1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sampoli-Benitez, B.A.
Hunter, M.J.
Meininger, D.P.
Komives, E.A.
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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
273
913
926
10.1006/jmbi.1997.1356
9367781
Structure of the fifth EGF-like domain of thrombomodulin: An EGF-like domain with a novel disulfide-bonding pattern.
1997
10.2210/pdb1adx/pdb
pdb_00001adx
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
4377.751
THROMBOMODULIN
FIFTH EGF-LIKE DOMAIN
1
man
polymer
TMEGF5
no
no
QMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDE
QMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDE
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
human
Homo
sample
9606
BLOOD
Homo sapiens
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1997-12-24
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1997-02-18
REL
REL
LOWEST ENERGY
50
14
TOCSY
NOESY DQF-COSY
E-COSY
5.5
298
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL REFERENCE ABOVE.
DISTANCE GEOMETRY AND SIMULATED ANNEALING
BRUNGER
refinement
X-PLOR
3.1
structure solution
DGII
structure solution
X-PLOR
500
Bruker
AMX500
600
Bruker
DRX600
GLN
1
n
1
GLN
1
A
MET
2
n
2
MET
2
A
PHE
3
n
3
PHE
3
A
CYS
4
n
4
CYS
4
A
ASN
5
n
5
ASN
5
A
GLN
6
n
6
GLN
6
A
THR
7
n
7
THR
7
A
ALA
8
n
8
ALA
8
A
CYS
9
n
9
CYS
9
A
PRO
10
n
10
PRO
10
A
ALA
11
n
11
ALA
11
A
ASP
12
n
12
ASP
12
A
CYS
13
n
13
CYS
13
A
ASP
14
n
14
ASP
14
A
PRO
15
n
15
PRO
15
A
ASN
16
n
16
ASN
16
A
THR
17
n
17
THR
17
A
GLN
18
n
18
GLN
18
A
ALA
19
n
19
ALA
19
A
SER
20
n
20
SER
20
A
CYS
21
n
21
CYS
21
A
GLU
22
n
22
GLU
22
A
CYS
23
n
23
CYS
23
A
PRO
24
n
24
PRO
24
A
GLU
25
n
25
GLU
25
A
GLY
26
n
26
GLY
26
A
TYR
27
n
27
TYR
27
A
ILE
28
n
28
ILE
28
A
LEU
29
n
29
LEU
29
A
ASP
30
n
30
ASP
30
A
ASP
31
n
31
ASP
31
A
GLY
32
n
32
GLY
32
A
PHE
33
n
33
PHE
33
A
ILE
34
n
34
ILE
34
A
CYS
35
n
35
CYS
35
A
THR
36
n
36
THR
36
A
ASP
37
n
37
ASP
37
A
ILE
38
n
38
ILE
38
A
ASP
39
n
39
ASP
39
A
GLU
40
n
40
GLU
40
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
2
-26.46
2.10
128.40
101.94
A
A
A
C
N
CD
CYS
PRO
PRO
9
10
10
Y
2
-21.18
2.10
128.40
107.22
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
3
-19.25
2.10
128.40
109.15
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
4
-23.36
2.10
128.40
105.04
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
5
-22.10
2.10
128.40
106.30
A
A
A
C
N
CD
CYS
PRO
PRO
9
10
10
Y
6
-19.19
2.10
128.40
109.21
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
8
-26.14
2.10
128.40
102.26
A
A
A
C
N
CD
CYS
PRO
PRO
9
10
10
Y
8
-21.03
2.10
128.40
107.37
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
10
-19.75
2.10
128.40
108.65
A
A
A
C
N
CD
CYS
PRO
PRO
23
24
24
Y
1
A
PHE
3
178.85
29.48
1
A
CYS
4
41.43
-159.80
1
A
GLN
6
86.08
41.44
1
A
THR
7
82.21
-40.11
1
A
ALA
8
-174.64
130.87
1
A
PRO
10
-66.28
-159.89
1
A
ASP
12
-60.34
90.41
1
A
CYS
13
-59.20
90.12
1
A
GLN
18
-41.82
96.88
1
A
ALA
19
-175.14
29.59
1
A
CYS
23
51.69
149.46
1
A
PRO
24
-53.26
-164.64
1
A
GLU
25
-54.22
90.03
1
A
ILE
28
79.85
117.39
1
A
LEU
29
-53.99
-165.42
1
A
PHE
33
44.88
26.20
1
A
ILE
38
-134.84
-38.32
1
A
ASP
39
-167.26
-89.52
2
A
MET
2
61.55
121.11
2
A
CYS
4
68.42
163.50
2
A
GLN
6
86.41
110.34
2
A
THR
7
31.42
-88.90
2
A
CYS
9
-157.97
-122.51
2
A
ALA
11
66.57
100.70
2
A
THR
17
178.65
53.49
2
A
GLN
18
-62.47
-164.40
2
A
CYS
23
14.69
104.43
2
A
PRO
24
23.24
135.01
2
A
GLU
25
-56.62
92.76
2
A
ILE
28
98.45
113.30
2
A
LEU
29
-60.97
-154.45
2
A
ASP
30
101.50
173.86
2
A
PHE
33
54.96
19.09
2
A
THR
36
160.49
176.95
2
A
ASP
37
171.03
40.61
2
A
ILE
38
-159.92
29.37
2
A
ASP
39
171.91
67.08
3
A
PHE
3
-106.46
53.71
3
A
CYS
4
63.77
158.89
3
A
GLN
6
-109.76
-163.95
3
A
CYS
9
175.07
166.54
3
A
PRO
10
-53.79
-160.61
3
A
CYS
13
-43.07
94.32
3
A
THR
17
168.94
87.32
3
A
CYS
23
-1.25
118.76
3
A
PRO
24
4.08
64.77
3
A
GLU
25
24.05
96.14
3
A
ILE
28
51.75
153.40
3
A
PHE
33
44.89
26.66
3
A
ASP
37
160.83
90.87
4
A
PHE
3
-45.13
92.75
4
A
CYS
4
37.86
-158.11
4
A
ASN
5
-95.59
-141.61
4
A
ALA
8
66.96
156.25
4
A
ALA
11
74.18
-138.46
4
A
ASP
12
87.33
109.51
4
A
THR
17
-159.59
62.39
4
A
CYS
21
41.32
-174.55
4
A
GLU
22
42.18
29.93
4
A
CYS
23
-25.63
104.08
4
A
PRO
24
32.52
-162.21
4
A
GLU
25
-102.78
69.05
4
A
ILE
28
69.26
109.29
4
A
LEU
29
-51.16
-171.17
4
A
ASP
30
152.76
179.68
4
A
ASP
31
57.57
15.49
4
A
PHE
33
45.09
23.71
4
A
THR
36
90.10
129.94
4
A
ILE
38
27.83
85.02
5
A
ASN
5
59.91
-86.45
5
A
THR
7
34.80
-84.92
5
A
ALA
8
-163.37
82.60
5
A
CYS
9
-66.84
-162.42
5
A
ALA
11
64.31
84.02
5
A
CYS
13
36.90
72.84
5
A
THR
17
178.09
79.05
5
A
CYS
21
46.50
-171.93
5
A
CYS
23
-18.70
141.53
5
A
PRO
24
-34.33
156.89
5
A
GLU
25
-64.64
87.49
5
A
ILE
28
64.28
116.26
5
A
LEU
29
-55.36
-165.17
5
A
ASP
31
-43.82
107.89
5
A
THR
36
170.30
176.08
5
A
ASP
37
-139.13
-32.56
6
A
PHE
3
-105.78
57.70
6
A
CYS
4
35.57
101.49
6
A
ASN
5
37.78
60.02
6
A
GLN
6
38.07
-93.31
6
A
ALA
8
174.25
-177.33
6
A
CYS
9
164.13
159.67
6
A
PRO
10
-49.75
-143.45
6
A
ALA
11
-155.77
48.66
6
A
CYS
13
-63.20
88.43
6
A
THR
17
-153.28
55.54
6
A
SER
20
165.64
-113.12
6
A
CYS
21
-55.38
-163.94
6
A
CYS
23
-5.27
112.32
6
A
PRO
24
8.32
-134.17
6
A
ILE
28
79.52
107.60
6
A
LEU
29
-50.80
-176.12
6
A
ASP
30
160.54
161.05
6
A
ASP
31
76.63
-1.93
6
A
PHE
33
58.38
13.44
6
A
THR
36
162.80
177.45
6
A
ASP
37
-158.64
-59.21
7
A
MET
2
-150.80
26.14
7
A
PHE
3
36.14
80.65
7
A
CYS
4
50.55
-176.49
7
A
ASN
5
-108.19
-86.34
7
A
GLN
6
-52.21
-168.70
7
A
THR
7
-38.76
-30.18
7
A
ALA
8
172.14
136.75
7
A
PRO
10
-76.18
-161.45
7
A
ALA
11
-117.09
58.37
7
A
THR
17
-140.57
57.49
7
A
GLN
18
-63.12
93.64
7
A
ALA
19
-154.89
17.71
7
A
CYS
23
52.64
131.54
7
A
PRO
24
-40.11
99.15
7
A
GLU
25
40.76
83.26
7
A
TYR
27
-39.20
-36.18
7
A
ILE
28
87.58
112.95
7
A
LEU
29
-54.47
-179.44
7
A
ASP
30
155.74
174.53
7
A
PHE
33
56.80
13.83
7
A
THR
36
-46.30
174.25
7
A
ASP
37
-134.79
-62.33
7
A
ILE
38
-38.34
115.47
8
A
ASN
5
70.77
-7.44
8
A
GLN
6
168.98
73.01
8
A
THR
7
70.93
-81.17
8
A
CYS
9
-176.13
-125.23
8
A
ALA
11
51.31
83.20
8
A
CYS
13
30.10
93.95
8
A
ASN
16
-90.74
34.95
8
A
THR
17
176.55
79.95
8
A
SER
20
-44.86
165.11
8
A
CYS
21
38.58
-165.92
8
A
GLU
22
41.42
29.62
8
A
CYS
23
-7.52
103.92
8
A
PRO
24
19.53
-143.24
8
A
GLU
25
-105.86
56.39
8
A
ILE
28
52.00
124.42
8
A
LEU
29
-61.80
-166.34
8
A
ASP
30
-165.45
-162.09
8
A
ASP
31
-43.97
96.33
8
A
PHE
33
-75.66
27.78
8
A
THR
36
174.16
176.29
8
A
ASP
39
-110.82
50.71
9
A
MET
2
-170.61
147.51
9
A
CYS
4
39.92
93.10
9
A
ASN
5
40.53
-88.11
9
A
GLN
6
-176.13
134.43
9
A
THR
7
83.47
-43.65
9
A
ALA
8
162.05
128.34
9
A
PRO
10
-61.62
-151.48
9
A
ALA
11
-142.22
-140.34
9
A
ASP
12
93.07
9.93
9
A
CYS
13
40.59
102.97
9
A
ASP
14
-52.15
-175.04
9
A
GLN
18
32.14
35.95
9
A
ALA
19
-138.89
-156.62
9
A
CYS
23
-12.88
143.10
9
A
PRO
24
-36.90
163.18
9
A
ILE
28
58.61
126.33
9
A
LEU
29
-54.03
-167.30
9
A
CYS
35
-47.91
-86.30
9
A
THR
36
41.58
-166.44
9
A
ASP
37
-154.83
-32.22
9
A
ASP
39
-93.01
39.52
10
A
MET
2
-164.11
-149.46
10
A
PHE
3
-179.25
90.77
10
A
CYS
4
-27.64
107.55
10
A
ASN
5
-75.70
-139.83
10
A
GLN
6
39.17
36.01
10
A
THR
7
83.87
-42.88
10
A
ALA
8
178.61
169.70
10
A
PRO
10
-53.78
-160.08
10
A
CYS
13
39.56
51.09
10
A
THR
17
-167.05
73.45
10
A
GLN
18
-40.19
-94.40
10
A
ALA
19
37.97
-155.31
10
A
SER
20
48.60
-123.40
10
A
CYS
21
-39.44
157.01
10
A
PRO
24
2.30
116.95
10
A
GLU
25
-44.12
97.11
10
A
ILE
28
47.22
173.11
10
A
LEU
29
-77.41
-167.84
10
A
ASP
31
-43.10
98.98
10
A
PHE
33
48.57
27.16
10
A
THR
36
-56.88
-159.66
10
A
ASP
37
-164.52
24.66
11
A
PHE
3
-40.15
89.40
11
A
CYS
4
36.09
92.54
11
A
ASN
5
-29.71
-83.65
11
A
GLN
6
-42.46
169.20
11
A
ALA
8
178.37
103.81
11
A
PRO
10
-63.97
-163.09
11
A
ASP
12
-103.67
60.80
11
A
CYS
13
-37.42
110.67
11
A
ASN
16
-92.69
36.61
11
A
THR
17
-177.11
77.37
11
A
GLN
18
-93.54
39.14
11
A
SER
20
-60.75
-117.38
11
A
CYS
21
-47.55
173.55
11
A
PRO
24
-18.03
139.48
11
A
GLU
25
-63.08
89.50
11
A
TYR
27
-55.15
-170.40
11
A
ILE
28
168.16
161.10
11
A
LEU
29
-90.50
-133.85
11
A
ASP
30
152.81
91.47
11
A
ASP
31
44.05
26.30
11
A
THR
36
157.99
-49.21
11
A
ASP
37
75.64
124.89
12
A
MET
2
161.45
132.29
12
A
PHE
3
39.45
28.17
12
A
CYS
4
22.66
90.27
12
A
GLN
6
163.03
87.46
12
A
THR
7
44.94
27.72
12
A
ALA
8
73.18
171.38
12
A
CYS
9
176.54
144.53
12
A
PRO
10
-44.62
-170.19
12
A
ASP
12
-47.13
92.50
12
A
GLN
18
-88.46
33.52
12
A
CYS
21
-126.57
-159.44
12
A
CYS
23
-17.66
140.22
12
A
PRO
24
-34.58
155.84
12
A
GLU
25
-64.54
87.14
12
A
ILE
28
72.15
108.81
12
A
LEU
29
-61.89
-166.44
12
A
PHE
33
40.20
27.90
12
A
THR
36
163.03
172.58
12
A
ILE
38
-140.17
24.83
13
A
MET
2
64.90
124.18
13
A
GLN
6
176.93
166.23
13
A
CYS
9
177.51
165.09
13
A
PRO
10
-52.78
-162.30
13
A
CYS
13
-49.16
151.87
13
A
THR
17
-165.35
74.96
13
A
ALA
19
-51.57
89.38
13
A
SER
20
154.75
154.37
13
A
CYS
21
43.17
-169.85
13
A
CYS
23
-11.96
135.71
13
A
PRO
24
-26.58
82.86
13
A
GLU
25
5.44
65.86
13
A
ILE
28
87.51
111.81
13
A
LEU
29
-54.93
-176.19
13
A
ASP
30
158.96
164.96
13
A
CYS
35
-49.57
-98.51
13
A
THR
36
43.47
-168.81
13
A
ASP
37
-176.62
77.58
14
A
MET
2
72.60
-166.34
14
A
PHE
3
-66.97
86.20
14
A
CYS
4
-32.97
95.27
14
A
ASN
5
-125.52
-158.58
14
A
GLN
6
62.48
-103.66
14
A
ALA
8
58.47
126.77
14
A
PRO
10
-77.22
-158.45
14
A
ASP
12
-107.29
48.24
14
A
CYS
13
-41.87
106.67
14
A
THR
17
-171.42
74.74
14
A
GLN
18
-53.96
-107.37
14
A
ALA
19
41.42
-125.89
14
A
SER
20
42.56
-115.32
14
A
CYS
21
-57.27
-160.13
14
A
GLU
22
39.85
32.42
14
A
CYS
23
-3.86
125.96
14
A
PRO
24
-24.27
85.90
14
A
GLU
25
5.48
67.00
14
A
ILE
28
68.05
104.97
14
A
LEU
29
-57.98
-163.41
14
A
ASP
31
-43.85
105.58
14
A
PHE
33
52.72
19.54
14
A
THR
36
178.72
177.91
14
A
ASP
37
-169.38
-52.08
14
A
ASP
39
48.48
77.61
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, 14 STRUCTURES
1
Y
N
disulf
2.021
A
CYS
4
A
SG
CYS
4
1_555
A
CYS
9
A
SG
CYS
9
1_555
disulf
2.020
A
CYS
13
A
SG
CYS
13
1_555
A
CYS
21
A
SG
CYS
21
1_555
disulf
2.020
A
CYS
23
A
SG
CYS
23
1_555
A
CYS
35
A
SG
CYS
35
1_555
BLOOD COAGULATION
BLOOD COAGULATION, ANTICOAGULANT, FIBRINOGEN, PEPTIDE SYNTHESIS, PROTEIN C, THROMBIN, DISULFIDE BONDS
TRBM_HUMAN
UNP
1
1
P07204
MLGVLVLGALALAGLGFPAPAEPQPGGSQCVEHDCFALYPGPATFLNASQICDGLRGHLMTVRSSVAADVISLLLNGDGG
VGRRRLWIGLQLPPGCGDPKRLGPLRGFQWVTGDNNTSYSRWARLDLNGAPLCGPLCVAVSAAEATVPSEPIWEEQQCEV
KADGFLCEFHFPATCRPLAVEPGAAAAAVSITYGTPFAARGADFQALPVGSSAAVAPLGLQLMCTAPPGAVQGHWAREAP
GAWDCSVENGGCEHACNAIPGAPRCQCPAGAALQADGRSCTASATQSCNDLCEHFCVPNPDQPGSYSCMCETGYRLAADQ
HRCEDVDDCILEPSPCPQRCVNTQGGFECHCYPNYDLVDGECVEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHE
PHRCQMFCNQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNLPGTFECICGPDSALARHIGTDC
DSGKVDGGDSGSGEPPPSPTPGSTLTPPAVGLVHSGLLIGISIASLCLVVALLALLCHLRKKQGAARAKMEYKCAAPSKE
VVLQHVRTERTPQRL
405
444
1ADX
1
40
P07204
A
1
1
40
1
P 1