1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hoshino, M.
Hagihara, Y.
Nishii, I.
Yamazaki, T.
Kato, H.
Goto, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
304
927
939
10.1006/jmbi.2000.4243
11124037
Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance.
2000
10.2210/pdb1g4g/pdb
pdb_00001g4g
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9755.360
BETA2-GLYCOPROTEIN I
1
man
polymer
no
no
TKASCKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDA
SDVKPC
TKASCKLPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDA
SDVKPC
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
human
Homo
Pichia
sample
9606
Homo sapiens
4922
Pichia pastoris
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2000-11-15
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
ENSEMBLE OF 20 STRUCTURES
RCSB
Y
RCSB
2000-10-27
REL
1
3D_15N-separated_NOESY
3D_13C-separated_NOESY
HNCO-TROSY
HMQC-J
HNHB
HN(CO)HB
N15-TOCSY
0.12
6.0
ambient
298
K
the structures are based on a total of 1402 restraints, 1288 are NOE-derived distance constraints, 88 dihedral angle restraints, 26 distance restraints from hydrogen bonds
simulated annealing
minimized average structure
1mM beta2-glycoprotein I domain V U-15N; 20mM Na-phosphate buffer, pH 6.0; 90% H2O, 10% D2O
90% H2O/10% D2O
1mM beta2-glycoprotein I domain V U-15N,13C; 20mM Na-phosphate buffer, pD 6.0; 100% D2O
100% D2O
Brunger
structure solution
X-PLOR
3.841
Brunger
refinement
X-PLOR
3.841
600
Bruker
DRX
800
Bruker
DMX
THR
1
n
1
THR
1
A
LYS
2
n
2
LYS
2
A
ALA
3
n
3
ALA
3
A
SER
4
n
4
SER
4
A
CYS
5
n
5
CYS
5
A
LYS
6
n
6
LYS
6
A
LEU
7
n
7
LEU
7
A
PRO
8
n
8
PRO
8
A
VAL
9
n
9
VAL
9
A
LYS
10
n
10
LYS
10
A
LYS
11
n
11
LYS
11
A
ALA
12
n
12
ALA
12
A
THR
13
n
13
THR
13
A
VAL
14
n
14
VAL
14
A
VAL
15
n
15
VAL
15
A
TYR
16
n
16
TYR
16
A
GLN
17
n
17
GLN
17
A
GLY
18
n
18
GLY
18
A
GLU
19
n
19
GLU
19
A
ARG
20
n
20
ARG
20
A
VAL
21
n
21
VAL
21
A
LYS
22
n
22
LYS
22
A
ILE
23
n
23
ILE
23
A
GLN
24
n
24
GLN
24
A
GLU
25
n
25
GLU
25
A
LYS
26
n
26
LYS
26
A
PHE
27
n
27
PHE
27
A
LYS
28
n
28
LYS
28
A
ASN
29
n
29
ASN
29
A
GLY
30
n
30
GLY
30
A
MET
31
n
31
MET
31
A
LEU
32
n
32
LEU
32
A
HIS
33
n
33
HIS
33
A
GLY
34
n
34
GLY
34
A
ASP
35
n
35
ASP
35
A
LYS
36
n
36
LYS
36
A
VAL
37
n
37
VAL
37
A
SER
38
n
38
SER
38
A
PHE
39
n
39
PHE
39
A
PHE
40
n
40
PHE
40
A
CYS
41
n
41
CYS
41
A
LYS
42
n
42
LYS
42
A
ASN
43
n
43
ASN
43
A
LYS
44
n
44
LYS
44
A
GLU
45
n
45
GLU
45
A
LYS
46
n
46
LYS
46
A
LYS
47
n
47
LYS
47
A
CYS
48
n
48
CYS
48
A
SER
49
n
49
SER
49
A
TYR
50
n
50
TYR
50
A
THR
51
n
51
THR
51
A
GLU
52
n
52
GLU
52
A
ASP
53
n
53
ASP
53
A
ALA
54
n
54
ALA
54
A
GLN
55
n
55
GLN
55
A
CYS
56
n
56
CYS
56
A
ILE
57
n
57
ILE
57
A
ASP
58
n
58
ASP
58
A
GLY
59
n
59
GLY
59
A
THR
60
n
60
THR
60
A
ILE
61
n
61
ILE
61
A
GLU
62
n
62
GLU
62
A
VAL
63
n
63
VAL
63
A
PRO
64
n
64
PRO
64
A
LYS
65
n
65
LYS
65
A
CYS
66
n
66
CYS
66
A
PHE
67
n
67
PHE
67
A
LYS
68
n
68
LYS
68
A
GLU
69
n
69
GLU
69
A
HIS
70
n
70
HIS
70
A
SER
71
n
71
SER
71
A
SER
72
n
72
SER
72
A
LEU
73
n
73
LEU
73
A
ALA
74
n
74
ALA
74
A
PHE
75
n
75
PHE
75
A
TRP
76
n
76
TRP
76
A
LYS
77
n
77
LYS
77
A
THR
78
n
78
THR
78
A
ASP
79
n
79
ASP
79
A
ALA
80
n
80
ALA
80
A
SER
81
n
81
SER
81
A
ASP
82
n
82
ASP
82
A
VAL
83
n
83
VAL
83
A
LYS
84
n
84
LYS
84
A
PRO
85
n
85
PRO
85
A
CYS
86
n
86
CYS
86
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
O
VAL
14
A
O
VAL
14
A
N
VAL
21
A
N
VAL
21
A
N
ASN
43
A
N
ASN
43
A
O
CYS
48
A
O
CYS
48
A
N
ILE
57
A
N
ILE
57
A
O
THR
60
A
O
THR
60
1
A
A
O
H
ASP
ASP
79
82
1.49
1
A
A
H
O
ASN
CYS
43
48
1.52
1
A
A
H
O
CYS
MET
5
31
1.54
1
A
A
H
OD1
ALA
ASP
3
58
1.56
1
A
A
O
H
LYS
GLU
22
25
1.59
1
A
ARG
20
0.153
SIDE CHAIN
1
A
SER
4
-54.67
-178.47
1
A
CYS
5
-101.78
-145.10
1
A
LEU
7
-39.65
100.65
1
A
LYS
11
-148.21
43.13
1
A
ASN
29
-100.24
51.79
1
A
ASP
58
-53.60
97.33
1
A
PHE
67
-55.10
172.65
1
A
HIS
70
-160.12
-35.87
1
A
SER
71
46.44
95.53
1
A
SER
72
-55.34
-164.08
1
A
LEU
73
57.40
71.13
1
A
PHE
75
-106.34
-159.58
1
A
TRP
76
-60.20
94.18
1
A
LYS
77
-178.87
108.41
minimized average
NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I
1
N
N
A
ILE
23
A
ILE
23
HELX_P
A
PHE
27
A
PHE
27
1
1
5
A
ASP
79
A
ASP
79
HELX_P
A
VAL
83
A
VAL
83
5
2
5
disulf
2.020
A
CYS
5
A
SG
CYS
5
1_555
A
CYS
56
A
SG
CYS
56
1_555
disulf
2.021
A
CYS
41
A
SG
CYS
41
1_555
A
CYS
66
A
SG
CYS
66
1_555
disulf
2.022
A
CYS
48
A
SG
CYS
48
1_555
A
CYS
86
A
SG
CYS
86
1_555
SIGNALING PROTEIN
short consensus repeat, sushi-domain, SIGNALING PROTEIN
APOH_HUMAN
UNP
1
260
P02749
CKASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDA
SDVKPC
260
345
1G4G
1
86
P02749
A
1
1
86
1
CYS
conflict
THR
1
1G4G
A
P02749
UNP
260
1
1
VAL
variant
LEU
7
1G4G
A
P02749
UNP
266
7
2
3
anti-parallel
anti-parallel
anti-parallel
A
THR
13
A
THR
13
A
VAL
15
A
VAL
15
A
ARG
20
A
ARG
20
A
LYS
22
A
LYS
22
A
LYS
36
A
LYS
36
A
ASN
43
A
ASN
43
A
CYS
48
A
CYS
48
A
ILE
57
A
ILE
57
A
THR
60
A
THR
60
A
ILE
61
A
ILE
61
1
P 1