1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Liu, G.
Koga, N.
Koga, R.
Xiao, R.
Hamilton, K.
Kohan, E.
Acton, T.B.
Kornhaber, G.
Everett, J.K.
Baker, D.
Montelione, G.T.
Northeast Structural Genomics Consortium (NESG)
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
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
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
Nature
NATUAS
0006
0028-0836
491
222
227
10.1038/nature11600
23135467
Principles for designing ideal protein structures.
2012
10.2210/pdb2lvb/pdb
pdb_00002lvb
12671.152
DE NOVO DESIGNED PFK fold PROTEIN
1
man
polymer
no
no
MGKVLLVISTDTNIISSVQERAKHNYPGREIRTATSSQDIRDIIKSMKDNGKPLVVFVNGASQNDVNEFQNEAKKEGVSY
DVLKSTDPEELTQRVREFLKTAGSLEHHHHHH
MGKVLLVISTDTNIISSVQERAKHNYPGREIRTATSSQDIRDIIKSMKDNGKPLVVFVNGASQNDVNEFQNEAKKEGVSY
DVLKSTDPEELTQRVREFLKTAGSLEHHHHHH
A
NESG-OR250
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
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
sample
32630
artificial gene
562
Escherichia coli
BL21(DE3)pMgK
pET29b+
Northeast Structural Genomics Consortium
NESG
PSI:Biology
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Database references
Database references
Database references
Data collection
Database references
Other
1
0
2012-08-08
1
1
2012-10-31
1
2
2012-11-07
1
3
2013-01-23
1
4
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
Y
BMRB
Y
RCSB
2012-06-30
REL
REL
REL
REL
target function
100
20
2D 1H-15N HSQC
2D 1H-13C HSQC
3D HNCO
3D CBCA(CO)NH
3D HNCACB
3D 1H-13C arom NOESY
3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
3D HCCH-TOCSY
2D 1H-13C HSQC
0.784
mM
[U-100% 13C; U-100% 15N]
100
mM
5
mM
0.02
%
10
mM
0.854
mM
[U-100% 13C; U-100% 15N]
100
mM
5
mM
0.02
%
10
mM
6.5
ambient
298
K
distance geometry, simulated annealing, torsion angle dynamics, molecular dynamics
1
lowest energy
0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5, 90% H2O/10% D2O
90% H2O/10% D2O
0.854 mM [U-100% 13C; U-100% 15N] OR250.003, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5, 90% H2O/10% D2O
90% H2O/10% D2O
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
Brunger, Adams, Clore, Gros, Nilges and Read
geometry optimization
CNS
Guntert, Mumenthaler and Wuthrich
refinement
CYANA
3.0
Guntert, Mumenthaler and Wuthrich
geometry optimization
CYANA
3.0
Guntert, Mumenthaler and Wuthrich
structure solution
CYANA
3.0
Huang, Tejero, Powers and Montelione
data analysis
AutoStructure
2.1
Huang, Tejero, Powers and Montelione
refinement
AutoStructure
2.1
Zimmerman, Moseley, Kulikowski and Montelione
data analysis
AutoAssign
2.1
Zimmerman, Moseley, Kulikowski and Montelione
chemical shift assignment
AutoAssign
2.1
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Bartels et al.
data analysis
XEASY
Bartels et al.
peak picking
XEASY
Bartels et al.
chemical shift assignment
XEASY
Bruker Biospin
collection
TopSpin
Varian
collection
VnmrJ
Goddard
data analysis
Sparky
Shen, Cornilescu, Delaglio and Bax
geometry optimization
TALOS+
Bhattacharya, Montelione
structure validation
PSVS
800
Bruker
AVANCE
Bruker Avance
600
Varian
INOVA
Varian INOVA
MET
1
n
1
MET
1
A
GLY
2
n
2
GLY
2
A
LYS
3
n
3
LYS
3
A
VAL
4
n
4
VAL
4
A
LEU
5
n
5
LEU
5
A
LEU
6
n
6
LEU
6
A
VAL
7
n
7
VAL
7
A
ILE
8
n
8
ILE
8
A
SER
9
n
9
SER
9
A
THR
10
n
10
THR
10
A
ASP
11
n
11
ASP
11
A
THR
12
n
12
THR
12
A
ASN
13
n
13
ASN
13
A
ILE
14
n
14
ILE
14
A
ILE
15
n
15
ILE
15
A
SER
16
n
16
SER
16
A
SER
17
n
17
SER
17
A
VAL
18
n
18
VAL
18
A
GLN
19
n
19
GLN
19
A
GLU
20
n
20
GLU
20
A
ARG
21
n
21
ARG
21
A
ALA
22
n
22
ALA
22
A
LYS
23
n
23
LYS
23
A
HIS
24
n
24
HIS
24
A
ASN
25
n
25
ASN
25
A
TYR
26
n
26
TYR
26
A
PRO
27
n
27
PRO
27
A
GLY
28
n
28
GLY
28
A
ARG
29
n
29
ARG
29
A
GLU
30
n
30
GLU
30
A
ILE
31
n
31
ILE
31
A
ARG
32
n
32
ARG
32
A
THR
33
n
33
THR
33
A
ALA
34
n
34
ALA
34
A
THR
35
n
35
THR
35
A
SER
36
n
36
SER
36
A
SER
37
n
37
SER
37
A
GLN
38
n
38
GLN
38
A
ASP
39
n
39
ASP
39
A
ILE
40
n
40
ILE
40
A
ARG
41
n
41
ARG
41
A
ASP
42
n
42
ASP
42
A
ILE
43
n
43
ILE
43
A
ILE
44
n
44
ILE
44
A
LYS
45
n
45
LYS
45
A
SER
46
n
46
SER
46
A
MET
47
n
47
MET
47
A
LYS
48
n
48
LYS
48
A
ASP
49
n
49
ASP
49
A
ASN
50
n
50
ASN
50
A
GLY
51
n
51
GLY
51
A
LYS
52
n
52
LYS
52
A
PRO
53
n
53
PRO
53
A
LEU
54
n
54
LEU
54
A
VAL
55
n
55
VAL
55
A
VAL
56
n
56
VAL
56
A
PHE
57
n
57
PHE
57
A
VAL
58
n
58
VAL
58
A
ASN
59
n
59
ASN
59
A
GLY
60
n
60
GLY
60
A
ALA
61
n
61
ALA
61
A
SER
62
n
62
SER
62
A
GLN
63
n
63
GLN
63
A
ASN
64
n
64
ASN
64
A
ASP
65
n
65
ASP
65
A
VAL
66
n
66
VAL
66
A
ASN
67
n
67
ASN
67
A
GLU
68
n
68
GLU
68
A
PHE
69
n
69
PHE
69
A
GLN
70
n
70
GLN
70
A
ASN
71
n
71
ASN
71
A
GLU
72
n
72
GLU
72
A
ALA
73
n
73
ALA
73
A
LYS
74
n
74
LYS
74
A
LYS
75
n
75
LYS
75
A
GLU
76
n
76
GLU
76
A
GLY
77
n
77
GLY
77
A
VAL
78
n
78
VAL
78
A
SER
79
n
79
SER
79
A
TYR
80
n
80
TYR
80
A
ASP
81
n
81
ASP
81
A
VAL
82
n
82
VAL
82
A
LEU
83
n
83
LEU
83
A
LYS
84
n
84
LYS
84
A
SER
85
n
85
SER
85
A
THR
86
n
86
THR
86
A
ASP
87
n
87
ASP
87
A
PRO
88
n
88
PRO
88
A
GLU
89
n
89
GLU
89
A
GLU
90
n
90
GLU
90
A
LEU
91
n
91
LEU
91
A
THR
92
n
92
THR
92
A
GLN
93
n
93
GLN
93
A
ARG
94
n
94
ARG
94
A
VAL
95
n
95
VAL
95
A
ARG
96
n
96
ARG
96
A
GLU
97
n
97
GLU
97
A
PHE
98
n
98
PHE
98
A
LEU
99
n
99
LEU
99
A
LYS
100
n
100
LYS
100
A
THR
101
n
101
THR
101
A
ALA
102
n
102
ALA
102
A
GLY
103
n
103
GLY
103
A
SER
104
n
104
SER
104
A
LEU
105
n
105
LEU
105
A
GLU
106
n
106
GLU
106
A
HIS
107
n
107
HIS
107
A
HIS
108
n
108
HIS
108
A
HIS
109
n
109
HIS
109
A
HIS
110
n
110
HIS
110
A
HIS
111
n
111
HIS
111
A
HIS
112
n
112
HIS
112
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
ARG
32
A
N
ARG
32
A
O
PHE
57
A
O
PHE
57
A
O
VAL
58
A
O
VAL
58
A
N
VAL
7
A
N
VAL
7
A
N
LEU
6
A
N
LEU
6
A
O
LEU
83
A
O
LEU
83
1
A
ASN
50
-147.14
-61.61
1
A
PRO
53
-62.44
97.10
1
A
SER
104
-162.64
91.05
1
A
HIS
108
-69.10
99.17
1
A
HIS
110
-150.03
87.20
2
A
PRO
27
-68.23
89.48
2
A
PRO
53
-67.12
92.40
2
A
HIS
108
-67.22
87.75
3
A
HIS
111
-138.57
-67.33
4
A
LEU
105
-79.73
-166.93
4
A
HIS
108
-64.93
89.20
5
A
SER
36
-170.31
-174.39
5
A
SER
104
-72.58
-87.36
5
A
HIS
111
-166.05
-166.46
6
A
PRO
27
-82.37
30.66
6
A
THR
35
-133.92
-32.58
6
A
ASN
59
-65.67
84.99
6
A
THR
86
-140.13
-10.94
6
A
HIS
107
-69.96
93.60
7
A
SER
79
-68.45
89.79
7
A
SER
104
52.68
-71.53
8
A
SER
79
-65.73
94.81
8
A
HIS
111
-154.41
42.07
9
A
ASN
59
-62.07
89.10
9
A
HIS
108
-68.63
96.28
10
A
HIS
111
-153.46
68.34
11
A
THR
35
-130.22
-49.48
11
A
ASP
49
-91.47
-62.02
11
A
ASN
59
-68.06
81.80
12
A
GLU
106
-105.83
-93.95
12
A
HIS
107
57.36
-84.75
12
A
HIS
109
-84.84
43.33
12
A
HIS
110
-152.48
86.82
14
A
THR
86
-144.84
16.51
14
A
SER
104
-158.76
-6.25
14
A
HIS
110
-146.89
36.34
15
A
SER
104
-61.57
95.02
16
A
TYR
26
-115.79
79.73
17
A
LEU
105
-62.84
98.16
17
A
HIS
108
-65.98
90.95
17
A
HIS
110
63.71
85.15
18
A
SER
104
74.55
-39.30
19
A
ASN
50
-149.04
-33.07
19
A
SER
79
-67.85
91.68
19
A
GLU
106
-55.64
87.07
19
A
HIS
110
48.27
94.98
20
A
ASP
11
-69.95
92.19
20
A
HIS
109
-61.96
97.32
lowest energy, model 1
Solution NMR Structure DE NOVO DESIGNED PFK fold PROTEIN, Northeast Structural Genomics Consortium (NESG) Target OR250
1
N
N
A
ASP
11
A
ASP
11
HELX_P
A
TYR
26
A
TYR
26
1
1
16
A
SER
36
A
SER
36
HELX_P
A
ASN
50
A
ASN
50
1
2
15
A
SER
62
A
SER
62
HELX_P
A
LYS
75
A
LYS
75
1
3
14
A
ASP
87
A
ASP
87
HELX_P
A
LEU
105
A
LEU
105
1
4
19
DE NOVO PROTEIN
Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein Structure Initiative, DE NOVO PROTEIN
2LVB
PDB
1
2LVB
1
112
2LVB
1
112
2LVB
A
1
1
112
4
parallel
parallel
parallel
A
ARG
32
A
ARG
32
A
ALA
34
A
ALA
34
A
PRO
53
A
PRO
53
A
ASN
59
A
ASN
59
A
LYS
3
A
LYS
3
A
SER
9
A
SER
9
A
SER
79
A
SER
79
A
LYS
84
A
LYS
84