1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
O'Leary, J.M.
Hamilton, J.m.
Deane, C.M.
Valeyev, N.V.
Sandell, L.J.
Downing, A.K.
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 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
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
279
53857
53866
10.1074/jbc.M409225200
15466413
Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA
2004
US
PROTEIN EXPR.PURIF.
PEXPEJ
0757
1096-0279
Identification and removal of O-linked and non-covalently linked sugars from recombinant protein produced using Pichia pastoris
2004
10.2210/pdb1u5m/pdb
pdb_00001u5m
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
7981.009
alpha 1 type II collagen isoform 1
Exon2
T67A, T71A, S73A
1
man
polymer
collagen II, alpha-1 polypeptide; cartilage collagen; chondrocalcin, included; COL11A3, formerly
no
no
YVEFQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPADLAAAA
YVEFQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPADLAAAA
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
human
Homo
Pichia
sample
COL2A1
9606
Homo sapiens
4922
Pichia pastoris
GS115
plasmid
pPICK9K-CRcolIIA
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
2004-10-05
1
1
2008-04-30
1
2
2011-07-13
1
3
2021-10-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Pair of fibronectin type I domains
RCSB
Y
RCSB
2004-07-28
REL
REL
Sequential assignments were made using triple resonance techniques. Disulfide bond connectivity was determined using NOESY data acquired at different temperatures.
target function
600
20
3D_15N-separated_NOESY
HMQC-J
2D NOESY
50 mM potassium phosphate
6.0
ambient
298
K
semi-automated assignment and torsion angle dynamics
1,2
closest to the average
0.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
0.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 99.9% D2O
99.9% D2O
0.8mM U-15N,13C exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
Guntert, P.
structure solution
CYANA
1.0.6
Guntert, P.
refinement
CYANA
1.0.6
600
GE
OMEGA
750
GE
OMEGA
TYR
1
n
1
TYR
1
A
VAL
2
n
2
VAL
2
A
GLU
3
n
3
GLU
3
A
PHE
4
n
4
PHE
4
A
GLN
5
n
5
GLN
5
A
GLU
6
n
6
GLU
6
A
ALA
7
n
7
ALA
7
A
GLY
8
n
8
GLY
8
A
SER
9
n
9
SER
9
A
CYS
10
n
10
CYS
10
A
VAL
11
n
11
VAL
11
A
GLN
12
n
12
GLN
12
A
ASP
13
n
13
ASP
13
A
GLY
14
n
14
GLY
14
A
GLN
15
n
15
GLN
15
A
ARG
16
n
16
ARG
16
A
TYR
17
n
17
TYR
17
A
ASN
18
n
18
ASN
18
A
ASP
19
n
19
ASP
19
A
LYS
20
n
20
LYS
20
A
ASP
21
n
21
ASP
21
A
VAL
22
n
22
VAL
22
A
TRP
23
n
23
TRP
23
A
LYS
24
n
24
LYS
24
A
PRO
25
n
25
PRO
25
A
GLU
26
n
26
GLU
26
A
PRO
27
n
27
PRO
27
A
CYS
28
n
28
CYS
28
A
ARG
29
n
29
ARG
29
A
ILE
30
n
30
ILE
30
A
CYS
31
n
31
CYS
31
A
VAL
32
n
32
VAL
32
A
CYS
33
n
33
CYS
33
A
ASP
34
n
34
ASP
34
A
THR
35
n
35
THR
35
A
GLY
36
n
36
GLY
36
A
THR
37
n
37
THR
37
A
VAL
38
n
38
VAL
38
A
LEU
39
n
39
LEU
39
A
CYS
40
n
40
CYS
40
A
ASP
41
n
41
ASP
41
A
ASP
42
n
42
ASP
42
A
ILE
43
n
43
ILE
43
A
ILE
44
n
44
ILE
44
A
CYS
45
n
45
CYS
45
A
GLU
46
n
46
GLU
46
A
ASP
47
n
47
ASP
47
A
VAL
48
n
48
VAL
48
A
LYS
49
n
49
LYS
49
A
ASP
50
n
50
ASP
50
A
CYS
51
n
51
CYS
51
A
LEU
52
n
52
LEU
52
A
SER
53
n
53
SER
53
A
PRO
54
n
54
PRO
54
A
GLU
55
n
55
GLU
55
A
ILE
56
n
56
ILE
56
A
PRO
57
n
57
PRO
57
A
PHE
58
n
58
PHE
58
A
GLY
59
n
59
GLY
59
A
GLU
60
n
60
GLU
60
A
CYS
61
n
61
CYS
61
A
CYS
62
n
62
CYS
62
A
PRO
63
n
63
PRO
63
A
ILE
64
n
64
ILE
64
A
CYS
65
n
65
CYS
65
A
PRO
66
n
66
PRO
66
A
ALA
67
n
67
ALA
67
A
ASP
68
n
68
ASP
68
A
LEU
69
n
69
LEU
69
A
ALA
70
n
70
ALA
70
A
ALA
71
n
71
ALA
71
A
ALA
72
n
72
ALA
72
A
ALA
73
n
73
ALA
73
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
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
CYS
10
A
N
CYS
10
A
O
TYR
17
A
O
TYR
17
A
N
TRP
23
A
N
TRP
23
A
O
CYS
31
A
O
CYS
31
A
N
VAL
32
A
N
VAL
32
A
O
LEU
39
A
O
LEU
39
4
A
A
H
O
ASP
THR
34
37
1.52
5
A
A
H
O
ASP
THR
34
37
1.59
6
A
A
H
O
ASP
THR
34
37
1.51
7
A
A
H
O
ASP
THR
34
37
1.54
9
A
A
H
O
ASP
THR
34
37
1.54
9
A
A
H
OD1
ASN
ASP
18
21
1.58
10
A
A
O
HE2
GLY
GLU
59
60
1.54
10
A
A
H
O
ASP
THR
34
37
1.56
16
A
A
H
O
ASP
THR
34
37
1.52
20
A
A
OE1
HE2
GLU
GLU
46
60
1.55
20
A
A
H
OD2
ASN
ASP
18
21
1.55
1
A
GLU
3
49.85
86.89
1
A
ALA
7
60.87
150.02
1
A
ASP
47
177.92
-161.64
1
A
LYS
49
-114.08
-78.07
1
A
CYS
51
44.25
-153.17
1
A
LEU
52
-137.08
-71.14
1
A
PHE
58
56.26
-95.82
1
A
GLU
60
-128.58
-147.66
1
A
ASP
68
-174.86
-50.88
1
A
ALA
70
60.52
74.96
2
A
SER
9
179.98
153.99
2
A
ASN
18
-54.70
-170.43
2
A
CYS
28
-169.22
-36.95
2
A
ASP
50
166.77
-33.28
2
A
CYS
51
64.51
166.23
2
A
LEU
52
-49.46
-96.74
2
A
PHE
58
36.31
44.59
2
A
GLU
60
-137.55
-77.57
2
A
CYS
61
-178.28
-38.03
2
A
ALA
67
-68.34
-150.96
2
A
ALA
70
56.59
173.91
2
A
ALA
72
74.94
-59.92
3
A
VAL
2
-173.32
134.54
3
A
ASN
18
-59.80
-177.86
3
A
ILE
43
-69.31
98.95
3
A
GLU
46
-56.47
105.81
3
A
VAL
48
65.00
140.80
3
A
LYS
49
-94.75
46.45
3
A
ASP
50
-145.49
27.49
3
A
LEU
52
-69.81
-90.11
3
A
PHE
58
36.85
43.80
3
A
GLU
60
-136.22
-135.62
3
A
ALA
67
-145.33
53.19
3
A
ASP
68
-161.87
49.09
3
A
ALA
71
-163.52
-62.37
4
A
GLU
3
-145.12
-60.26
4
A
PHE
4
50.24
90.52
4
A
ASN
18
-56.15
175.58
4
A
ASP
47
-168.45
33.39
4
A
LYS
49
-111.12
-77.62
4
A
ASP
50
-147.73
55.45
4
A
CYS
51
-48.37
163.25
4
A
LEU
52
-50.26
-76.27
4
A
GLU
60
-141.35
-149.76
4
A
ALA
67
-101.90
75.94
4
A
ASP
68
-154.83
-49.25
5
A
PHE
4
51.13
94.09
5
A
SER
9
62.72
157.24
5
A
ASP
47
-152.79
89.09
5
A
VAL
48
66.35
149.34
5
A
PHE
58
36.66
40.27
5
A
GLU
60
-135.23
-139.87
5
A
ALA
67
68.51
-68.86
5
A
ASP
68
-179.63
56.91
5
A
LEU
69
56.03
178.48
5
A
ALA
70
-103.15
61.34
5
A
ALA
72
-163.52
-61.40
6
A
GLU
3
68.41
166.69
6
A
GLN
5
66.66
130.48
6
A
ALA
7
63.07
93.13
6
A
SER
9
63.34
167.08
6
A
ASN
18
-56.10
-175.52
6
A
ASP
21
-38.35
155.79
6
A
THR
35
55.91
17.89
6
A
ASP
47
-164.01
30.55
6
A
ASP
50
-148.04
49.80
6
A
LEU
52
-135.63
-48.95
6
A
GLU
60
-134.91
-144.21
6
A
ASP
68
52.95
77.55
7
A
VAL
2
-163.82
-43.96
7
A
GLU
3
-40.58
155.45
7
A
GLU
6
60.03
164.78
7
A
ASN
18
-53.93
-172.27
7
A
ASP
21
-39.96
157.86
7
A
ASP
47
-165.58
40.98
7
A
LYS
49
-134.47
-61.72
7
A
LEU
52
-152.60
-47.97
7
A
PHE
58
39.95
83.12
7
A
ALA
67
66.97
-72.13
7
A
ASP
68
-178.53
60.23
7
A
ALA
70
54.86
78.33
7
A
ALA
72
-177.90
133.29
8
A
GLU
6
61.24
114.31
8
A
ASP
50
39.87
53.78
8
A
LEU
52
-40.72
-83.07
8
A
PHE
58
41.09
84.43
8
A
ASP
68
-177.62
37.31
8
A
ALA
71
45.04
90.76
8
A
ALA
72
51.60
81.00
9
A
GLU
3
66.81
83.77
9
A
PHE
4
-167.12
91.80
9
A
ASN
18
-54.47
-175.05
9
A
ASP
21
-36.50
143.01
9
A
VAL
48
-93.22
-103.10
9
A
LYS
49
-156.57
-86.35
9
A
LEU
52
-45.58
-89.35
9
A
PHE
58
42.75
84.83
9
A
PRO
66
-74.97
-169.80
9
A
ALA
67
-94.44
46.76
9
A
LEU
69
-40.39
159.54
9
A
ALA
71
-57.87
-73.28
10
A
THR
35
38.08
76.04
10
A
LYS
49
-142.51
-69.79
10
A
LEU
52
-73.93
-88.34
10
A
GLU
60
-145.35
-150.43
10
A
ALA
67
-49.87
95.62
10
A
ASP
68
172.23
-43.14
10
A
LEU
69
39.58
52.50
10
A
ALA
72
179.51
-58.49
11
A
PHE
4
49.98
92.97
11
A
ALA
7
-145.69
-62.58
11
A
ASN
18
-54.56
-170.69
11
A
CYS
28
-169.46
-36.66
11
A
CYS
33
-68.70
70.63
11
A
ASP
50
170.44
-34.28
11
A
CYS
51
58.56
163.05
11
A
LEU
52
-39.65
-86.68
11
A
PHE
58
35.72
40.69
11
A
GLU
60
-134.70
-75.84
11
A
CYS
61
-179.51
-38.22
11
A
ASP
68
-156.90
83.84
11
A
LEU
69
39.66
83.99
11
A
ALA
71
-105.29
-60.10
12
A
ASN
18
-75.34
-164.97
12
A
CYS
28
-169.40
-36.58
12
A
ASP
50
86.36
-45.36
12
A
CYS
51
60.99
-162.01
12
A
PHE
58
36.40
40.12
12
A
GLU
60
-134.21
-76.13
12
A
CYS
61
-178.87
-38.71
12
A
PRO
66
-75.08
-168.68
12
A
ALA
70
41.87
79.67
12
A
ALA
72
60.74
150.48
13
A
VAL
2
56.43
96.05
13
A
GLU
3
-165.28
96.00
13
A
GLU
6
-117.62
71.45
13
A
ALA
7
-174.48
103.50
13
A
SER
9
62.71
103.02
13
A
ASN
18
-61.54
-172.99
13
A
ASP
21
-50.67
103.30
13
A
CYS
28
-169.76
-36.79
13
A
CYS
33
-108.28
66.77
13
A
LYS
49
-96.99
40.88
13
A
ASP
50
-144.53
39.83
13
A
LEU
52
-78.66
-86.35
13
A
PHE
58
35.43
41.83
13
A
GLU
60
-135.02
-75.64
13
A
CYS
61
-178.57
-38.56
13
A
ALA
70
58.99
158.85
13
A
ALA
71
-175.04
68.76
14
A
GLU
3
170.58
143.12
14
A
PHE
4
-128.65
-51.83
14
A
GLN
5
58.26
159.94
14
A
ALA
7
-172.64
-60.64
14
A
ASN
18
-52.69
-175.34
14
A
CYS
28
-169.52
-37.25
14
A
VAL
48
-46.35
165.88
14
A
LYS
49
-126.25
-67.49
14
A
ASP
50
-154.03
55.14
14
A
LEU
52
-93.69
-68.09
14
A
PHE
58
35.01
45.01
14
A
GLU
60
-138.04
-74.28
14
A
CYS
61
178.73
-37.45
14
A
ALA
67
-111.74
69.49
14
A
ASP
68
-147.54
-50.73
14
A
ALA
72
59.69
84.46
15
A
VAL
2
-42.74
154.72
15
A
GLU
3
58.36
113.23
15
A
GLU
6
65.08
117.57
15
A
ALA
7
-176.26
123.07
15
A
ASN
18
-60.69
-159.89
15
A
CYS
28
-169.51
-36.54
15
A
VAL
48
-130.91
-106.27
15
A
LYS
49
-159.68
-73.82
15
A
CYS
51
-67.65
-164.69
15
A
LEU
52
-96.94
-66.39
15
A
PHE
58
33.69
40.67
15
A
GLU
60
-134.62
-76.03
15
A
CYS
61
-178.32
-38.62
15
A
ALA
67
-74.96
-157.84
15
A
ALA
70
57.11
101.76
15
A
ALA
72
64.01
169.15
16
A
PHE
4
-48.33
156.98
16
A
SER
9
-51.43
172.07
16
A
ASN
18
-47.58
172.51
16
A
CYS
28
-169.72
-36.05
16
A
PHE
58
35.35
39.92
16
A
GLU
60
-133.59
-76.29
16
A
CYS
61
-178.38
-38.63
16
A
ALA
67
-52.83
-98.00
16
A
LEU
69
-160.38
89.82
16
A
ALA
70
57.90
91.92
17
A
VAL
2
-142.42
-47.27
17
A
GLU
3
-63.48
89.65
17
A
GLN
5
81.27
-51.67
17
A
GLU
6
63.51
151.61
17
A
ALA
7
-49.78
171.97
17
A
SER
9
175.08
149.75
17
A
ASN
18
-71.39
-161.26
17
A
CYS
28
-169.24
-37.11
17
A
CYS
33
-69.84
67.20
17
A
CYS
51
-57.33
-163.71
17
A
PHE
58
35.19
42.10
17
A
GLU
60
-135.84
-72.15
17
A
CYS
61
179.76
-37.79
17
A
ALA
70
172.61
168.06
17
A
ALA
71
56.02
100.06
18
A
GLU
3
-174.29
100.00
18
A
GLN
5
58.78
161.14
18
A
ALA
7
-50.11
102.30
18
A
SER
9
62.02
170.89
18
A
ASN
18
-52.07
-176.80
18
A
ASP
21
-53.48
104.20
18
A
CYS
28
-169.97
-36.14
18
A
ASP
47
175.73
-176.31
18
A
LYS
49
-92.11
45.69
18
A
ASP
50
-149.89
52.93
18
A
LEU
52
-60.17
-85.47
18
A
PHE
58
35.70
43.64
18
A
GLU
60
-136.42
-76.94
18
A
CYS
61
-178.96
-37.36
18
A
ASP
68
169.84
79.99
18
A
LEU
69
63.59
-80.68
18
A
ALA
70
-162.47
111.51
18
A
ALA
71
62.06
177.36
19
A
VAL
2
-176.10
-39.78
19
A
ASN
18
-79.49
-169.80
19
A
CYS
28
-169.79
-36.32
19
A
CYS
51
-64.36
-153.09
19
A
LEU
52
-148.89
-65.55
19
A
PHE
58
35.20
43.89
19
A
GLU
60
-135.79
-75.75
19
A
CYS
61
-179.32
-36.60
19
A
ASP
68
174.80
85.74
19
A
LEU
69
52.03
-179.25
20
A
GLU
3
-171.76
120.14
20
A
GLU
6
60.05
153.74
20
A
ALA
7
-161.59
91.52
20
A
ASN
18
-58.24
-161.54
20
A
CYS
28
-169.53
-36.52
20
A
ASP
47
-109.61
-166.15
20
A
VAL
48
68.65
106.93
20
A
ASP
50
-149.46
41.68
20
A
LEU
52
-40.35
-75.70
20
A
PHE
58
33.56
42.03
20
A
GLU
60
-135.77
-74.54
20
A
CYS
61
-179.49
-38.27
20
A
ALA
67
-166.94
97.53
20
A
ASP
68
-139.11
-47.85
Structure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA
1
N
N
disulf
1.999
A
CYS
10
A
SG
CYS
10
1_555
A
CYS
33
A
SG
CYS
33
1_555
disulf
1.991
A
CYS
28
A
SG
CYS
28
1_555
A
CYS
61
A
SG
CYS
61
1_555
disulf
1.998
A
CYS
31
A
SG
CYS
31
1_555
A
CYS
40
A
SG
CYS
40
1_555
disulf
2.054
A
CYS
45
A
SG
CYS
45
1_555
A
CYS
62
A
SG
CYS
62
1_555
disulf
2.145
A
CYS
51
A
SG
CYS
51
1_555
A
CYS
65
A
SG
CYS
65
1_555
STRUCTURAL PROTEIN
5 disulfide bonds, two sub-domain architecture, beta-sheet, STRUCTURAL PROTEIN
CO2A1_HUMAN
UNP
1
25
P02458
GQDVQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPTDLATAS
25
97
1U5M
1
73
P02458
A
1
1
73
1
GLY
cloning artifact
TYR
1
1U5M
A
P02458
UNP
25
1
1
GLN
cloning artifact
VAL
2
1U5M
A
P02458
UNP
26
2
1
ASP
cloning artifact
GLU
3
1U5M
A
P02458
UNP
27
3
1
VAL
cloning artifact
PHE
4
1U5M
A
P02458
UNP
28
4
1
THR
engineered mutation
ALA
67
1U5M
A
P02458
UNP
91
67
1
THR
engineered mutation
ALA
71
1U5M
A
P02458
UNP
95
71
1
SER
engineered mutation
ALA
73
1U5M
A
P02458
UNP
97
73
2
3
anti-parallel
anti-parallel
anti-parallel
A
CYS
10
A
CYS
10
A
VAL
11
A
VAL
11
A
ARG
16
A
ARG
16
A
TYR
17
A
TYR
17
A
VAL
22
A
VAL
22
A
TRP
23
A
TRP
23
A
ARG
29
A
ARG
29
A
ASP
34
A
ASP
34
A
THR
37
A
THR
37
A
ASP
42
A
ASP
42