5
Delaglio, F.
processing
NMRPipe
20031121
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.932
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
900
Bruker
AVANCE
GLY
1
n
1
GLY
1
A
SER
2
n
2
SER
2
A
SER
3
n
3
SER
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
SER
6
n
6
SER
6
A
GLY
7
n
7
GLY
7
A
PRO
8
n
8
PRO
8
A
SER
9
n
9
SER
9
A
THR
10
n
10
THR
10
A
VAL
11
n
11
VAL
11
A
PRO
12
n
12
PRO
12
A
ILE
13
n
13
ILE
13
A
MET
14
n
14
MET
14
A
HIS
15
n
15
HIS
15
A
GLN
16
n
16
GLN
16
A
VAL
17
n
17
VAL
17
A
SER
18
n
18
SER
18
A
ALA
19
n
19
ALA
19
A
THR
20
n
20
THR
20
A
MET
21
n
21
MET
21
A
ARG
22
n
22
ARG
22
A
SER
23
n
23
SER
23
A
ILE
24
n
24
ILE
24
A
THR
25
n
25
THR
25
A
LEU
26
n
26
LEU
26
A
SER
27
n
27
SER
27
A
TRP
28
n
28
TRP
28
A
PRO
29
n
29
PRO
29
A
GLN
30
n
30
GLN
30
A
PRO
31
n
31
PRO
31
A
GLU
32
n
32
GLU
32
A
GLN
33
n
33
GLN
33
A
PRO
34
n
34
PRO
34
A
ASN
35
n
35
ASN
35
A
GLY
36
n
36
GLY
36
A
ILE
37
n
37
ILE
37
A
ILE
38
n
38
ILE
38
A
LEU
39
n
39
LEU
39
A
ASP
40
n
40
ASP
40
A
TYR
41
n
41
TYR
41
A
GLU
42
n
42
GLU
42
A
ILE
43
n
43
ILE
43
A
ARG
44
n
44
ARG
44
A
TYR
45
n
45
TYR
45
A
TYR
46
n
46
TYR
46
A
GLU
47
n
47
GLU
47
A
LYS
48
n
48
LYS
48
A
GLU
49
n
49
GLU
49
A
HIS
50
n
50
HIS
50
A
ASN
51
n
51
ASN
51
A
GLU
52
n
52
GLU
52
A
PHE
53
n
53
PHE
53
A
ASN
54
n
54
ASN
54
A
SER
55
n
55
SER
55
A
SER
56
n
56
SER
56
A
MET
57
n
57
MET
57
A
ALA
58
n
58
ALA
58
A
ARG
59
n
59
ARG
59
A
SER
60
n
60
SER
60
A
GLN
61
n
61
GLN
61
A
THR
62
n
62
THR
62
A
ASN
63
n
63
ASN
63
A
THR
64
n
64
THR
64
A
ALA
65
n
65
ALA
65
A
ARG
66
n
66
ARG
66
A
ILE
67
n
67
ILE
67
A
ASP
68
n
68
ASP
68
A
GLY
69
n
69
GLY
69
A
LEU
70
n
70
LEU
70
A
ARG
71
n
71
ARG
71
A
PRO
72
n
72
PRO
72
A
GLY
73
n
73
GLY
73
A
MET
74
n
74
MET
74
A
VAL
75
n
75
VAL
75
A
TYR
76
n
76
TYR
76
A
VAL
77
n
77
VAL
77
A
VAL
78
n
78
VAL
78
A
GLN
79
n
79
GLN
79
A
VAL
80
n
80
VAL
80
A
ARG
81
n
81
ARG
81
A
ALA
82
n
82
ALA
82
A
ARG
83
n
83
ARG
83
A
THR
84
n
84
THR
84
A
VAL
85
n
85
VAL
85
A
ALA
86
n
86
ALA
86
A
GLY
87
n
87
GLY
87
A
TYR
88
n
88
TYR
88
A
GLY
89
n
89
GLY
89
A
LYS
90
n
90
LYS
90
A
PHE
91
n
91
PHE
91
A
SER
92
n
92
SER
92
A
GLY
93
n
93
GLY
93
A
LYS
94
n
94
LYS
94
A
MET
95
n
95
MET
95
A
CYS
96
n
96
CYS
96
A
PHE
97
n
97
PHE
97
A
GLN
98
n
98
GLN
98
A
THR
99
n
99
THR
99
A
LEU
100
n
100
LEU
100
A
THR
101
n
101
THR
101
A
ASP
102
n
102
ASP
102
A
SER
103
n
103
SER
103
A
GLY
104
n
104
GLY
104
A
PRO
105
n
105
PRO
105
A
SER
106
n
106
SER
106
A
SER
107
n
107
SER
107
A
GLY
108
n
108
GLY
108
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
HIS
15
A
N
HIS
15
A
O
SER
27
A
O
SER
27
A
N
ILE
24
A
N
ILE
24
A
O
ILE
67
A
O
ILE
67
A
O
ALA
58
A
O
ALA
58
A
N
ILE
43
A
N
ILE
43
A
N
GLU
42
A
N
GLU
42
A
O
ARG
81
A
O
ARG
81
A
N
ALA
82
A
N
ALA
82
A
O
GLY
89
A
O
GLY
89
A
O
ALA
58
A
O
ALA
58
A
N
ILE
43
A
N
ILE
43
A
N
GLU
42
A
N
GLU
42
A
O
ARG
81
A
O
ARG
81
A
N
TYR
76
A
N
TYR
76
A
O
PHE
97
A
O
PHE
97
1
A
SER
9
-56.91
-174.87
1
A
ALA
19
-173.92
145.66
1
A
GLN
33
-118.43
56.05
1
A
PRO
34
-69.75
0.38
1
A
ASP
102
-98.08
43.42
2
A
PRO
34
-69.72
2.41
2
A
SER
103
-125.84
-56.75
3
A
SER
9
-59.85
-179.31
3
A
GLN
33
-118.55
53.20
3
A
PRO
34
-69.75
1.97
3
A
LYS
94
-40.67
155.44
4
A
SER
3
-56.91
105.67
4
A
SER
9
-48.80
175.46
4
A
ALA
19
-171.72
142.69
4
A
PRO
34
-69.75
0.43
4
A
ASN
35
42.07
25.04
4
A
ILE
37
-37.63
141.85
4
A
ASN
54
-78.56
49.21
4
A
SER
103
-173.98
149.64
4
A
SER
106
34.62
47.53
5
A
PRO
34
-69.76
0.42
5
A
ASN
35
45.73
29.36
6
A
SER
9
-64.73
-179.46
6
A
GLN
33
-119.95
53.83
6
A
ILE
37
-52.27
107.75
6
A
ASN
54
-104.56
61.42
6
A
SER
107
-59.76
176.66
7
A
SER
5
-41.62
154.86
7
A
SER
9
-50.94
175.69
8
A
SER
2
-36.64
105.74
8
A
SER
9
-51.94
175.57
8
A
PRO
34
-69.76
2.57
8
A
ASN
54
-94.76
48.78
8
A
PRO
105
-69.73
-178.68
8
A
SER
106
-173.36
145.55
9
A
SER
2
-88.71
42.44
9
A
ALA
19
-175.03
145.75
9
A
PRO
34
-69.75
0.83
9
A
ASN
35
42.79
25.31
9
A
ILE
37
-39.97
134.46
9
A
ASP
102
-86.90
39.44
10
A
ALA
19
-172.30
146.59
10
A
PRO
29
-69.75
-179.45
10
A
GLN
33
-119.55
51.11
10
A
PRO
34
-69.81
2.35
10
A
SER
107
-55.78
176.17
11
A
SER
9
-56.88
171.08
12
A
GLN
33
-119.55
50.41
12
A
PRO
34
-69.78
2.40
12
A
ASN
54
-104.36
53.93
13
A
SER
9
-46.16
158.61
13
A
ALA
19
-174.73
146.73
13
A
GLN
33
-118.29
50.58
13
A
ASN
54
-92.80
51.95
13
A
SER
106
-103.78
41.97
14
A
SER
9
-57.87
174.34
14
A
PRO
34
-69.70
0.80
14
A
ILE
37
-39.13
143.22
14
A
GLU
47
-36.36
122.88
14
A
ASN
54
-104.63
55.11
14
A
LYS
94
-38.01
132.20
14
A
THR
99
-61.73
-179.71
15
A
SER
2
-65.47
94.31
15
A
SER
9
-48.99
176.58
15
A
VAL
11
-36.39
138.06
15
A
GLN
33
-118.80
56.87
15
A
ILE
37
-56.15
105.10
15
A
ASN
54
-102.58
66.11
16
A
SER
9
-55.47
-177.22
16
A
PRO
34
-69.81
2.97
16
A
GLU
47
-38.31
140.22
16
A
ASN
54
-102.58
41.37
17
A
SER
6
37.86
33.99
17
A
SER
9
-48.73
161.25
17
A
PRO
34
-69.75
2.40
17
A
ASN
35
48.99
28.32
17
A
SER
103
36.86
37.84
18
A
SER
3
-173.64
113.96
18
A
SER
6
-59.27
106.10
18
A
SER
9
-47.48
168.15
18
A
LYS
94
-37.76
131.77
18
A
ASP
102
-83.03
47.66
18
A
SER
103
-94.82
-66.98
19
A
SER
9
-59.41
-176.29
19
A
PRO
34
-69.73
2.09
19
A
ASN
35
48.13
27.50
19
A
ILE
37
-57.17
107.16
20
A
SER
9
-48.13
172.59
20
A
ALA
19
-174.46
149.04
20
A
PRO
34
-69.81
0.90
20
A
ASN
35
46.65
29.01
Solution structures of the fn3 domain of human ephrin type-B receptor 1
1
N
N
SIGNALING PROTEIN
Tyrosine-protein kinase receptor EPH-2, NET, HEK6, ELK, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN
EPHB1_HUMAN
UNP
1
434
P54762
434
528
2DJS
8
102
P54762
A
1
8
102
1
cloning artifact
GLY
1
2DJS
A
P54762
UNP
1
1
cloning artifact
SER
2
2DJS
A
P54762
UNP
2
1
cloning artifact
SER
3
2DJS
A
P54762
UNP
3
1
cloning artifact
GLY
4
2DJS
A
P54762
UNP
4
1
cloning artifact
SER
5
2DJS
A
P54762
UNP
5
1
cloning artifact
SER
6
2DJS
A
P54762
UNP
6
1
cloning artifact
GLY
7
2DJS
A
P54762
UNP
7
1
cloning artifact
SER
103
2DJS
A
P54762
UNP
103
1
cloning artifact
GLY
104
2DJS
A
P54762
UNP
104
1
cloning artifact
PRO
105
2DJS
A
P54762
UNP
105
1
cloning artifact
SER
106
2DJS
A
P54762
UNP
106
1
cloning artifact
SER
107
2DJS
A
P54762
UNP
107
1
cloning artifact
GLY
108
2DJS
A
P54762
UNP
108
3
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
HIS
15
A
HIS
15
A
ALA
19
A
ALA
19
A
SER
23
A
SER
23
A
SER
27
A
SER
27
A
THR
64
A
THR
64
A
ASP
68
A
ASP
68
A
SER
56
A
SER
56
A
SER
60
A
SER
60
A
ILE
38
A
ILE
38
A
GLU
47
A
GLU
47
A
VAL
75
A
VAL
75
A
THR
84
A
THR
84
A
TYR
88
A
TYR
88
A
PHE
91
A
PHE
91
A
SER
56
A
SER
56
A
SER
60
A
SER
60
A
ILE
38
A
ILE
38
A
GLU
47
A
GLU
47
A
VAL
75
A
VAL
75
A
THR
84
A
THR
84
A
MET
95
A
MET
95
A
GLN
98
A
GLN
98