0.027855
0.016082
0.000000
0.000000
0.032164
0.000000
0.000000
0.000000
0.007115
0.00000
0.00000
0.00000
Kuhlman, B.
Dantas, G.
Ireton, G.C.
Varani, G.
Stoddard, B.L.
Baker, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
35.900
35.900
140.554
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
H2 O
18.015
WATER
non-polymer
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 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
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
US
Science
SCIEAS
0038
0036-8075
302
1364
1368
10.1126/science.1089427
14631033
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
2003
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2003-03-24
ADSC QUANTUM 210
DOUBLE CRYSTAL Si(111)
SAD
M
x-ray
1
0.9793
1.0
8.2.1
ALS
0.9793
SYNCHROTRON
ALS BEAMLINE 8.2.1
12130.249
TOP7
1
man
polymer
18.015
water
7
nat
water
no
yes
(MSE)GDIQVQVNIDDNGKNFDYTYTVTTESELQKVLNEL(MSE)DYIKKQGAKRVRISITARTKKEAEKFAAILIKVFA
ELGYNDINVTFDGDTVTVEGQLEGGSLEHHHHHH
MGDIQVQVNIDDNGKNFDYTYTVTTESELQKVLNELMDYIKKQGAKRVRISITARTKKEAEKFAAILIKVFAELGYNDIN
VTFDGDTVTVEGQLEGGSLEHHHHHH
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
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
Escherichia
sample
Computationally Designed Sequence
562
Escherichia coli
BL21(DE3) pLysS
PLASMID
pet29b(+)
1
2.16
42.94
VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING
6.6
15-20% PEG3350 250mM Ammonium Formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, temperature 298K
298
repository
Initial release
Version format compliance
Version format compliance
1
0
2003-11-25
1
1
2008-04-29
1
2
2011-07-13
RCSB
Y
RCSB
2003-09-11
REL
REL
HOH
water
WAT
1
2
HOH
HOH
107
A
WAT
2
2
HOH
HOH
108
A
WAT
3
2
HOH
HOH
109
A
WAT
4
2
HOH
HOH
110
A
WAT
5
2
HOH
HOH
111
A
WAT
6
2
HOH
HOH
112
A
WAT
7
2
HOH
HOH
113
A
n
1
1
A
n
2
2
A
ASP
3
n
3
ASP
3
A
ILE
4
n
4
ILE
4
A
GLN
5
n
5
GLN
5
A
VAL
6
n
6
VAL
6
A
GLN
7
n
7
GLN
7
A
VAL
8
n
8
VAL
8
A
ASN
9
n
9
ASN
9
A
ILE
10
n
10
ILE
10
A
ASP
11
n
11
ASP
11
A
ASP
12
n
12
ASP
12
A
ASN
13
n
13
ASN
13
A
GLY
14
n
14
GLY
14
A
LYS
15
n
15
LYS
15
A
ASN
16
n
16
ASN
16
A
PHE
17
n
17
PHE
17
A
ASP
18
n
18
ASP
18
A
TYR
19
n
19
TYR
19
A
THR
20
n
20
THR
20
A
TYR
21
n
21
TYR
21
A
THR
22
n
22
THR
22
A
VAL
23
n
23
VAL
23
A
THR
24
n
24
THR
24
A
THR
25
n
25
THR
25
A
GLU
26
n
26
GLU
26
A
SER
27
n
27
SER
27
A
GLU
28
n
28
GLU
28
A
LEU
29
n
29
LEU
29
A
GLN
30
n
30
GLN
30
A
LYS
31
n
31
LYS
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
ASN
34
n
34
ASN
34
A
GLU
35
n
35
GLU
35
A
LEU
36
n
36
LEU
36
A
MSE
37
n
37
MSE
37
A
ASP
38
n
38
ASP
38
A
TYR
39
n
39
TYR
39
A
ILE
40
n
40
ILE
40
A
LYS
41
n
41
LYS
41
A
LYS
42
n
42
LYS
42
A
GLN
43
n
43
GLN
43
A
GLY
44
n
44
GLY
44
A
ALA
45
n
45
ALA
45
A
LYS
46
n
46
LYS
46
A
ARG
47
n
47
ARG
47
A
VAL
48
n
48
VAL
48
A
ARG
49
n
49
ARG
49
A
ILE
50
n
50
ILE
50
A
SER
51
n
51
SER
51
A
ILE
52
n
52
ILE
52
A
THR
53
n
53
THR
53
A
ALA
54
n
54
ALA
54
A
ARG
55
n
55
ARG
55
A
THR
56
n
56
THR
56
A
LYS
57
n
57
LYS
57
A
LYS
58
n
58
LYS
58
A
GLU
59
n
59
GLU
59
A
ALA
60
n
60
ALA
60
A
GLU
61
n
61
GLU
61
A
LYS
62
n
62
LYS
62
A
PHE
63
n
63
PHE
63
A
ALA
64
n
64
ALA
64
A
ALA
65
n
65
ALA
65
A
ILE
66
n
66
ILE
66
A
LEU
67
n
67
LEU
67
A
ILE
68
n
68
ILE
68
A
LYS
69
n
69
LYS
69
A
VAL
70
n
70
VAL
70
A
PHE
71
n
71
PHE
71
A
ALA
72
n
72
ALA
72
A
GLU
73
n
73
GLU
73
A
LEU
74
n
74
LEU
74
A
GLY
75
n
75
GLY
75
A
TYR
76
n
76
TYR
76
A
ASN
77
n
77
ASN
77
A
ASP
78
n
78
ASP
78
A
ILE
79
n
79
ILE
79
A
ASN
80
n
80
ASN
80
A
VAL
81
n
81
VAL
81
A
THR
82
n
82
THR
82
A
PHE
83
n
83
PHE
83
A
ASP
84
n
84
ASP
84
A
GLY
85
n
85
GLY
85
A
ASP
86
n
86
ASP
86
A
THR
87
n
87
THR
87
A
VAL
88
n
88
VAL
88
A
THR
89
n
89
THR
89
A
VAL
90
n
90
VAL
90
A
GLU
91
n
91
GLU
91
A
GLY
92
n
92
GLY
92
A
GLN
93
n
93
GLN
93
A
LEU
94
n
94
LEU
94
A
n
95
95
A
n
96
96
A
n
97
97
A
n
98
98
A
n
99
99
A
n
100
100
A
n
101
101
A
n
102
102
A
n
103
103
A
n
104
104
A
n
105
105
A
n
106
106
A
author_defined_assembly
1
monomeric
A
MSE
37
SELENOMETHIONINE
A
MSE
37
MET
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
O
TYR
19
A
O
TYR
19
A
N
VAL
8
A
N
VAL
8
A
N
ASN
9
A
N
ASN
9
A
O
ARG
49
A
O
ARG
49
A
N
VAL
48
A
N
VAL
48
A
O
GLY
92
A
O
GLY
92
A
O
THR
89
A
O
THR
89
A
N
THR
82
A
N
THR
82
1
A
CG
LYS
15
A
CG
LYS
15
1
Y
1
A
CD
LYS
15
A
CD
LYS
15
1
Y
1
A
CE
LYS
15
A
CE
LYS
15
1
Y
1
A
NZ
LYS
15
A
NZ
LYS
15
1
Y
1
A
CG
PHE
17
A
CG
PHE
17
1
Y
1
A
CD1
PHE
17
A
CD1
PHE
17
1
Y
1
A
CD2
PHE
17
A
CD2
PHE
17
1
Y
1
A
CE1
PHE
17
A
CE1
PHE
17
1
Y
1
A
CE2
PHE
17
A
CE2
PHE
17
1
Y
1
A
CZ
PHE
17
A
CZ
PHE
17
1
Y
1
A
OG
SER
27
A
OG
SER
27
1
Y
1
A
CG
GLN
30
A
CG
GLN
30
1
Y
1
A
CD
GLN
30
A
CD
GLN
30
1
Y
1
A
OE1
GLN
30
A
OE1
GLN
30
1
Y
1
A
NE2
GLN
30
A
NE2
GLN
30
1
Y
1
A
CG
LYS
31
A
CG
LYS
31
1
Y
1
A
CD
LYS
31
A
CD
LYS
31
1
Y
1
A
CE
LYS
31
A
CE
LYS
31
1
Y
1
A
NZ
LYS
31
A
NZ
LYS
31
1
Y
1
A
CG
ASN
34
A
CG
ASN
34
1
Y
1
A
OD1
ASN
34
A
OD1
ASN
34
1
Y
1
A
ND2
ASN
34
A
ND2
ASN
34
1
Y
1
A
CG
LEU
36
A
CG
LEU
36
1
Y
1
A
CD1
LEU
36
A
CD1
LEU
36
1
Y
1
A
CD2
LEU
36
A
CD2
LEU
36
1
Y
1
A
CG
LYS
46
A
CG
LYS
46
1
Y
1
A
CD
LYS
46
A
CD
LYS
46
1
Y
1
A
CE
LYS
46
A
CE
LYS
46
1
Y
1
A
NZ
LYS
46
A
NZ
LYS
46
1
Y
1
A
CG
ARG
47
A
CG
ARG
47
1
Y
1
A
CD
ARG
47
A
CD
ARG
47
1
Y
1
A
NE
ARG
47
A
NE
ARG
47
1
Y
1
A
CZ
ARG
47
A
CZ
ARG
47
1
Y
1
A
NH1
ARG
47
A
NH1
ARG
47
1
Y
1
A
NH2
ARG
47
A
NH2
ARG
47
1
Y
1
A
CG
ARG
55
A
CG
ARG
55
1
Y
1
A
CD
ARG
55
A
CD
ARG
55
1
Y
1
A
NE
ARG
55
A
NE
ARG
55
1
Y
1
A
CZ
ARG
55
A
CZ
ARG
55
1
Y
1
A
NH1
ARG
55
A
NH1
ARG
55
1
Y
1
A
NH2
ARG
55
A
NH2
ARG
55
1
Y
1
A
CG
LYS
62
A
CG
LYS
62
1
Y
1
A
CD
LYS
62
A
CD
LYS
62
1
Y
1
A
CE
LYS
62
A
CE
LYS
62
1
Y
1
A
NZ
LYS
62
A
NZ
LYS
62
1
Y
1
A
CG
GLU
73
A
CG
GLU
73
1
Y
1
A
CD
GLU
73
A
CD
GLU
73
1
Y
1
A
OE1
GLU
73
A
OE1
GLU
73
1
Y
1
A
OE2
GLU
73
A
OE2
GLU
73
1
Y
1
A
MSE
1
A
MSE
1
1
Y
1
A
GLY
2
A
GLY
2
1
Y
1
A
GLU
95
A
GLU
95
1
Y
1
A
GLY
96
A
GLY
96
1
Y
1
A
GLY
97
A
GLY
97
1
Y
1
A
SER
98
A
SER
98
1
Y
1
A
LEU
99
A
LEU
99
1
Y
1
A
GLU
100
A
GLU
100
1
Y
1
A
HIS
101
A
HIS
101
1
Y
1
A
HIS
102
A
HIS
102
1
Y
1
A
HIS
103
A
HIS
103
1
Y
1
A
HIS
104
A
HIS
104
1
Y
1
A
HIS
105
A
HIS
105
1
Y
1
A
HIS
106
A
HIS
106
1
Y
1
A
A
ND2
ND2
ASN
ASN
80
80
1.96
1_555
4_555
1
A
A
CD1
CD1
ILE
ILE
68
68
1.98
1_555
4_555
1
A
ASP
12
-168.83
80.22
1
A
ASN
13
43.86
102.49
1
A
THR
24
-158.71
81.00
1
A
THR
25
-176.78
-36.94
1
A
GLU
26
68.87
-7.45
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
65.5
10.54
9.56
0.00
10.54
0.00
-21.07
0.293
0.016
0.268
0.268
2.50
18.71
346
6736
6736
5.1
96.1
RANDOM
1873860.40
1873860.40
0
1
GROUP
THROUGHOUT
0.0
SAD
Engh & Huber
FLAT MODEL
55.2431
0.300247
0.46
0.42
5
0.45
0.47
2.50
18.71
7
692
0
0
685
0.008
1.4
26.3
0.73
0.37
0.055
0.353
2.66
45
1009
6
4.3
91.3
30.2
2.5
50.0
1QYS
6979
0.0
0.0
0.045
1
37.8
100
0.344
2.5
2.59
5.0
100
refinement
CNS
1.1
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
CNS
TOP7
Crystal structure of Top7: A computationally designed protein with a novel fold
1
N
N
2
N
N
A
SER
27
A
SER
27
HELX_P
A
GLY
44
A
GLY
44
1
1
18
A
THR
56
A
THR
56
HELX_P
A
LEU
74
A
LEU
74
1
2
19
covale
1.328
A
LEU
36
A
C
LEU
36
1_555
A
MSE
37
A
N
MSE
37
1_555
covale
1.327
A
MSE
37
A
C
MSE
37
1_555
A
ASP
38
A
N
ASP
38
1_555
DE NOVO PROTEIN
alpha-beta, computationally designed, novel fold, DE NOVO PROTEIN
1QYS
PDB
1
1QYS
1
106
1QYS
1
106
1QYS
A
1
1
106
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ASN
16
A
ASN
16
A
VAL
23
A
VAL
23
A
ILE
4
A
ILE
4
A
ASP
11
A
ASP
11
A
ARG
47
A
ARG
47
A
THR
53
A
THR
53
A
THR
87
A
THR
87
A
GLN
93
A
GLN
93
A
ASP
78
A
ASP
78
A
ASP
84
A
ASP
84
154
P 32 2 1