1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Xu, X.
Eletsky, A.
Mills, J.L.
Pulavarti, S.V.S.R.K.
Lee, D.
Kohan, E.
Janjua, H.
Xiao, R.
Acton, T.B.
Everett, J.K.
Montelione, G.T.
Szyperski, 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
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
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
To be Published
0353
Solution NMR Structure of Homeobox 2 Domain from Human ZHX1 repressor, Northeast Structural Genomics Consortium (NESG) Target HR7907F
10.2210/pdb2ly9/pdb
pdb_00002ly9
8710.016
Zinc fingers and homeoboxes protein 1
DNA binding Homeobox 2 residues 462-532
1
man
polymer
no
no
SHMPDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHLNN
SHMPDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHLNN
A
NESG-HR7907F
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
human
sample
ZHX1
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)pMgK
pET15Avi6HT_NESG
Northeast Structural Genomics Consortium
NESG
PSI:Biology
database_2
pdbx_database_status
pdbx_nmr_software
struct_ref_seq_dif
repository
Initial release
Data collection
Database references
Other
1
0
2012-11-14
1
1
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
Y
BMRB
Y
RCSB
2012-09-14
REL
REL
REL
REL
875
278
176
217
204
0
0
36
36
target function
100
20
2D 1H-15N HSQC
2D 1H-13C HSQC
3D HNCO
(4,3)D GFT CABCA(CO)NHN
(4,3)D GFT HNNCABCA
2D 1H-13C HSQC
(4,3)D GFT HCCH-COSY alipahtic
3D (H)CCH-TOCSY aliphatic
3D 13C/15N-edited NOESY
(4,3)D GFT HABCAB(CO)NH
3D (H)CCH-COSY aromatic
0.4
mM
[U-100% 13C; U-100% 15N]
0.02
%
10
mM
5
mM
100
mM
1
%
20
mM
50
uM
0.3
mM
[5% 13C; U-100% 15N]
0.02
%
10
mM
5
mM
100
mM
1
%
20
mM
50
uM
6.5
1
atm
298
K
STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD NMR ENSEMBLE INFORMATION
simulated annealing
1
lowest energy
0.4 mM [U-100% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
0.3 mM [5% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
Keller and Wuthrich
peak picking
CARA
1.8.4
Keller and Wuthrich
chemical shift assignment
CARA
1.8.4
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
AS-DP
1.0
Huang, Tejero, Powers and Montelione
refinement
AS-DP
1.0
Zimmerman, Moseley, Kulikowski and Montelione
data analysis
AutoAssign
2.3.0
Zimmerman, Moseley, Kulikowski and Montelione
chemical shift assignment
AutoAssign
2.3.0
Bartels et al.
data analysis
XEASY
Varian
collection
VnmrJ
Shen, Cornilescu, Delaglio and Bax
geometry optimization
TALOS+
Bhattacharya, Montelione
structure validation
PSVS
600
Varian
INOVA
Varian INOVA
750
Varian
INOVA
Varian INOVA
SER
1
n
1
SER
1
A
HIS
2
n
2
HIS
2
A
MET
3
n
3
MET
3
A
PRO
4
n
4
PRO
4
A
ASP
5
n
5
ASP
5
A
SER
6
n
6
SER
6
A
PHE
7
n
7
PHE
7
A
GLY
8
n
8
GLY
8
A
ILE
9
n
9
ILE
9
A
ARG
10
n
10
ARG
10
A
ALA
11
n
11
ALA
11
A
LYS
12
n
12
LYS
12
A
LYS
13
n
13
LYS
13
A
THR
14
n
14
THR
14
A
LYS
15
n
15
LYS
15
A
GLU
16
n
16
GLU
16
A
GLN
17
n
17
GLN
17
A
LEU
18
n
18
LEU
18
A
ALA
19
n
19
ALA
19
A
GLU
20
n
20
GLU
20
A
LEU
21
n
21
LEU
21
A
LYS
22
n
22
LYS
22
A
VAL
23
n
23
VAL
23
A
SER
24
n
24
SER
24
A
TYR
25
n
25
TYR
25
A
LEU
26
n
26
LEU
26
A
LYS
27
n
27
LYS
27
A
ASN
28
n
28
ASN
28
A
GLN
29
n
29
GLN
29
A
PHE
30
n
30
PHE
30
A
PRO
31
n
31
PRO
31
A
HIS
32
n
32
HIS
32
A
ASP
33
n
33
ASP
33
A
SER
34
n
34
SER
34
A
GLU
35
n
35
GLU
35
A
ILE
36
n
36
ILE
36
A
ILE
37
n
37
ILE
37
A
ARG
38
n
38
ARG
38
A
LEU
39
n
39
LEU
39
A
MET
40
n
40
MET
40
A
LYS
41
n
41
LYS
41
A
ILE
42
n
42
ILE
42
A
THR
43
n
43
THR
43
A
GLY
44
n
44
GLY
44
A
LEU
45
n
45
LEU
45
A
THR
46
n
46
THR
46
A
LYS
47
n
47
LYS
47
A
GLY
48
n
48
GLY
48
A
GLU
49
n
49
GLU
49
A
ILE
50
n
50
ILE
50
A
LYS
51
n
51
LYS
51
A
LYS
52
n
52
LYS
52
A
TRP
53
n
53
TRP
53
A
PHE
54
n
54
PHE
54
A
SER
55
n
55
SER
55
A
ASP
56
n
56
ASP
56
A
THR
57
n
57
THR
57
A
ARG
58
n
58
ARG
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
GLN
61
n
61
GLN
61
A
ARG
62
n
62
ARG
62
A
ASN
63
n
63
ASN
63
A
SER
64
n
64
SER
64
A
LYS
65
n
65
LYS
65
A
SER
66
n
66
SER
66
A
ASN
67
n
67
ASN
67
A
GLN
68
n
68
GLN
68
A
CYS
69
n
69
CYS
69
A
LEU
70
n
70
LEU
70
A
HIS
71
n
71
HIS
71
A
LEU
72
n
72
LEU
72
A
ASN
73
n
73
ASN
73
A
ASN
74
n
74
ASN
74
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
1
A
HIS
2
-130.79
-46.19
1
A
SER
6
-150.74
12.13
1
A
ARG
10
59.34
19.29
1
A
SER
66
72.89
-60.53
1
A
ASN
67
-84.31
-70.56
2
A
MET
3
64.68
103.40
2
A
ASP
5
-67.34
87.23
2
A
ALA
11
58.16
-159.57
2
A
LYS
13
-69.45
99.41
2
A
CYS
69
66.63
-175.73
2
A
LEU
70
75.39
-70.41
3
A
ASP
5
71.75
134.10
3
A
ALA
11
72.62
-73.22
3
A
THR
43
-90.65
-61.62
3
A
SER
66
65.05
172.62
3
A
ASN
73
-66.43
97.61
4
A
PRO
4
-53.39
105.91
4
A
ILE
9
-63.49
99.56
4
A
ARG
10
61.54
-72.72
4
A
ALA
11
-67.97
92.38
4
A
ASN
63
-107.08
45.66
5
A
MET
3
71.46
151.28
5
A
PRO
4
-56.02
92.59
5
A
PHE
7
-62.20
95.35
5
A
ASN
67
55.79
-154.28
5
A
LEU
70
-154.80
-66.92
6
A
HIS
2
-158.53
16.06
6
A
MET
3
-153.23
86.63
6
A
SER
6
-117.41
-79.89
6
A
HIS
32
-62.68
-79.35
6
A
ASP
33
-179.73
-52.15
6
A
CYS
69
67.38
86.85
7
A
ASP
5
-84.89
32.19
7
A
PHE
7
62.41
90.06
7
A
ARG
10
-156.09
-41.76
7
A
LYS
13
66.66
177.25
7
A
HIS
32
-68.73
-70.95
7
A
ASP
33
-159.32
-43.23
8
A
PHE
7
-121.61
-53.18
8
A
ARG
10
64.17
89.75
8
A
ASN
28
-164.85
100.44
8
A
HIS
32
-79.99
-71.32
8
A
ASP
33
-155.40
-54.95
8
A
GLN
61
-91.93
-60.69
8
A
LYS
65
-86.85
-82.47
8
A
SER
66
-178.32
-67.06
8
A
ASN
67
59.05
103.44
8
A
LEU
70
-83.20
43.33
9
A
ASP
5
-148.49
-76.45
9
A
SER
6
68.52
-65.41
9
A
PHE
7
66.85
-78.97
9
A
LYS
12
-160.77
-42.59
9
A
ASN
28
-171.83
142.12
9
A
GLN
68
-73.35
-157.87
9
A
CYS
69
-69.74
82.02
10
A
PHE
7
-65.74
87.78
10
A
ALA
11
59.79
-159.85
10
A
LYS
13
57.92
-171.77
10
A
SER
64
-69.60
92.26
10
A
ASN
67
60.47
76.93
11
A
ARG
10
-138.62
-55.19
11
A
ALA
11
-150.96
41.33
11
A
ASN
67
57.13
79.46
12
A
PHE
7
-100.02
-166.69
12
A
SER
66
-164.61
100.65
12
A
ASN
67
64.89
136.06
12
A
GLN
68
-159.26
-56.69
12
A
LEU
72
54.00
77.05
13
A
SER
6
68.34
156.13
13
A
ILE
9
-66.67
98.70
13
A
ASN
28
-160.34
103.43
13
A
HIS
32
-89.67
-91.52
13
A
ASP
33
-147.32
-57.22
13
A
SER
64
-164.54
-47.13
13
A
LYS
65
64.03
-178.06
13
A
CYS
69
-67.84
97.97
14
A
MET
3
-57.07
105.01
14
A
LYS
13
-57.02
105.62
14
A
HIS
32
-87.02
-75.89
14
A
ASP
33
-150.95
-58.37
14
A
LYS
65
68.68
110.05
15
A
MET
3
66.77
89.40
15
A
ALA
11
64.07
100.32
15
A
ILE
42
-92.37
-64.61
15
A
ASN
63
-68.59
86.87
15
A
ASN
67
-69.32
96.20
15
A
LEU
70
60.72
90.56
15
A
HIS
71
69.08
113.43
16
A
ASP
5
-74.08
-78.88
16
A
SER
6
53.46
71.88
16
A
ARG
62
-147.99
27.89
16
A
ASN
63
-58.96
106.62
16
A
ASN
67
63.19
-178.40
16
A
CYS
69
60.97
93.53
17
A
MET
3
67.30
162.39
17
A
PRO
4
-74.04
39.70
17
A
SER
6
-178.88
112.96
17
A
ARG
10
-135.33
-70.09
17
A
ASN
67
68.32
171.65
17
A
HIS
71
69.56
119.92
18
A
PHE
7
-63.44
96.40
18
A
ALA
11
-152.43
27.82
18
A
LYS
13
67.58
114.79
18
A
CYS
69
-90.61
-91.24
19
A
PRO
4
-89.01
41.80
19
A
ASN
28
-174.56
142.19
19
A
PHE
30
-114.69
79.91
19
A
HIS
32
-73.74
-77.34
19
A
ASP
33
-158.25
-58.16
19
A
ARG
62
-156.41
-16.88
19
A
SER
64
-55.55
96.28
19
A
SER
66
71.14
64.67
19
A
CYS
69
62.14
72.92
19
A
HIS
71
-49.59
101.99
20
A
HIS
2
64.67
99.46
20
A
MET
3
70.05
153.62
20
A
ARG
62
-161.59
-55.09
20
A
ASN
63
61.50
-175.84
20
A
SER
64
-142.93
-53.90
20
A
LYS
65
-165.17
-40.32
20
A
GLN
68
54.87
84.53
20
A
ASN
73
-58.21
90.93
lowest energy, model 1
Solution NMR Structure of Homeobox 2 Domain from Human ZHX1 repressor, Northeast Structural Genomics Consortium (NESG) Target HR7907F
1
N
N
A
THR
14
A
THR
14
HELX_P
A
ASN
28
A
ASN
28
1
1
15
A
HIS
32
A
HIS
32
HELX_P
A
GLY
44
A
GLY
44
1
2
13
A
THR
46
A
THR
46
HELX_P
A
GLN
61
A
GLN
61
1
3
16
TRANSCRIPTION
Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein Structure Initiative, TRANSCRIPTION
ZHX1_HUMAN
UNP
1
462
Q9UKY1
PDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHLNN
462
532
2LY9
4
74
Q9UKY1
A
1
4
74
1
expression tag
SER
1
2LY9
A
Q9UKY1
UNP
1
1
expression tag
HIS
2
2LY9
A
Q9UKY1
UNP
2
1
expression tag
MET
3
2LY9
A
Q9UKY1
UNP
3