1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Ertekin, A.
Janjua, H.
Kohan, E.
Shastry, R.
Pederson, K.
Prestegard, J.H.
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
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
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 CDK2-associated protein 2 (CDK2AP2, Deleted in Oral Cancer 1 Related protein, DOC-1R)
10.2210/pdb2m1l/pdb
pdb_00002m1l
7644.793
Cyclin-dependent kinase 2-associated protein 2
UNP residues 61-126
2
man
polymer
CDK2-associated protein 2, DOC-1-related protein, DOC-1R
no
no
SHMAMKPPGAQGSQSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIHARALVRECLAETERNART
SHMAMKPPGAQGSQSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIHARALVRECLAETERNART
A,B
NESG-HR8910C
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
sample
CDK2AP2, DOC1R
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)pMgK
pET15Nano6HT_NESG
Northeast Structural Genomics Consortium
NESG
PSI:Biology
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_ref_seq_dif
repository
Initial release
Data collection
Database references
Other
1
0
2013-01-09
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
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
Y
BMRB
Y
RCSB
2012-11-30
REL
REL
REL
REL
1914
437
476
523
478
50
51
structures with the lowest energy
100
20
2D 1H-15N HSQC
2D 1H-13C HSQC
3D HNCO
3D CBCA(CO)NH
3D HNCACB
3D CBCA(CO)NH
3D HBHA(CO)NH
3D HN(CA)CO
3D 1H-13C NOESY aliphatic
3D 1H-15N NOESY
3D 13C-filtered NOESY aliphatic
2D 13C-filtered NOESY aromatic
2D 1H-13C high res (L/V methyl stereospecific assignment)
3D HCCH-TOCSY
3D HCCH-COSY
3D HCCH-TOCSY
3D 1H-13C NOESY aromatic
5.0
mg/mL
[U-100% 13C; U-100% 15N]
1
%
0.02
%
10
mM
5
mM
200
mM
20
mM
5
%
5.0
mg/mL
[U-100% 13C; U-100% 15N]
15.0
mg/mL
0.02
%
10
mM
5
mM
200
mM
20
mM
5
%
1
%
0.3
mM
[U-100% 15N]
0.02
%
10
mM
5
mM
200
mM
20
mM
5
%
1
%
4.2
%
5.0
mg/mL
[U-5% 13C; U-100% 15N]
1
%
0.02
%
10
mM
5
mM
200
mM
20
mM
5
%
6.5
ambient
298
K
Structure determination of this symmetric homodimer was performed iteratively using CYANA 3.02. The 20 structures out of 100 with lowest target function were further refined by restrained molecular dynamics/energy minimization in explicit water using CNS 1.3. Residual dipolar couplings and backbone dihedral angle constraints for the ordered regions were applied at all stages of the structure determination
simulated annealing
1
lowest energy
5.0 mg/mL [U-100% 13C; U-100% 15N] HR8910C.003, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 95% H2O/5% D2O
95% H2O/5% D2O
5.0 mg/mL [U-100% 13C; U-100% 15N] HR8910C, 15.0 mg/mL HR8910C, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 1 x Proteinase Inhibitors, 95% H2O/5% D2O
95% H2O/5% D2O
0.3 mM [U-100% 15N] HR8910C, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 1 x Proteinase Inhibitors, 4.2 % PEG, 95% H2O/5% D2O
95% H2O/5% D2O
5.0 mg/mL [U-5% 13C; U-100% 15N] HR8910C.005, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 95% H2O/5% D2O
95% H2O/5% D2O
Brunger, Adams, Clore, Gros, Nilges and Read
refinement,structure solution,geometry optimization
CNS
1.3
Guntert, Mumenthaler and Wuthrich
refinement,geometry optimization,structure solution
CYANA
3.02
Zimmerman, Moseley, Kulikowski and Montelione
data analysis,chemical shift assignment
AutoAssign
2.1
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
2.0
Bruker Biospin
collection
TopSpin
2.1
Bahrami, Markley, Assadi, and Eghbalnia
chemical shift assignment
PINE
1.0
Goddard
data analysis
Sparky
3.112
Shen, Cornilescu, Delaglio and Bax
geometry optimization
TALOS+
PALES (Zweckstetter, Bax)
geometry optimization
PALES
Bhattacharya, Montelione
structure validation
PSVS
1.4
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.3
800
Bruker
AVANCE
Bruker Avance
SER
58
n
1
SER
58
A
HIS
59
n
2
HIS
59
A
MET
60
n
3
MET
60
A
ALA
61
n
4
ALA
61
A
MET
62
n
5
MET
62
A
LYS
63
n
6
LYS
63
A
PRO
64
n
7
PRO
64
A
PRO
65
n
8
PRO
65
A
GLY
66
n
9
GLY
66
A
ALA
67
n
10
ALA
67
A
GLN
68
n
11
GLN
68
A
GLY
69
n
12
GLY
69
A
SER
70
n
13
SER
70
A
GLN
71
n
14
GLN
71
A
SER
72
n
15
SER
72
A
THR
73
n
16
THR
73
A
TYR
74
n
17
TYR
74
A
THR
75
n
18
THR
75
A
ASP
76
n
19
ASP
76
A
LEU
77
n
20
LEU
77
A
LEU
78
n
21
LEU
78
A
SER
79
n
22
SER
79
A
VAL
80
n
23
VAL
80
A
ILE
81
n
24
ILE
81
A
GLU
82
n
25
GLU
82
A
GLU
83
n
26
GLU
83
A
MET
84
n
27
MET
84
A
GLY
85
n
28
GLY
85
A
LYS
86
n
29
LYS
86
A
GLU
87
n
30
GLU
87
A
ILE
88
n
31
ILE
88
A
ARG
89
n
32
ARG
89
A
PRO
90
n
33
PRO
90
A
THR
91
n
34
THR
91
A
TYR
92
n
35
TYR
92
A
ALA
93
n
36
ALA
93
A
GLY
94
n
37
GLY
94
A
SER
95
n
38
SER
95
A
LYS
96
n
39
LYS
96
A
SER
97
n
40
SER
97
A
ALA
98
n
41
ALA
98
A
MET
99
n
42
MET
99
A
GLU
100
n
43
GLU
100
A
ARG
101
n
44
ARG
101
A
LEU
102
n
45
LEU
102
A
LYS
103
n
46
LYS
103
A
ARG
104
n
47
ARG
104
A
GLY
105
n
48
GLY
105
A
ILE
106
n
49
ILE
106
A
ILE
107
n
50
ILE
107
A
HIS
108
n
51
HIS
108
A
ALA
109
n
52
ALA
109
A
ARG
110
n
53
ARG
110
A
ALA
111
n
54
ALA
111
A
LEU
112
n
55
LEU
112
A
VAL
113
n
56
VAL
113
A
ARG
114
n
57
ARG
114
A
GLU
115
n
58
GLU
115
A
CYS
116
n
59
CYS
116
A
LEU
117
n
60
LEU
117
A
ALA
118
n
61
ALA
118
A
GLU
119
n
62
GLU
119
A
THR
120
n
63
THR
120
A
GLU
121
n
64
GLU
121
A
ARG
122
n
65
ARG
122
A
ASN
123
n
66
ASN
123
A
ALA
124
n
67
ALA
124
A
ARG
125
n
68
ARG
125
A
THR
126
n
69
THR
126
A
SER
58
n
1
SER
58
B
HIS
59
n
2
HIS
59
B
MET
60
n
3
MET
60
B
ALA
61
n
4
ALA
61
B
MET
62
n
5
MET
62
B
LYS
63
n
6
LYS
63
B
PRO
64
n
7
PRO
64
B
PRO
65
n
8
PRO
65
B
GLY
66
n
9
GLY
66
B
ALA
67
n
10
ALA
67
B
GLN
68
n
11
GLN
68
B
GLY
69
n
12
GLY
69
B
SER
70
n
13
SER
70
B
GLN
71
n
14
GLN
71
B
SER
72
n
15
SER
72
B
THR
73
n
16
THR
73
B
TYR
74
n
17
TYR
74
B
THR
75
n
18
THR
75
B
ASP
76
n
19
ASP
76
B
LEU
77
n
20
LEU
77
B
LEU
78
n
21
LEU
78
B
SER
79
n
22
SER
79
B
VAL
80
n
23
VAL
80
B
ILE
81
n
24
ILE
81
B
GLU
82
n
25
GLU
82
B
GLU
83
n
26
GLU
83
B
MET
84
n
27
MET
84
B
GLY
85
n
28
GLY
85
B
LYS
86
n
29
LYS
86
B
GLU
87
n
30
GLU
87
B
ILE
88
n
31
ILE
88
B
ARG
89
n
32
ARG
89
B
PRO
90
n
33
PRO
90
B
THR
91
n
34
THR
91
B
TYR
92
n
35
TYR
92
B
ALA
93
n
36
ALA
93
B
GLY
94
n
37
GLY
94
B
SER
95
n
38
SER
95
B
LYS
96
n
39
LYS
96
B
SER
97
n
40
SER
97
B
ALA
98
n
41
ALA
98
B
MET
99
n
42
MET
99
B
GLU
100
n
43
GLU
100
B
ARG
101
n
44
ARG
101
B
LEU
102
n
45
LEU
102
B
LYS
103
n
46
LYS
103
B
ARG
104
n
47
ARG
104
B
GLY
105
n
48
GLY
105
B
ILE
106
n
49
ILE
106
B
ILE
107
n
50
ILE
107
B
HIS
108
n
51
HIS
108
B
ALA
109
n
52
ALA
109
B
ARG
110
n
53
ARG
110
B
ALA
111
n
54
ALA
111
B
LEU
112
n
55
LEU
112
B
VAL
113
n
56
VAL
113
B
ARG
114
n
57
ARG
114
B
GLU
115
n
58
GLU
115
B
CYS
116
n
59
CYS
116
B
LEU
117
n
60
LEU
117
B
ALA
118
n
61
ALA
118
B
GLU
119
n
62
GLU
119
B
THR
120
n
63
THR
120
B
GLU
121
n
64
GLU
121
B
ARG
122
n
65
ARG
122
B
ASN
123
n
66
ASN
123
B
ALA
124
n
67
ALA
124
B
ARG
125
n
68
ARG
125
B
THR
126
n
69
THR
126
B
author_defined_assembly
2
dimeric
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
ALA
61
-158.65
75.47
1
A
ALA
67
-70.26
-74.93
1
A
SER
70
-157.85
26.65
1
A
GLN
71
-154.87
34.24
1
A
ALA
124
-155.84
83.05
1
A
ARG
125
-102.53
-67.62
1
B
ALA
67
-167.14
-70.81
1
B
ASN
123
-78.91
-84.98
2
A
LYS
63
-158.77
81.00
2
A
ALA
67
-66.56
97.26
2
A
GLN
68
-155.08
-156.53
2
B
ALA
61
-66.61
93.67
2
B
LYS
63
-166.40
94.91
2
B
PRO
65
-61.75
92.65
3
A
ALA
67
-62.32
91.74
3
B
LYS
63
-159.78
66.09
3
B
ALA
67
-142.89
-157.79
3
B
GLN
68
-60.27
93.87
3
B
SER
70
-53.47
105.97
3
B
GLN
71
-170.49
106.20
3
B
ALA
124
-66.56
95.71
4
A
MET
60
-50.01
100.50
4
A
ALA
61
-169.52
79.80
4
A
PRO
65
-60.66
84.97
4
B
PRO
65
-58.83
102.66
4
B
ALA
67
-53.98
106.68
4
B
GLN
68
-165.65
-54.45
4
B
SER
70
-168.15
-48.72
4
B
SER
95
-67.29
99.14
5
A
MET
62
-53.54
92.37
5
A
LYS
63
-170.16
74.34
5
A
SER
70
-118.46
-169.70
5
B
MET
62
-90.48
-147.59
5
B
LYS
63
74.55
107.29
5
B
PRO
64
-15.16
88.80
5
B
GLN
68
-161.84
-37.10
5
B
GLN
71
57.80
16.92
6
A
LYS
63
-152.70
61.42
6
A
PRO
65
-62.91
96.10
6
A
ALA
67
-151.24
-44.16
6
B
ALA
61
-153.77
45.56
6
B
PRO
65
-58.97
95.97
6
B
GLN
68
68.77
121.87
6
B
SER
95
-69.78
99.18
7
A
MET
62
-121.87
-169.95
7
A
LYS
63
63.89
89.59
7
A
ALA
67
-133.93
-77.14
7
A
GLN
68
-96.43
-156.16
7
B
MET
60
-170.71
114.01
7
B
ALA
61
-143.83
31.41
7
B
SER
70
-142.18
28.96
7
B
GLN
71
-146.90
35.91
8
A
PRO
65
-52.86
104.01
8
B
MET
60
-103.29
76.64
8
B
LYS
63
70.82
85.61
8
B
PRO
65
-68.93
-173.12
9
A
LYS
63
57.91
76.00
9
A
PRO
65
-46.66
99.74
9
A
SER
95
-69.84
99.04
9
B
HIS
59
-160.05
119.84
9
B
LYS
63
74.62
112.19
9
B
PRO
64
-35.39
113.51
10
A
HIS
59
-143.37
13.50
10
A
GLN
71
46.48
25.94
11
B
MET
62
-66.73
95.59
11
B
PRO
65
-60.45
93.63
11
B
ALA
67
57.45
-77.99
11
B
GLN
68
-68.05
94.34
11
B
GLN
71
52.89
5.07
12
A
PRO
65
-68.84
99.17
12
A
GLN
68
-148.12
-53.94
12
B
ALA
67
-56.28
106.77
13
A
PRO
65
-61.49
89.43
13
B
HIS
59
-68.81
90.80
13
B
PRO
65
-77.63
43.56
13
B
SER
70
-178.01
123.27
13
B
GLN
71
-60.97
96.01
14
A
LYS
63
36.12
77.79
14
A
GLN
68
-149.77
-19.61
14
A
GLN
71
-95.50
36.33
14
A
ASN
123
-105.86
51.61
14
B
LYS
63
68.66
89.47
15
A
ALA
61
-66.00
99.20
15
A
ASN
123
-67.52
99.67
15
B
MET
60
-131.65
-55.79
15
B
LYS
63
-150.60
82.91
15
B
SER
70
76.68
-41.04
15
B
ASN
123
-78.45
-91.87
15
B
ALA
124
176.45
-178.70
16
A
HIS
59
-69.66
90.20
16
A
SER
95
-64.33
97.55
16
A
ALA
124
-69.78
86.11
16
B
HIS
59
60.64
70.53
16
B
LYS
63
58.63
90.34
17
A
LYS
63
-154.14
74.75
17
A
ALA
67
-65.50
95.90
17
A
GLN
68
-69.32
82.39
17
A
SER
70
67.14
-73.32
17
A
SER
95
-66.89
99.26
17
A
ARG
125
-68.22
92.30
17
B
GLN
71
-66.16
96.48
18
A
LYS
63
58.24
94.43
18
A
PRO
65
-59.85
96.24
18
B
MET
60
-156.64
85.40
18
B
ALA
61
-170.58
39.71
18
B
PRO
65
-62.90
92.18
18
B
GLN
71
37.96
39.96
19
A
GLN
68
-63.16
94.73
19
B
PRO
65
-76.21
31.63
20
A
MET
60
61.25
87.39
20
A
ALA
124
-69.23
95.15
20
B
HIS
59
-161.51
118.01
20
B
ALA
61
-69.53
93.69
lowest energy, model 1
Solution NMR Structure of Cyclin-dependent kinase 2-associated protein 2 (CDK2AP2, DOC-1R) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8910C
1
N
N
1
N
N
A
GLN
71
A
GLN
14
HELX_P
A
LYS
86
A
LYS
29
1
1
16
A
GLU
87
A
GLU
30
HELX_P
A
ALA
93
A
ALA
36
1
2
7
A
SER
95
A
SER
38
HELX_P
A
GLU
121
A
GLU
64
1
3
27
B
GLN
71
B
GLN
14
HELX_P
B
GLU
87
B
GLU
30
1
4
17
B
GLU
87
B
GLU
30
HELX_P
B
ALA
93
B
ALA
36
1
5
7
B
SER
95
B
SER
38
HELX_P
B
ALA
124
B
ALA
67
1
6
30
CELL CYCLE
Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, PSI-Biology, Protein Structure Initiative, CELL CYCLE
CDKA2_HUMAN
UNP
1
61
O75956
AMKPPGAQGSQSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIHARALVRECLAETERNART
61
126
2M1L
61
126
O75956
A
1
4
69
61
126
2M1L
61
126
O75956
B
1
4
69
1
expression tag
SER
58
2M1L
A
O75956
UNP
1
1
expression tag
HIS
59
2M1L
A
O75956
UNP
2
1
expression tag
MET
60
2M1L
A
O75956
UNP
3
2
expression tag
SER
58
2M1L
B
O75956
UNP
1
2
expression tag
HIS
59
2M1L
B
O75956
UNP
2
2
expression tag
MET
60
2M1L
B
O75956
UNP
3