1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Clayton, D.J.
Brereton, I.M.
Kroon, P.A.
Smith, R.
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
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 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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
NE
FEBS Lett.
FEBLAL
0165
0014-5793
479
118
122
10.1016/S0014-5793(00)01842-1
10981718
Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities.
2000
10.2210/pdb1f8z/pdb
pdb_00001f8z
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
4392.759
LOW-DENSITY LIPOPROTEIN RECEPTOR
SIXTH LIGAND-BINDING MODULE
1
syn
polymer
40.078
CALCIUM ION
1
syn
non-polymer
no
no
ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN
ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN
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
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
2000-10-18
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
1LDL contains the first ligand-binding module of the LDL receptor
1LDR contains the second ligand-binding module of the LDL receptor
RCSB
Y
RCSB
2000-07-05
REL
REL
CA
CALCIUM ION
Peptide synthesis - based on the human sequence
sample
structures with the least restraint violations, structures with the lowest energy
50
20
2D NOESY
DQF-COSY
E-COSY
10 mM
5.50
1
atm
298
K
Structures are based on 552 distance constraints, 18 backbone angle restraints
and 14 sidechain angle restraints
Structure determination by
Torsion angle dynamics,
Molecular dynamics
3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate
90% H2O/10% D2O
3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate
100% D2O
Bruker
collection
XwinNMR
Bruker
processing
AURELIA
Xia & Bartels
processing
XEASY
Peter Guntert
structure solution
DYANA
1.5
Axel Brunger
structure solution
X-PLOR
3.1
Axel Brunger
refinement
X-PLOR
3.1
750
Bruker
DMX
CA
40
2
CA
CA
40
A
ALA
1
n
1
ALA
1
A
THR
2
n
2
THR
2
A
CYS
3
n
3
CYS
3
A
ARG
4
n
4
ARG
4
A
PRO
5
n
5
PRO
5
A
ASP
6
n
6
ASP
6
A
GLU
7
n
7
GLU
7
A
PHE
8
n
8
PHE
8
A
GLN
9
n
9
GLN
9
A
CYS
10
n
10
CYS
10
A
SER
11
n
11
SER
11
A
ASP
12
n
12
ASP
12
A
GLY
13
n
13
GLY
13
A
ASN
14
n
14
ASN
14
A
CYS
15
n
15
CYS
15
A
ILE
16
n
16
ILE
16
A
HIS
17
n
17
HIS
17
A
GLY
18
n
18
GLY
18
A
SER
19
n
19
SER
19
A
ARG
20
n
20
ARG
20
A
GLN
21
n
21
GLN
21
A
CYS
22
n
22
CYS
22
A
ASP
23
n
23
ASP
23
A
ARG
24
n
24
ARG
24
A
GLU
25
n
25
GLU
25
A
TYR
26
n
26
TYR
26
A
ASP
27
n
27
ASP
27
A
CYS
28
n
28
CYS
28
A
LYS
29
n
29
LYS
29
A
ASP
30
n
30
ASP
30
A
MET
31
n
31
MET
31
A
SER
32
n
32
SER
32
A
ASP
33
n
33
ASP
33
A
GLU
34
n
34
GLU
34
A
VAL
35
n
35
VAL
35
A
GLY
36
n
36
GLY
36
A
CYS
37
n
37
CYS
37
A
VAL
38
n
38
VAL
38
A
ASN
39
n
39
ASN
39
A
author_defined_assembly
1
monomeric
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
23
A
OD1
ASP
23
1_555
61.5
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
25
A
O
GLU
25
1_555
138.9
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
25
A
O
GLU
25
1_555
117.7
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
25
A
N
GLU
25
1_555
129.9
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
25
A
N
GLU
25
1_555
68.5
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
25
A
N
GLU
25
1_555
69.3
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
TYR
26
A
N
TYR
26
1_555
179.5
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
TYR
26
A
N
TYR
26
1_555
118.0
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
TYR
26
A
N
TYR
26
1_555
41.0
A
GLU
25
A
N
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
TYR
26
A
N
TYR
26
1_555
49.7
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
27
A
OD2
ASP
27
1_555
62.9
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
27
A
OD2
ASP
27
1_555
113.1
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
27
A
OD2
ASP
27
1_555
84.2
A
GLU
25
A
N
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
27
A
OD2
ASP
27
1_555
148.8
A
TYR
26
A
N
TYR
26
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
27
A
OD2
ASP
27
1_555
117.3
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
87.2
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
140.9
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
101.2
A
GLU
25
A
N
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
134.6
A
TYR
26
A
N
TYR
26
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
93.3
A
ASP
27
A
OD2
ASP
27
1_555
A
CA
40
B
CA
CA
1_555
A
ASP
33
A
OD2
ASP
33
1_555
65.0
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
70.2
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
66.2
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
150.4
A
GLU
25
A
N
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
87.3
A
TYR
26
A
N
TYR
26
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
109.8
A
ASP
27
A
OD2
ASP
27
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
122.7
A
ASP
33
A
OD2
ASP
33
1_555
A
CA
40
B
CA
CA
1_555
A
GLU
34
A
OE2
GLU
34
1_555
82.1
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
PHE
8
A
N
PHE
8
A
O
ILE
16
A
O
ILE
16
1
6.70
1.10
114.20
120.90
A
A
A
CA
CB
SG
CYS
CYS
CYS
15
15
15
N
1
7.66
1.10
114.20
121.86
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
2
7.84
1.10
114.20
122.04
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
3
6.78
1.10
114.20
120.98
A
A
A
CA
CB
SG
CYS
CYS
CYS
15
15
15
N
3
7.22
1.10
114.20
121.42
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
4
6.80
1.10
114.20
121.00
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
6
-3.05
0.50
120.30
117.25
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
20
20
20
N
7
7.83
1.10
114.20
122.03
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
8
7.47
1.10
114.20
121.67
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
9
7.34
1.10
114.20
121.54
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
11
7.48
1.10
114.20
121.68
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
12
7.31
1.10
114.20
121.51
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
13
7.03
1.10
114.20
121.23
A
A
A
CA
CB
SG
CYS
CYS
CYS
15
15
15
N
13
6.87
1.10
114.20
121.07
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
14
7.84
1.10
114.20
122.04
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
15
7.22
1.10
114.20
121.42
A
A
A
CA
CB
SG
CYS
CYS
CYS
15
15
15
N
15
8.28
1.10
114.20
122.48
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
16
7.45
1.10
114.20
121.65
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
17
8.30
1.10
114.20
122.50
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
18
7.65
1.10
114.20
121.85
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
19
6.69
1.10
114.20
120.89
A
A
A
CA
CB
SG
CYS
CYS
CYS
15
15
15
N
19
7.28
1.10
114.20
121.48
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
20
7.71
1.10
114.20
121.91
A
A
A
CA
CB
SG
CYS
CYS
CYS
22
22
22
N
1
A
ASP
23
-150.33
3.39
1
A
GLU
25
-92.60
38.03
1
A
TYR
26
-2.20
75.85
1
A
MET
31
56.81
17.15
2
A
CYS
22
68.06
63.86
2
A
ASP
23
-150.42
9.97
2
A
ARG
24
43.10
28.23
2
A
GLU
25
-101.65
41.38
2
A
TYR
26
1.07
80.39
2
A
MET
31
55.80
17.41
3
A
ASP
23
-150.61
3.64
3
A
GLU
25
-93.95
39.82
3
A
TYR
26
-3.96
79.06
3
A
MET
31
51.23
11.17
4
A
ASP
23
-141.70
-5.07
4
A
GLU
25
-98.48
44.71
4
A
TYR
26
-2.60
82.95
4
A
MET
31
46.11
16.46
5
A
CYS
22
67.67
65.00
5
A
ASP
23
-150.48
1.11
5
A
GLU
25
-89.99
40.48
5
A
TYR
26
1.40
76.31
5
A
MET
31
57.51
12.54
5
A
VAL
38
-102.93
46.80
6
A
ASP
23
-150.18
2.49
6
A
GLU
25
-98.37
43.65
6
A
TYR
26
-3.66
83.97
6
A
MET
31
53.72
14.48
6
A
CYS
37
-52.57
-75.50
7
A
ASP
23
-150.45
6.44
7
A
ARG
24
48.95
29.96
7
A
GLU
25
-92.29
41.92
7
A
TYR
26
-5.74
79.79
7
A
MET
31
59.42
15.90
8
A
ASP
23
-150.60
6.64
8
A
GLU
25
-92.12
41.76
8
A
TYR
26
-6.52
76.96
8
A
MET
31
54.65
13.40
8
A
VAL
38
-95.19
43.16
9
A
ASP
23
-150.43
9.32
9
A
GLU
25
-97.83
45.38
9
A
TYR
26
-11.39
85.73
9
A
MET
31
52.17
15.65
10
A
ASP
23
-150.56
12.17
10
A
ARG
24
39.90
33.62
10
A
GLU
25
-96.73
40.15
10
A
TYR
26
1.36
76.82
10
A
CYS
37
-68.87
-73.42
11
A
CYS
22
63.48
61.59
11
A
ASP
23
-143.53
-0.20
11
A
ARG
24
45.09
26.95
11
A
GLU
25
-100.53
46.36
11
A
TYR
26
4.29
76.68
11
A
MET
31
58.40
13.17
12
A
ASP
23
-150.64
3.58
12
A
GLU
25
-92.16
39.62
12
A
TYR
26
-2.35
76.68
12
A
MET
31
54.76
16.26
13
A
ASP
23
-150.37
6.45
13
A
GLU
25
-94.34
40.16
13
A
TYR
26
-3.44
77.92
13
A
MET
31
57.21
13.28
14
A
CYS
22
65.18
60.04
14
A
ASP
23
-150.28
8.03
14
A
ARG
24
44.39
29.93
14
A
GLU
25
-94.76
42.91
14
A
TYR
26
-2.94
78.90
14
A
MET
31
55.99
13.62
15
A
CYS
22
67.70
60.85
15
A
ASP
23
-142.34
-5.38
15
A
GLU
25
-99.93
41.58
15
A
TYR
26
9.76
70.78
15
A
CYS
37
-77.36
-74.32
15
A
VAL
38
-101.35
45.94
16
A
ASP
23
-150.52
2.85
16
A
GLU
25
-94.19
42.76
16
A
TYR
26
-6.25
82.72
16
A
MET
31
51.23
13.45
17
A
CYS
22
65.39
60.08
17
A
ASP
23
-147.49
-4.39
17
A
GLU
25
-96.77
36.00
17
A
TYR
26
5.84
73.87
17
A
MET
31
59.13
14.72
17
A
CYS
37
-59.53
-71.94
17
A
VAL
38
-96.40
43.35
18
A
ASP
23
-150.39
5.47
18
A
GLU
25
-93.98
41.45
18
A
TYR
26
-5.40
77.35
18
A
MET
31
55.44
15.89
19
A
ASP
23
-150.36
4.65
19
A
GLU
25
-93.93
39.35
19
A
TYR
26
0.35
76.89
19
A
MET
31
56.49
14.36
20
A
GLU
25
-98.49
44.69
20
A
TYR
26
-11.66
80.12
20
A
MET
31
57.42
6.67
20
A
CYS
37
-69.01
-70.49
NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR
1
N
N
2
N
N
A
MET
31
A
MET
31
HELX_P
A
VAL
35
A
VAL
35
5
1
5
disulf
2.019
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
15
A
SG
CYS
15
1_555
disulf
2.019
A
CYS
10
A
SG
CYS
10
1_555
A
CYS
28
A
SG
CYS
28
1_555
disulf
2.020
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
37
A
SG
CYS
37
1_555
metalc
2.791
A
ARG
20
A
O
ARG
20
1_555
A
CA
40
B
CA
CA
1_555
metalc
2.647
A
ASP
23
A
OD1
ASP
23
1_555
A
CA
40
B
CA
CA
1_555
metalc
3.186
A
GLU
25
A
O
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
metalc
3.021
A
GLU
25
A
N
GLU
25
1_555
A
CA
40
B
CA
CA
1_555
metalc
3.248
A
TYR
26
A
N
TYR
26
1_555
A
CA
40
B
CA
CA
1_555
metalc
2.635
A
ASP
27
A
OD2
ASP
27
1_555
A
CA
40
B
CA
CA
1_555
metalc
2.632
A
ASP
33
A
OD2
ASP
33
1_555
A
CA
40
B
CA
CA
1_555
metalc
2.619
A
GLU
34
A
OE2
GLU
34
1_555
A
CA
40
B
CA
CA
1_555
LIPID BINDING PROTEIN
LDL receptor, ligand-binding domain, calcium-binding, familial hypercholesterolemia, LIPID BINDING PROTEIN
LDLR_HUMAN
UNP
1
234
P01130
ATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVN
234
272
1F8Z
1
39
P01130
A
1
1
39
2
anti-parallel
A
GLU
7
A
GLU
7
A
GLN
9
A
GLN
9
A
CYS
15
A
CYS
15
A
HIS
17
A
HIS
17
BINDING SITE FOR RESIDUE CA A 40
A
CA
40
Software
7
A
ARG
20
A
ARG
20
7
1_555
A
ASP
23
A
ASP
23
7
1_555
A
GLU
25
A
GLU
25
7
1_555
A
TYR
26
A
TYR
26
7
1_555
A
ASP
27
A
ASP
27
7
1_555
A
ASP
33
A
ASP
33
7
1_555
A
GLU
34
A
GLU
34
7
1_555
1
P 1