1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Pineda-Lucena, A.
Arrowsmith, C.H.
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
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
12
1136
1140
10.1110/ps.0240903
12717036
A novel member of the split beta-alpha-beta fold: Solution structure of the
hypothetical protein YML108W from Saccharomyces cerevisiae. Ontario Centre for Structural Proteomics target (YST0204_1_105); Northeast Structural Genomics Target (YT601).
2003
10.2210/pdb1n6z/pdb
pdb_00001n6z
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
12355.082
Hypothetical 12.3 kDa protein in ZDS2-URA5 intergenic region
YML108W
1
man
polymer
no
no
MSKSNTYRMLVLLEDDTKINKEDEKFLKGKPGKMHEFVDELILPFNVDELDELNTWFDKFDAEICIPNEGHIKYEISSDG
LIVLMLDKEIEEVVEKVKKFVEENN
MSKSNTYRMLVLLEDDTKINKEDEKFLKGKPGKMHEFVDELILPFNVDELDELNTWFDKFDAEICIPNEGHIKYEISSDG
LIVLMLDKEIEEVVEKVKKFVEENN
A
YT601
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
baker's yeast
Saccharomyces
Escherichia
sample
YML108W OR YM8339.11
4932
Saccharomyces cerevisiae
562
Escherichia coli
Northeast Structural Genomics Consortium
NESG
PSI, Protein Structure Initiative
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2003-05-06
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
The protein that was structurally determined
also contains a His tag prior to
the sequence listed in the SEQRES.
The His tag sequence is MGSSHHHHHHSSGLVPRGSH.
These His tag residues were missing in the
electron density.
Y
RCSB
Y
RCSB
2002-11-12
REL
REL
THIS STRUCTURE WAS DETERMINED USING STANDARD 3D HETERONUECLEAR NMR TECHNIQUES
structures with the lowest energy
200
10
3D_13C-separated_NOESY
3D_15N-separated_NOESY
900E-3
6.5
AMBIENT
298
K
torsion angle dynamics
1
lowest energy
1 mM, U-15N,13C 25 mM sodium phosphate (pH=6.5), 450 mM NaCl, 1 mM DTT
95% H20/5% D2O
DELAGLIO ET AL.
processing
NMRPipe
2.1
GUNTERT ET AL.
structure solution
DYANA
1.5
BARTELS ET AL.
data analysis
XEASY
1.3.14
HERRMANN ET AL.
structure solution
CYANA
1.0.5
GUNTERT ET AL.
refinement
DYANA
1.5
600
Varian
UNITY
MET
1
n
1
MET
1
A
SER
2
n
2
SER
2
A
LYS
3
n
3
LYS
3
A
SER
4
n
4
SER
4
A
ASN
5
n
5
ASN
5
A
THR
6
n
6
THR
6
A
TYR
7
n
7
TYR
7
A
ARG
8
n
8
ARG
8
A
MET
9
n
9
MET
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
LEU
12
n
12
LEU
12
A
LEU
13
n
13
LEU
13
A
GLU
14
n
14
GLU
14
A
ASP
15
n
15
ASP
15
A
ASP
16
n
16
ASP
16
A
THR
17
n
17
THR
17
A
LYS
18
n
18
LYS
18
A
ILE
19
n
19
ILE
19
A
ASN
20
n
20
ASN
20
A
LYS
21
n
21
LYS
21
A
GLU
22
n
22
GLU
22
A
ASP
23
n
23
ASP
23
A
GLU
24
n
24
GLU
24
A
LYS
25
n
25
LYS
25
A
PHE
26
n
26
PHE
26
A
LEU
27
n
27
LEU
27
A
LYS
28
n
28
LYS
28
A
GLY
29
n
29
GLY
29
A
LYS
30
n
30
LYS
30
A
PRO
31
n
31
PRO
31
A
GLY
32
n
32
GLY
32
A
LYS
33
n
33
LYS
33
A
MET
34
n
34
MET
34
A
HIS
35
n
35
HIS
35
A
GLU
36
n
36
GLU
36
A
PHE
37
n
37
PHE
37
A
VAL
38
n
38
VAL
38
A
ASP
39
n
39
ASP
39
A
GLU
40
n
40
GLU
40
A
LEU
41
n
41
LEU
41
A
ILE
42
n
42
ILE
42
A
LEU
43
n
43
LEU
43
A
PRO
44
n
44
PRO
44
A
PHE
45
n
45
PHE
45
A
ASN
46
n
46
ASN
46
A
VAL
47
n
47
VAL
47
A
ASP
48
n
48
ASP
48
A
GLU
49
n
49
GLU
49
A
LEU
50
n
50
LEU
50
A
ASP
51
n
51
ASP
51
A
GLU
52
n
52
GLU
52
A
LEU
53
n
53
LEU
53
A
ASN
54
n
54
ASN
54
A
THR
55
n
55
THR
55
A
TRP
56
n
56
TRP
56
A
PHE
57
n
57
PHE
57
A
ASP
58
n
58
ASP
58
A
LYS
59
n
59
LYS
59
A
PHE
60
n
60
PHE
60
A
ASP
61
n
61
ASP
61
A
ALA
62
n
62
ALA
62
A
GLU
63
n
63
GLU
63
A
ILE
64
n
64
ILE
64
A
CYS
65
n
65
CYS
65
A
ILE
66
n
66
ILE
66
A
PRO
67
n
67
PRO
67
A
ASN
68
n
68
ASN
68
A
GLU
69
n
69
GLU
69
A
GLY
70
n
70
GLY
70
A
HIS
71
n
71
HIS
71
A
ILE
72
n
72
ILE
72
A
LYS
73
n
73
LYS
73
A
TYR
74
n
74
TYR
74
A
GLU
75
n
75
GLU
75
A
ILE
76
n
76
ILE
76
A
SER
77
n
77
SER
77
A
SER
78
n
78
SER
78
A
ASP
79
n
79
ASP
79
A
GLY
80
n
80
GLY
80
A
LEU
81
n
81
LEU
81
A
ILE
82
n
82
ILE
82
A
VAL
83
n
83
VAL
83
A
LEU
84
n
84
LEU
84
A
MET
85
n
85
MET
85
A
LEU
86
n
86
LEU
86
A
ASP
87
n
87
ASP
87
A
LYS
88
n
88
LYS
88
A
GLU
89
n
89
GLU
89
A
ILE
90
n
90
ILE
90
A
GLU
91
n
91
GLU
91
A
GLU
92
n
92
GLU
92
A
VAL
93
n
93
VAL
93
A
VAL
94
n
94
VAL
94
A
GLU
95
n
95
GLU
95
A
LYS
96
n
96
LYS
96
A
VAL
97
n
97
VAL
97
A
LYS
98
n
98
LYS
98
A
LYS
99
n
99
LYS
99
A
PHE
100
n
100
PHE
100
A
VAL
101
n
101
VAL
101
A
GLU
102
n
102
GLU
102
A
GLU
103
n
103
GLU
103
A
ASN
104
n
104
ASN
104
A
ASN
105
n
105
ASN
105
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
O
LEU
41
A
O
LEU
41
A
N
MET
9
A
N
MET
9
A
N
LEU
10
A
N
LEU
10
A
O
LEU
84
A
O
LEU
84
A
O
LEU
81
A
O
LEU
81
A
N
SER
77
A
N
SER
77
1
A
A
H
O
SER
LEU
77
81
1.53
1
A
A
O
H
SER
GLY
77
80
1.57
2
A
A
H
O
SER
LEU
77
81
1.50
2
A
A
O
H
LEU
LEU
10
84
1.58
2
A
A
O
HD21
LEU
ASN
50
54
1.58
2
A
A
O
H
SER
GLY
77
80
1.59
3
A
A
H
O
SER
LEU
77
81
1.51
3
A
A
O
H
LEU
PHE
53
57
1.54
4
A
A
H
O
SER
LEU
77
81
1.50
4
A
A
O
H
SER
GLY
77
80
1.53
5
A
A
O
H
GLU
LEU
49
53
1.55
5
A
A
O
H
SER
GLY
77
80
1.58
5
A
A
H
O
MET
LEU
9
41
1.59
6
A
A
O
HD22
SER
ASN
4
46
1.49
6
A
A
O
H
SER
GLY
77
80
1.56
6
A
A
O
HD21
VAL
ASN
101
105
1.58
7
A
A
H
O
SER
LEU
77
81
1.50
7
A
A
O
H
SER
GLY
77
80
1.55
7
A
A
H
O
MET
LEU
9
41
1.57
7
A
A
O
H
TRP
PHE
56
60
1.59
7
A
A
O
HD21
VAL
ASN
101
105
1.59
7
A
A
O
H
VAL
VAL
93
97
1.59
7
A
A
O
H
ALA
ILE
62
66
1.60
8
A
A
H
O
SER
LEU
77
81
1.50
8
A
A
O
H
LEU
PHE
53
57
1.56
8
A
A
O
HD21
VAL
ASN
101
105
1.57
9
A
A
H
O
SER
LEU
77
81
1.50
9
A
A
H
O
MET
LEU
9
41
1.58
9
A
A
O
H
SER
GLY
77
80
1.60
9
A
A
O
H
LEU
LEU
10
84
1.60
10
A
A
H
O
SER
LEU
77
81
1.49
10
A
A
O
H
SER
GLY
77
80
1.54
10
A
A
O
H
LEU
PHE
53
57
1.57
10
A
A
O
H
VAL
VAL
93
97
1.59
1
A
LYS
3
-49.18
154.23
1
A
ASN
5
-164.35
103.29
1
A
ASN
20
-63.77
-158.47
1
A
ASP
23
-144.98
-71.30
1
A
GLU
24
-161.20
100.22
1
A
LYS
28
-65.31
74.41
1
A
PRO
44
-75.00
42.89
1
A
ASP
48
-108.48
40.95
1
A
GLU
49
-151.61
35.47
2
A
SER
2
165.37
42.88
2
A
LYS
3
73.57
89.81
2
A
SER
4
-179.30
-174.56
2
A
LYS
18
-172.37
35.08
2
A
ASN
20
-64.93
-155.76
2
A
ASP
23
-147.12
-65.90
2
A
PHE
26
178.64
47.83
2
A
HIS
35
39.09
78.97
2
A
PRO
44
-74.99
41.53
2
A
GLU
49
-155.42
35.82
3
A
LYS
3
68.40
166.06
3
A
ASN
5
-161.40
108.29
3
A
THR
17
46.79
-174.77
3
A
ASN
20
-65.22
-152.78
3
A
ASP
23
-150.67
-66.56
3
A
PHE
26
179.25
79.21
3
A
HIS
35
46.56
71.60
3
A
PRO
44
-75.04
41.93
3
A
GLU
49
-162.96
38.50
4
A
SER
2
-129.61
-52.76
4
A
LYS
3
-152.75
50.52
4
A
THR
17
47.40
-174.79
4
A
ASN
20
-64.89
-152.27
4
A
ASP
23
-151.63
-65.75
4
A
PHE
26
-168.82
61.80
4
A
HIS
35
44.58
71.27
4
A
PRO
44
-74.95
40.51
4
A
GLU
49
-153.01
36.06
5
A
SER
2
39.17
35.34
5
A
SER
4
76.38
-55.88
5
A
ASN
5
174.07
122.41
5
A
LYS
18
-170.16
74.88
5
A
ASN
20
-65.10
-149.98
5
A
ASP
23
-153.08
-70.77
5
A
PHE
26
-178.60
76.97
5
A
HIS
35
45.86
74.89
5
A
PRO
44
-74.93
41.47
5
A
GLU
49
-159.35
32.62
6
A
SER
2
157.65
-32.34
6
A
LYS
3
-40.11
-70.34
6
A
ASN
5
79.41
97.11
6
A
TYR
7
-124.02
-169.29
6
A
LYS
18
179.18
79.35
6
A
ASN
20
-64.97
-159.96
6
A
ASP
23
-149.46
-67.39
6
A
GLU
24
-161.44
102.62
6
A
HIS
35
50.93
79.03
6
A
PRO
44
-75.11
41.63
6
A
GLU
49
-157.16
38.49
7
A
SER
2
-99.89
-63.58
7
A
THR
17
-58.16
171.85
7
A
LYS
18
-157.83
53.98
7
A
ASN
20
-62.70
-156.13
7
A
ASP
23
-143.12
-66.33
7
A
LYS
28
-61.84
-76.83
7
A
PRO
44
-74.85
41.60
7
A
ASP
48
-107.11
40.18
7
A
GLU
49
-154.18
37.04
8
A
SER
2
164.38
-29.07
8
A
LYS
3
-116.63
-73.56
8
A
SER
4
157.90
76.17
8
A
ASN
5
157.63
116.25
8
A
LYS
18
-177.59
36.50
8
A
ASN
20
-66.73
-162.68
8
A
ASP
23
-153.92
-69.52
8
A
HIS
35
69.54
73.70
8
A
PRO
44
-74.92
41.30
8
A
ASP
48
-108.25
40.64
8
A
GLU
49
-155.69
38.21
9
A
SER
4
160.92
44.13
9
A
ASN
5
172.41
107.48
9
A
TYR
7
-126.35
-169.08
9
A
THR
17
-53.40
97.46
9
A
ASN
20
-64.49
-157.01
9
A
ASP
23
-141.30
-70.69
9
A
GLU
24
-160.76
100.61
9
A
LYS
28
-67.79
68.75
9
A
HIS
35
-38.60
124.80
9
A
PRO
44
-75.00
41.80
9
A
ASP
48
-104.86
41.59
9
A
GLU
49
-150.38
30.05
10
A
LYS
3
-41.18
158.32
10
A
SER
4
79.58
-69.26
10
A
ASN
5
174.80
125.50
10
A
THR
17
45.54
-161.99
10
A
ASN
20
-65.56
-157.04
10
A
ASP
23
-142.38
-66.69
10
A
GLU
24
-160.44
100.03
10
A
LYS
28
-32.18
-91.43
10
A
HIS
35
50.61
73.11
10
A
PRO
44
-74.95
43.12
10
A
GLU
49
-152.02
34.67
Solution NMR Structure of Protein YML108W from Saccharomyces cerevisiae. A novel member of the split bab fold. Northeast Structural Genomics Consortium Target YT601.
1
N
N
A
GLU
49
A
GLU
49
HELX_P
A
ILE
66
A
ILE
66
1
1
18
A
ILE
90
A
ILE
90
HELX_P
A
ASN
105
A
ASN
105
1
2
16
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
STRUCTURAL PROTEOMICS, STRUCTURAL GENOMICS, OCSP, NESG, PROTEIN STRUCTURE INITIATIVE, PSI, Northeast Structural Genomics Consortium, UNKNOWN FUNCTION
YMK8_YEAST
UNP
1
1
Q03759
MSKSNTYRMLVLLEDDTKINKEDEKFLKGKPGKMHEFVDELILPFNVDELDELNTWFDKFDAEICIPNEGHIKYEISSDG
LIVLMLDKEIEEVVEKVKKFVEENN
1
105
1N6Z
1
105
Q03759
A
1
1
105
4
anti-parallel
parallel
anti-parallel
A
PHE
37
A
PHE
37
A
LEU
43
A
LEU
43
A
TYR
7
A
TYR
7
A
LEU
13
A
LEU
13
A
LEU
81
A
LEU
81
A
LEU
86
A
LEU
86
A
ILE
72
A
ILE
72
A
SER
77
A
SER
77