1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tolkatchev, D.
Wang, P.
Chen, Z.
Xu, P.
Ni, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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 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
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
Protein Sci.
PRCIEI
0795
0961-8368
17
711
724
10.1110/ps.073295308
18359860
Structure dissection of human progranulin identifies well-folded granulin/epithelin modules with unique functional activities.
2008
10.2210/pdb2jyt/pdb
pdb_00002jyt
7402.308
Granulin-5
1
man
polymer
Granulin C
no
no
AMVPCDNVSSCPSSDTCCQLTSGEWGCCPIPEAVCCSDHQHCCPQGYTCVAEGQCQKLAAALEHHHHHH
AMVPCDNVSSCPSSDTCCQLTSGEWGCCPIPEAVCCSDHQHCCPQGYTCVAEGQCQKLAAALEHHHHHH
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
human
Homo
Escherichia
sample
GRN
9606
Homo sapiens
562
Escherichia coli
Origami(DE3)
plasmid
pET-32
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2008-04-22
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
Carp granulin-1 fragment
Human granulin A fragment
Oryzain beta fragment
BMRB
Y
RCSB
2007-12-19
REL
REL
structures with the lowest energy
60
10
2D 1H-1H TOCSY
2D 1H-1H NOESY
inphase COSY
2D 1H-1H TOCSY
2D 1H-1H NOESY
2D 1H-13C HSQC
10
mM
150
mM
0.2
mM
0.5
mM
10
mM
150
mM
0.2
mM
0.5
mM
6.8
ambient
atm
298
K
6.8
ambient
atm
288
K
simulated annealing
1
lowest energy
10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 90% H2O/10% D2O
90% H2O/10% D2O
10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 100% D2O
100% D2O
Linge, O'Donoghue and Nilges
structure solution
ARIA
1.0
Johnson, One Moon Scientific
chemical shift assignment
NMRView
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Tripos
data analysis
SYBYL
Accelrys Software Inc.
data analysis
Insight II
Koradi, Billeter and Wuthrich
data analysis
MOLMOL
Linge, O'Donoghue and Nilges
refinement
ARIA
1.0
800
Bruker
AVANCE
Bruker Avance
500
Bruker
AVANCE
Bruker Avance
n
1
-1
A
n
2
0
A
VAL
1
n
3
VAL
1
A
PRO
2
n
4
PRO
2
A
CYS
3
n
5
CYS
3
A
ASP
4
n
6
ASP
4
A
ASN
5
n
7
ASN
5
A
VAL
6
n
8
VAL
6
A
SER
7
n
9
SER
7
A
SER
8
n
10
SER
8
A
CYS
9
n
11
CYS
9
A
PRO
10
n
12
PRO
10
A
SER
11
n
13
SER
11
A
SER
12
n
14
SER
12
A
ASP
13
n
15
ASP
13
A
THR
14
n
16
THR
14
A
CYS
15
n
17
CYS
15
A
CYS
16
n
18
CYS
16
A
GLN
17
n
19
GLN
17
A
LEU
18
n
20
LEU
18
A
THR
19
n
21
THR
19
A
SER
20
n
22
SER
20
A
GLY
21
n
23
GLY
21
A
GLU
22
n
24
GLU
22
A
TRP
23
n
25
TRP
23
A
GLY
24
n
26
GLY
24
A
CYS
25
n
27
CYS
25
A
CYS
26
n
28
CYS
26
A
PRO
27
n
29
PRO
27
A
ILE
28
n
30
ILE
28
A
PRO
29
n
31
PRO
29
A
GLU
30
n
32
GLU
30
A
ALA
31
n
33
ALA
31
A
VAL
32
n
34
VAL
32
A
CYS
33
n
35
CYS
33
A
CYS
34
n
36
CYS
34
A
SER
35
n
37
SER
35
A
ASP
36
n
38
ASP
36
A
HIS
37
n
39
HIS
37
A
GLN
38
n
40
GLN
38
A
HIS
39
n
41
HIS
39
A
CYS
40
n
42
CYS
40
A
CYS
41
n
43
CYS
41
A
PRO
42
n
44
PRO
42
A
GLN
43
n
45
GLN
43
A
GLY
44
n
46
GLY
44
A
TYR
45
n
47
TYR
45
A
THR
46
n
48
THR
46
A
CYS
47
n
49
CYS
47
A
VAL
48
n
50
VAL
48
A
ALA
49
n
51
ALA
49
A
GLU
50
n
52
GLU
50
A
GLY
51
n
53
GLY
51
A
GLN
52
n
54
GLN
52
A
CYS
53
n
55
CYS
53
A
GLN
54
n
56
GLN
54
A
LYS
55
n
57
LYS
55
A
n
58
56
A
n
59
57
A
n
60
58
A
n
61
59
A
n
62
60
A
n
63
61
A
n
64
62
A
n
65
63
A
n
66
64
A
n
67
65
A
n
68
66
A
n
69
67
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
N
THR
14
A
N
THR
16
A
O
CYS
26
A
O
CYS
28
A
N
THR
46
A
N
THR
48
A
O
GLN
54
A
O
GLN
56
1
A
ALA
-1
A
ALA
1
1
Y
1
A
MET
0
A
MET
2
1
Y
1
A
LEU
56
A
LEU
58
1
Y
1
A
ALA
57
A
ALA
59
1
Y
1
A
ALA
58
A
ALA
60
1
Y
1
A
ALA
59
A
ALA
61
1
Y
1
A
LEU
60
A
LEU
62
1
Y
1
A
GLU
61
A
GLU
63
1
Y
1
A
HIS
62
A
HIS
64
1
Y
1
A
HIS
63
A
HIS
65
1
Y
1
A
HIS
64
A
HIS
66
1
Y
1
A
HIS
65
A
HIS
67
1
Y
1
A
HIS
66
A
HIS
68
1
Y
1
A
HIS
67
A
HIS
69
1
Y
2
A
ALA
-1
A
ALA
1
1
Y
2
A
MET
0
A
MET
2
1
Y
2
A
LEU
56
A
LEU
58
1
Y
2
A
ALA
57
A
ALA
59
1
Y
2
A
ALA
58
A
ALA
60
1
Y
2
A
ALA
59
A
ALA
61
1
Y
2
A
LEU
60
A
LEU
62
1
Y
2
A
GLU
61
A
GLU
63
1
Y
2
A
HIS
62
A
HIS
64
1
Y
2
A
HIS
63
A
HIS
65
1
Y
2
A
HIS
64
A
HIS
66
1
Y
2
A
HIS
65
A
HIS
67
1
Y
2
A
HIS
66
A
HIS
68
1
Y
2
A
HIS
67
A
HIS
69
1
Y
3
A
ALA
-1
A
ALA
1
1
Y
3
A
MET
0
A
MET
2
1
Y
3
A
LEU
56
A
LEU
58
1
Y
3
A
ALA
57
A
ALA
59
1
Y
3
A
ALA
58
A
ALA
60
1
Y
3
A
ALA
59
A
ALA
61
1
Y
3
A
LEU
60
A
LEU
62
1
Y
3
A
GLU
61
A
GLU
63
1
Y
3
A
HIS
62
A
HIS
64
1
Y
3
A
HIS
63
A
HIS
65
1
Y
3
A
HIS
64
A
HIS
66
1
Y
3
A
HIS
65
A
HIS
67
1
Y
3
A
HIS
66
A
HIS
68
1
Y
3
A
HIS
67
A
HIS
69
1
Y
4
A
ALA
-1
A
ALA
1
1
Y
4
A
MET
0
A
MET
2
1
Y
4
A
LEU
56
A
LEU
58
1
Y
4
A
ALA
57
A
ALA
59
1
Y
4
A
ALA
58
A
ALA
60
1
Y
4
A
ALA
59
A
ALA
61
1
Y
4
A
LEU
60
A
LEU
62
1
Y
4
A
GLU
61
A
GLU
63
1
Y
4
A
HIS
62
A
HIS
64
1
Y
4
A
HIS
63
A
HIS
65
1
Y
4
A
HIS
64
A
HIS
66
1
Y
4
A
HIS
65
A
HIS
67
1
Y
4
A
HIS
66
A
HIS
68
1
Y
4
A
HIS
67
A
HIS
69
1
Y
5
A
ALA
-1
A
ALA
1
1
Y
5
A
MET
0
A
MET
2
1
Y
5
A
LEU
56
A
LEU
58
1
Y
5
A
ALA
57
A
ALA
59
1
Y
5
A
ALA
58
A
ALA
60
1
Y
5
A
ALA
59
A
ALA
61
1
Y
5
A
LEU
60
A
LEU
62
1
Y
5
A
GLU
61
A
GLU
63
1
Y
5
A
HIS
62
A
HIS
64
1
Y
5
A
HIS
63
A
HIS
65
1
Y
5
A
HIS
64
A
HIS
66
1
Y
5
A
HIS
65
A
HIS
67
1
Y
5
A
HIS
66
A
HIS
68
1
Y
5
A
HIS
67
A
HIS
69
1
Y
6
A
ALA
-1
A
ALA
1
1
Y
6
A
MET
0
A
MET
2
1
Y
6
A
LEU
56
A
LEU
58
1
Y
6
A
ALA
57
A
ALA
59
1
Y
6
A
ALA
58
A
ALA
60
1
Y
6
A
ALA
59
A
ALA
61
1
Y
6
A
LEU
60
A
LEU
62
1
Y
6
A
GLU
61
A
GLU
63
1
Y
6
A
HIS
62
A
HIS
64
1
Y
6
A
HIS
63
A
HIS
65
1
Y
6
A
HIS
64
A
HIS
66
1
Y
6
A
HIS
65
A
HIS
67
1
Y
6
A
HIS
66
A
HIS
68
1
Y
6
A
HIS
67
A
HIS
69
1
Y
7
A
ALA
-1
A
ALA
1
1
Y
7
A
MET
0
A
MET
2
1
Y
7
A
LEU
56
A
LEU
58
1
Y
7
A
ALA
57
A
ALA
59
1
Y
7
A
ALA
58
A
ALA
60
1
Y
7
A
ALA
59
A
ALA
61
1
Y
7
A
LEU
60
A
LEU
62
1
Y
7
A
GLU
61
A
GLU
63
1
Y
7
A
HIS
62
A
HIS
64
1
Y
7
A
HIS
63
A
HIS
65
1
Y
7
A
HIS
64
A
HIS
66
1
Y
7
A
HIS
65
A
HIS
67
1
Y
7
A
HIS
66
A
HIS
68
1
Y
7
A
HIS
67
A
HIS
69
1
Y
8
A
ALA
-1
A
ALA
1
1
Y
8
A
MET
0
A
MET
2
1
Y
8
A
LEU
56
A
LEU
58
1
Y
8
A
ALA
57
A
ALA
59
1
Y
8
A
ALA
58
A
ALA
60
1
Y
8
A
ALA
59
A
ALA
61
1
Y
8
A
LEU
60
A
LEU
62
1
Y
8
A
GLU
61
A
GLU
63
1
Y
8
A
HIS
62
A
HIS
64
1
Y
8
A
HIS
63
A
HIS
65
1
Y
8
A
HIS
64
A
HIS
66
1
Y
8
A
HIS
65
A
HIS
67
1
Y
8
A
HIS
66
A
HIS
68
1
Y
8
A
HIS
67
A
HIS
69
1
Y
9
A
ALA
-1
A
ALA
1
1
Y
9
A
MET
0
A
MET
2
1
Y
9
A
LEU
56
A
LEU
58
1
Y
9
A
ALA
57
A
ALA
59
1
Y
9
A
ALA
58
A
ALA
60
1
Y
9
A
ALA
59
A
ALA
61
1
Y
9
A
LEU
60
A
LEU
62
1
Y
9
A
GLU
61
A
GLU
63
1
Y
9
A
HIS
62
A
HIS
64
1
Y
9
A
HIS
63
A
HIS
65
1
Y
9
A
HIS
64
A
HIS
66
1
Y
9
A
HIS
65
A
HIS
67
1
Y
9
A
HIS
66
A
HIS
68
1
Y
9
A
HIS
67
A
HIS
69
1
Y
10
A
ALA
-1
A
ALA
1
1
Y
10
A
MET
0
A
MET
2
1
Y
10
A
LEU
56
A
LEU
58
1
Y
10
A
ALA
57
A
ALA
59
1
Y
10
A
ALA
58
A
ALA
60
1
Y
10
A
ALA
59
A
ALA
61
1
Y
10
A
LEU
60
A
LEU
62
1
Y
10
A
GLU
61
A
GLU
63
1
Y
10
A
HIS
62
A
HIS
64
1
Y
10
A
HIS
63
A
HIS
65
1
Y
10
A
HIS
64
A
HIS
66
1
Y
10
A
HIS
65
A
HIS
67
1
Y
10
A
HIS
66
A
HIS
68
1
Y
10
A
HIS
67
A
HIS
69
1
Y
1
A
CYS
3
-163.89
58.36
1
A
ASP
4
60.15
-175.29
1
A
SER
11
56.49
-167.64
1
A
LEU
18
-80.49
-142.20
1
A
SER
20
64.33
118.57
1
A
PRO
29
-96.49
39.94
1
A
GLU
30
54.62
78.17
1
A
ALA
49
59.33
12.47
2
A
PRO
2
-61.04
-87.36
2
A
CYS
3
55.48
-160.13
2
A
ASP
4
-81.40
-96.81
2
A
ASN
5
-170.98
-36.46
2
A
SER
8
-162.32
105.15
2
A
SER
11
56.58
-162.00
2
A
SER
12
-91.45
56.40
2
A
LEU
18
-80.78
-149.49
2
A
SER
20
-174.76
109.41
2
A
PRO
29
-96.21
41.21
2
A
GLU
30
60.34
86.41
2
A
SER
35
-161.18
-65.26
2
A
ASP
36
-97.05
-85.98
2
A
CYS
40
-61.63
85.14
2
A
GLU
50
59.16
105.41
3
A
ASP
4
62.89
167.03
3
A
LEU
18
-107.44
-166.40
3
A
THR
19
-96.50
59.34
3
A
SER
20
-168.64
-48.30
3
A
PRO
27
-68.30
11.33
3
A
ILE
28
65.70
146.46
3
A
PRO
29
-94.13
-142.18
3
A
GLU
30
-65.34
87.75
3
A
CYS
33
-171.62
132.33
3
A
SER
35
56.67
-159.25
3
A
HIS
39
-168.80
100.74
3
A
ALA
49
56.02
16.33
4
A
ASP
4
55.36
-162.93
4
A
ASN
5
-106.90
-105.03
4
A
VAL
6
60.41
-77.15
4
A
THR
19
-88.50
49.14
4
A
SER
20
-145.95
-49.72
4
A
GLU
30
66.65
-80.19
4
A
ALA
31
176.67
-174.80
4
A
SER
35
56.29
-96.39
4
A
GLN
38
-147.95
-33.05
4
A
PRO
42
-62.50
-161.64
5
A
CYS
3
57.06
-93.54
5
A
ASP
4
-127.04
-69.60
5
A
ASN
5
-171.44
-32.85
5
A
SER
11
55.04
-160.70
5
A
HIS
37
-164.39
-142.62
5
A
GLN
38
-82.57
42.87
5
A
HIS
39
54.28
-124.63
6
A
PRO
2
-66.19
-132.14
6
A
CYS
3
59.92
87.40
6
A
ASP
4
54.64
-157.24
6
A
ASN
5
-141.57
19.65
6
A
SER
11
48.65
-148.75
6
A
SER
12
-62.54
85.22
6
A
ASP
13
-166.83
114.26
6
A
LEU
18
-92.60
-155.13
6
A
PRO
27
-46.19
-82.20
6
A
ILE
28
179.51
136.25
6
A
GLU
30
56.20
82.61
6
A
HIS
37
63.80
-80.16
6
A
GLU
50
53.20
76.33
7
A
CYS
3
-169.26
-149.28
7
A
SER
11
46.22
-152.03
7
A
SER
12
-52.04
97.88
7
A
ASP
13
-166.79
106.36
7
A
ILE
28
62.09
162.12
7
A
PRO
29
-88.39
-139.13
7
A
GLU
30
-66.33
80.68
7
A
SER
35
58.28
-96.51
7
A
GLN
38
-66.46
86.71
7
A
HIS
39
-170.26
93.86
7
A
GLU
50
54.61
79.97
8
A
CYS
3
58.33
-169.69
8
A
ASP
4
57.93
-178.04
8
A
ASN
5
-168.85
-27.39
8
A
SER
12
-62.86
80.55
8
A
ASP
13
179.58
160.15
8
A
GLU
30
58.44
-107.06
8
A
ALA
31
173.67
-174.88
8
A
ASP
36
-162.80
-164.51
8
A
HIS
37
-102.78
-153.18
8
A
GLN
38
60.24
-103.67
9
A
PRO
2
-51.69
171.06
9
A
CYS
3
-107.53
-162.34
9
A
ASP
4
60.77
-156.91
9
A
SER
11
59.38
-179.07
9
A
SER
12
-65.24
89.61
9
A
ILE
28
44.10
109.96
9
A
PRO
29
-95.34
57.51
9
A
GLU
30
58.26
92.48
9
A
SER
35
52.99
-158.16
9
A
ASP
36
-72.40
-137.23
9
A
HIS
37
61.99
-91.77
9
A
HIS
39
-121.56
-57.59
9
A
GLU
50
51.27
82.69
10
A
PRO
2
-52.57
-72.69
10
A
CYS
3
53.12
-98.20
10
A
ASP
4
-125.43
-158.09
10
A
PRO
29
-85.94
37.77
10
A
HIS
37
-103.13
-164.74
10
A
GLU
50
57.52
83.47
Human Granulin C, isomer 1
1
N
N
disulf
2.030
A
CYS
3
A
SG
CYS
5
1_555
A
CYS
15
A
SG
CYS
17
1_555
disulf
2.030
A
CYS
9
A
SG
CYS
11
1_555
A
CYS
25
A
SG
CYS
27
1_555
disulf
2.031
A
CYS
34
A
SG
CYS
36
1_555
A
CYS
47
A
SG
CYS
49
1_555
disulf
2.032
A
CYS
41
A
SG
CYS
43
1_555
A
CYS
53
A
SG
CYS
55
1_555
CYTOKINE
Granulin C, epithelin, human, stack of hairpins, Alternative splicing, Cytokine, Glycoprotein, Polymorphism, Secreted
GRN_HUMAN
UNP
1
364
P28799
VPCDNVSSCPSSDTCCQLTSGEWGCCPIPEAVCCSDHQHCCPQGYTCVAEGQCQ
364
417
2JYT
1
54
P28799
A
1
3
56
1
expression tag
ALA
-1
2JYT
A
P28799
UNP
1
1
expression tag
MET
0
2JYT
A
P28799
UNP
2
1
expression tag
LYS
55
2JYT
A
P28799
UNP
57
1
expression tag
LEU
56
2JYT
A
P28799
UNP
58
1
expression tag
ALA
57
2JYT
A
P28799
UNP
59
1
expression tag
ALA
58
2JYT
A
P28799
UNP
60
1
expression tag
ALA
59
2JYT
A
P28799
UNP
61
1
expression tag
LEU
60
2JYT
A
P28799
UNP
62
1
expression tag
GLU
61
2JYT
A
P28799
UNP
63
1
expression tag
HIS
62
2JYT
A
P28799
UNP
64
1
expression tag
HIS
63
2JYT
A
P28799
UNP
65
1
expression tag
HIS
64
2JYT
A
P28799
UNP
66
1
expression tag
HIS
65
2JYT
A
P28799
UNP
67
1
expression tag
HIS
66
2JYT
A
P28799
UNP
68
1
expression tag
HIS
67
2JYT
A
P28799
UNP
69
2
2
anti-parallel
anti-parallel
A
THR
14
A
THR
16
A
GLN
17
A
GLN
19
A
TRP
23
A
TRP
25
A
CYS
26
A
CYS
28
A
THR
46
A
THR
48
A
VAL
48
A
VAL
50
A
GLN
52
A
GLN
54
A
GLN
54
A
GLN
56