1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kurniawan, N.D.
Aliabadizadeh, K.
Brereton, I.M.
Kroon, P.A.
Smith, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
Ca 2
40.078
CALCIUM ION
non-polymer
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
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
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
311
341
356
10.1006/jmbi.2001.4867
11478865
NMR structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-density lipoprotein receptor.
2001
US
Protein Sci.
PRCIEI
0795
0961-8368
9
1282
1293
NMR Structure of a Concatemer of the First and Second Ligand-Binding Modules of the Human Low-Density Lipoprotein Receptor
2000
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
283
837
862
10.1006/jmbi.1998.2115
An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components. An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases,epidermal growth factor precursor, and extracellular matrix components
1998
10.2210/pdb1i0u/pdb
pdb_00001i0u
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9001.013
LOW DENSITY LIPOPROTEIN RECEPTOR
EGF-AB CONCATEMER(RESIDUES 314-395)
1
man
polymer
40.078
CALCIUM ION
2
syn
non-polymer
LDL RECEPTOR
no
no
GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACK
AV
GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACK
AV
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
human
Homo
LIVER
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
DH5-ALPHA; BL21-DE3
PLASMID
PGEX-4T; PET-30A+
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-08-15
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1F5Y contains ligand binding modules (LB1-2) of the human LDL receptor
1LRX contains YWTD modules of the human LDL receptor
1HZ8 is the ensemble of 30 structures
RCSB
Y
PDBJ
2001-01-29
REL
REL
CA
CALCIUM ION
15N T1, T2, and NOE relaxations to obtain backbone dynamics information T1/T2 data were not used for structure refinement
Energy minimised average structure from 30 selected structure with lowest energy
100
1
HNHA
2D NOESY
2D NOESY
2D NOESY
DQF-COSY
3D_15N-separated_NOESY
0.060
5.5
ambient
310
K
0.060
5.5
ambient
283
K
0.060
5.5
ambient
295
K
The structures are based on: 874 NOE restraints, 64 phi dihedral angles, 14 chi1 dihedral angles, 14 hydrogen bonds, 9 calcium ion ligand restraints
1. Torsion angles dynamics 2. Restrained molecular dynamics with calcium 3. Energy minimisation
1mM EGF-AB, 20mM CaCl2
95% H2O/5% D2O
1mM EGF-AB, 20mM CaCl2
99% D2O
1mM 15N-EGF-AB, 20mM CaCl2
95% H2O/5% D2O
1.5mM EGF-A, 20mM CaCl2
99% D2O
1.5mM EGF-A, 20mM CaCl2
95% H2O/5% D2O
Bruker
collection
XwinNMR
2.6
T. Goddard & D. G. Kneller
processing
Sparky
3.95
P. Guntert
structure solution
DYANA
1.5
A. Brunger
refinement
X-PLOR
3.85
R. Koradi
data analysis
MOLMOL
2.6
750
Bruker
DMX
CA
83
2
CA
CA
83
A
CA
84
2
CA
CA
84
A
GLY
1
n
1
GLY
1
A
THR
2
n
2
THR
2
A
ASN
3
n
3
ASN
3
A
GLU
4
n
4
GLU
4
A
CYS
5
n
5
CYS
5
A
LEU
6
n
6
LEU
6
A
ASP
7
n
7
ASP
7
A
ASN
8
n
8
ASN
8
A
ASN
9
n
9
ASN
9
A
GLY
10
n
10
GLY
10
A
GLY
11
n
11
GLY
11
A
CYS
12
n
12
CYS
12
A
SER
13
n
13
SER
13
A
HIS
14
n
14
HIS
14
A
VAL
15
n
15
VAL
15
A
CYS
16
n
16
CYS
16
A
ASN
17
n
17
ASN
17
A
ASP
18
n
18
ASP
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
ILE
21
n
21
ILE
21
A
GLY
22
n
22
GLY
22
A
TYR
23
n
23
TYR
23
A
GLU
24
n
24
GLU
24
A
CYS
25
n
25
CYS
25
A
LEU
26
n
26
LEU
26
A
CYS
27
n
27
CYS
27
A
PRO
28
n
28
PRO
28
A
ASP
29
n
29
ASP
29
A
GLY
30
n
30
GLY
30
A
PHE
31
n
31
PHE
31
A
GLN
32
n
32
GLN
32
A
LEU
33
n
33
LEU
33
A
VAL
34
n
34
VAL
34
A
ALA
35
n
35
ALA
35
A
GLN
36
n
36
GLN
36
A
ARG
37
n
37
ARG
37
A
ARG
38
n
38
ARG
38
A
CYS
39
n
39
CYS
39
A
GLU
40
n
40
GLU
40
A
ASP
41
n
41
ASP
41
A
ILE
42
n
42
ILE
42
A
ASP
43
n
43
ASP
43
A
GLU
44
n
44
GLU
44
A
CYS
45
n
45
CYS
45
A
GLN
46
n
46
GLN
46
A
ASP
47
n
47
ASP
47
A
PRO
48
n
48
PRO
48
A
ASP
49
n
49
ASP
49
A
THR
50
n
50
THR
50
A
CYS
51
n
51
CYS
51
A
SER
52
n
52
SER
52
A
GLN
53
n
53
GLN
53
A
LEU
54
n
54
LEU
54
A
CYS
55
n
55
CYS
55
A
VAL
56
n
56
VAL
56
A
ASN
57
n
57
ASN
57
A
LEU
58
n
58
LEU
58
A
GLU
59
n
59
GLU
59
A
GLY
60
n
60
GLY
60
A
GLY
61
n
61
GLY
61
A
TYR
62
n
62
TYR
62
A
LYS
63
n
63
LYS
63
A
CYS
64
n
64
CYS
64
A
GLN
65
n
65
GLN
65
A
CYS
66
n
66
CYS
66
A
GLU
67
n
67
GLU
67
A
GLU
68
n
68
GLU
68
A
GLY
69
n
69
GLY
69
A
PHE
70
n
70
PHE
70
A
GLN
71
n
71
GLN
71
A
LEU
72
n
72
LEU
72
A
ASP
73
n
73
ASP
73
A
PRO
74
n
74
PRO
74
A
HIS
75
n
75
HIS
75
A
THR
76
n
76
THR
76
A
LYS
77
n
77
LYS
77
A
ALA
78
n
78
ALA
78
A
CYS
79
n
79
CYS
79
A
LYS
80
n
80
LYS
80
A
ALA
81
n
81
ALA
81
A
VAL
82
n
82
VAL
82
A
author_defined_assembly
1
monomeric
A
THR
2
A
O
THR
2
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
OE1
GLU
4
1_555
104.2
A
THR
2
A
O
THR
2
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
OE2
GLU
4
1_555
58.2
A
GLU
4
A
OE1
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
OE2
GLU
4
1_555
46.9
A
THR
2
A
O
THR
2
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
N
GLU
4
1_555
78.1
A
GLU
4
A
OE1
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
N
GLU
4
1_555
75.3
A
GLU
4
A
OE2
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
GLU
4
A
N
GLU
4
1_555
59.9
A
THR
2
A
O
THR
2
1_555
A
CA
83
B
CA
CA
1_555
A
ASP
18
A
OD1
ASP
18
1_555
61.9
A
GLU
4
A
OE1
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
ASP
18
A
OD1
ASP
18
1_555
76.6
A
GLU
4
A
OE2
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
ASP
18
A
OD1
ASP
18
1_555
64.2
A
GLU
4
A
N
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
A
ASP
18
A
OD1
ASP
18
1_555
122.6
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
A
ILE
42
A
O
ILE
42
1_555
65.9
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
A
GLU
44
A
OE1
GLU
44
1_555
106.4
A
ILE
42
A
O
ILE
42
1_555
A
CA
84
C
CA
CA
1_555
A
GLU
44
A
OE1
GLU
44
1_555
89.8
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
A
GLU
44
A
OE2
GLU
44
1_555
62.8
A
ILE
42
A
O
ILE
42
1_555
A
CA
84
C
CA
CA
1_555
A
GLU
44
A
OE2
GLU
44
1_555
58.1
A
GLU
44
A
OE1
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
A
GLU
44
A
OE2
GLU
44
1_555
46.6
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
A
ASN
57
A
OD1
ASN
57
1_555
162.2
A
ILE
42
A
O
ILE
42
1_555
A
CA
84
C
CA
CA
1_555
A
ASN
57
A
OD1
ASN
57
1_555
101.4
A
GLU
44
A
OE1
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
A
ASN
57
A
OD1
ASN
57
1_555
59.5
A
GLU
44
A
OE2
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
A
ASN
57
A
OD1
ASN
57
1_555
100.2
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
A
LEU
58
A
O
LEU
58
1_555
131.0
A
ILE
42
A
O
ILE
42
1_555
A
CA
84
C
CA
CA
1_555
A
LEU
58
A
O
LEU
58
1_555
144.2
A
GLU
44
A
OE1
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
A
LEU
58
A
O
LEU
58
1_555
109.5
A
GLU
44
A
OE2
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
A
LEU
58
A
O
LEU
58
1_555
153.8
A
ASN
57
A
OD1
ASN
57
1_555
A
CA
84
C
CA
CA
1_555
A
LEU
58
A
O
LEU
58
1_555
66.7
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
ASN
17
A
O
ASN
17
A
N
GLU
24
A
N
GLU
24
A
O
ALA
35
A
O
ALA
35
A
N
ARG
38
A
N
ARG
38
A
N
VAL
56
A
N
VAL
56
A
O
LYS
63
A
O
LYS
63
A
N
GLN
71
A
N
GLN
71
A
O
LYS
80
A
O
LYS
80
1
8.58
1.10
114.20
122.78
A
A
A
CA
CB
SG
CYS
CYS
CYS
55
55
55
N
1
7.12
1.10
114.20
121.32
A
A
A
CA
CB
SG
CYS
CYS
CYS
64
64
64
N
1
12.01
1.10
114.20
126.21
A
A
A
CA
CB
SG
CYS
CYS
CYS
66
66
66
N
1
A
THR
2
-64.57
-172.40
1
A
ASN
9
-41.75
87.69
1
A
CYS
12
-105.01
-129.77
1
A
SER
13
-159.98
35.05
1
A
HIS
14
-109.78
-104.48
1
A
ASP
18
-52.36
86.55
1
A
TYR
23
-34.32
154.44
1
A
VAL
34
-79.74
-76.11
1
A
GLN
36
65.01
-66.96
1
A
ASP
49
-140.77
-40.84
1
A
THR
50
-75.57
-102.30
1
A
GLN
53
-111.79
-113.69
1
A
LEU
58
-176.35
-152.91
1
A
GLU
68
47.75
-79.00
1
A
THR
76
-140.05
-37.79
SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR
1
N
N
2
N
N
2
N
N
A
ASN
8
A
ASN
8
HELX_P
A
CYS
12
A
CYS
12
5
1
5
disulf
2.018
A
CYS
5
A
SG
CYS
5
1_555
A
CYS
16
A
SG
CYS
16
1_555
disulf
2.016
A
CYS
12
A
SG
CYS
12
1_555
A
CYS
25
A
SG
CYS
25
1_555
disulf
2.017
A
CYS
27
A
SG
CYS
27
1_555
A
CYS
39
A
SG
CYS
39
1_555
disulf
2.017
A
CYS
45
A
SG
CYS
45
1_555
A
CYS
55
A
SG
CYS
55
1_555
disulf
2.022
A
CYS
51
A
SG
CYS
51
1_555
A
CYS
64
A
SG
CYS
64
1_555
disulf
2.018
A
CYS
66
A
SG
CYS
66
1_555
A
CYS
79
A
SG
CYS
79
1_555
metalc
2.834
A
THR
2
A
O
THR
2
1_555
A
CA
83
B
CA
CA
1_555
metalc
2.693
A
GLU
4
A
OE1
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
metalc
2.749
A
GLU
4
A
OE2
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
metalc
3.165
A
GLU
4
A
N
GLU
4
1_555
A
CA
83
B
CA
CA
1_555
metalc
2.705
A
ASP
18
A
OD1
ASP
18
1_555
A
CA
83
B
CA
CA
1_555
metalc
2.724
A
ASP
41
A
OD2
ASP
41
1_555
A
CA
84
C
CA
CA
1_555
metalc
2.698
A
ILE
42
A
O
ILE
42
1_555
A
CA
84
C
CA
CA
1_555
metalc
2.713
A
GLU
44
A
OE1
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
metalc
2.759
A
GLU
44
A
OE2
GLU
44
1_555
A
CA
84
C
CA
CA
1_555
metalc
2.669
A
ASN
57
A
OD1
ASN
57
1_555
A
CA
84
C
CA
CA
1_555
metalc
2.760
A
LEU
58
A
O
LEU
58
1_555
A
CA
84
C
CA
CA
1_555
LIPID BINDING PROTEIN
anti-parallel beta strands, calcium binding sites, LIPID BINDING PROTEIN
LDLR_HUMAN
UNP
1
314
P01130
314
395
1I0U
1
82
P01130
A
1
1
82
2
2
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
15
A
VAL
15
A
ASN
17
A
ASN
17
A
GLU
24
A
GLU
24
A
LEU
26
A
LEU
26
A
GLN
32
A
GLN
32
A
ALA
35
A
ALA
35
A
ARG
38
A
ARG
38
A
GLU
40
A
GLU
40
A
CYS
55
A
CYS
55
A
VAL
56
A
VAL
56
A
LYS
63
A
LYS
63
A
CYS
64
A
CYS
64
A
PHE
70
A
PHE
70
A
LEU
72
A
LEU
72
A
CYS
79
A
CYS
79
A
ALA
81
A
ALA
81
BINDING SITE FOR RESIDUE CA A 83
A
CA
83
Software
4
BINDING SITE FOR RESIDUE CA A 84
A
CA
84
Software
6
A
THR
2
A
THR
2
4
1_555
A
ASN
3
A
ASN
3
4
1_555
A
GLU
4
A
GLU
4
4
1_555
A
ASP
18
A
ASP
18
4
1_555
A
ASP
41
A
ASP
41
6
1_555
A
ILE
42
A
ILE
42
6
1_555
A
GLU
44
A
GLU
44
6
1_555
A
ASN
57
A
ASN
57
6
1_555
A
LEU
58
A
LEU
58
6
1_555
A
GLY
60
A
GLY
60
6
1_555