1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kalodimos, C.G.
Bonvin, A.M.J.J.
Salinas, R.K.
Wechselberger, R.
Boelens, R.
Kaptein, R.
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
UK
EMBO J.
EMJODG
0897
0261-4189
21
2866
2876
10.1093/emboj/cdf318
12065400
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.
2002
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
98
6039
6044
10.1073/pnas.101129898
Strong DNA binding by covalently linked dimeric lac headpiece: evidence for the crucial role of the hinge helices
2001
10.2210/pdb1l1m/pdb
pdb_00001l1m
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
Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli.
7143.645
5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'
1
syn
polymer
Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli.
6974.534
5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
1
syn
polymer
6822.755
Lactose operon repressor
N-terminal DNA-binding domain, Residues 1-62
V52C
2
man
polymer
no
no
(DG)(DA)(DA)(DT)(DT)(DG)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DA)(DT)(DA)(DA)(DC)(DA)(DA)
(DT)(DT)(DT)
GAATTGTGAGCGGATAACAATTT
C
polydeoxyribonucleotide
no
no
(DA)(DA)(DA)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DC)(DA)(DA)
(DT)(DT)(DC)
AAATTGTTATCCGCTCACAATTC
D
polydeoxyribonucleotide
no
no
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRCAQQLAGKQSL
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRCAQQLAGKQSL
A,B
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
Escherichia
Escherichia
sample
LACI
562
Escherichia coli
562
Escherichia coli
DH9
PLASMID
PGP1-2,PET-HP62
0.122
1
19
C
1
D
23
0.621
C_DG1:DC23_D
1
2.776
-0.396
-0.084
-0.195
0.857
1
20
C
2
D
22
-2.858
C_DA2:DT22_D
2
0.733
-0.005
-0.120
-0.290
-1.446
1
20
C
3
D
21
0.159
C_DA3:DT21_D
3
0.327
0.126
-0.003
-0.213
0.444
1
20
C
4
D
20
2.221
C_DT4:DA20_D
4
2.365
-0.128
-0.050
-0.135
1.750
1
20
C
5
D
19
-4.220
C_DT5:DA19_D
5
3.877
-0.189
-0.237
-0.258
-0.368
1
19
C
6
D
18
3.908
C_DG6:DC18_D
6
5.025
-0.003
-0.114
-0.088
0.220
1
20
C
7
D
17
-0.762
C_DT7:DA17_D
7
3.478
0.019
-0.080
-0.175
-0.345
1
19
C
8
D
16
0.180
C_DG8:DC16_D
8
6.469
-0.055
-0.308
-0.205
-1.395
1
20
C
9
D
15
-0.616
C_DA9:DT15_D
9
6.571
0.232
-0.238
-0.115
1.486
1
19
C
10
D
14
6.396
C_DG10:DC14_D
10
3.889
-0.816
-0.105
-0.225
-2.885
1
19
C
11
D
13
-5.233
C_DC11:DG13_D
11
7.447
-0.126
-0.211
-0.092
0.738
1
19
C
12
D
12
-7.950
C_DG12:DC12_D
12
10.482
-0.294
-0.316
-0.260
-0.579
1
19
C
13
D
11
4.532
C_DG13:DC11_D
13
6.890
-0.151
-0.182
-0.079
-3.756
1
20
C
14
D
10
-5.149
C_DA14:DT10_D
14
10.646
-0.318
-0.205
-0.131
1.028
1
20
C
15
D
9
-8.185
C_DT15:DA9_D
15
3.752
-0.252
0.002
-0.087
3.049
1
20
C
16
D
8
-8.769
C_DA16:DT8_D
16
3.898
0.051
0.074
-0.105
-3.202
1
20
C
17
D
7
-4.543
C_DA17:DT7_D
17
8.362
0.003
-0.402
-0.306
-1.428
1
19
C
18
D
6
-1.285
C_DC18:DG6_D
18
4.843
-0.136
0.032
-0.175
-4.780
1
20
C
19
D
5
-8.760
C_DA19:DT5_D
19
-0.849
0.208
-0.175
-0.158
-1.132
1
20
C
20
D
4
0.835
C_DA20:DT4_D
20
2.500
0.183
-0.133
-0.154
1.068
1
20
C
21
D
3
1.399
C_DT21:DA3_D
21
0.469
-0.178
-0.006
-0.149
-0.323
1
20
C
22
D
2
-1.278
C_DT22:DA2_D
22
-2.398
0.059
-0.084
-0.266
-0.012
1
20
C
23
D
1
-4.572
C_DT23:DA1_D
23
1.000
-0.008
-0.123
-0.196
3.046
38.642
C
C
1
2
4.364
D
D
23
22
3.067
2.885
-0.321
-0.218
CC_DG1DA2:DT22DC23_DD
1
-0.410
0.620
38.537
-0.661
0.439
3.065
37.771
C
C
2
3
3.849
D
D
22
21
3.096
2.487
-0.006
-0.221
CC_DA2DA3:DT21DT22_DD
2
-3.413
5.283
37.543
-0.645
-0.407
2.984
34.035
C
C
3
4
5.285
D
D
21
20
3.048
3.089
0.077
-0.575
CC_DA3DT4:DA20DT21_DD
3
-0.410
0.701
33.896
-1.438
-0.192
2.856
33.865
C
C
4
5
18.510
D
D
20
19
3.161
10.584
0.008
-0.438
CC_DT4DT5:DA19DA20_DD
4
4.118
-7.201
31.956
-2.368
0.616
2.895
36.256
C
C
5
6
14.268
D
D
19
18
3.093
8.793
0.602
-0.357
CC_DT5DG6:DC18DA19_DD
5
-1.588
2.577
35.173
-1.720
-1.174
3.258
36.512
C
C
6
7
-2.022
D
D
18
17
3.257
-1.266
-0.244
-0.359
CC_DG6DT7:DA17DC18_DD
6
1.247
-1.991
36.471
-0.398
0.561
3.061
35.501
C
C
7
8
6.446
D
D
17
16
3.118
3.922
0.098
-0.381
CC_DT7DG8:DC16DA17_DD
7
1.325
-2.178
35.267
-1.169
0.023
3.190
35.883
C
C
8
9
5.898
D
D
16
15
3.250
3.628
0.079
-0.447
CC_DG8DA9:DT15DC16_DD
8
-0.027
0.045
35.705
-1.239
-0.132
3.305
31.997
C
C
9
10
-4.304
D
D
15
14
3.333
-2.368
0.474
-0.428
CC_DA9DG10:DC14DT15_DD
9
-2.676
4.864
31.802
-0.340
-1.352
3.006
39.604
C
C
10
11
10.759
D
D
14
13
3.163
7.250
-0.886
-0.375
CC_DG10DC11:DG13DC14_DD
10
1.792
-2.659
38.922
-1.361
1.507
3.737
43.438
C
C
11
12
55.976
D
D
13
12
3.547
35.717
0.649
2.025
CC_DC11DG12:DC12DG13_DD
11
0.986
-1.545
25.116
-2.278
-0.738
2.534
34.467
C
C
12
13
21.418
D
D
12
11
3.137
12.371
0.908
-0.651
CC_DG12DG13:DC11DC12_DD
12
-5.387
9.327
31.791
-2.837
-2.289
3.328
34.122
C
C
13
14
12.759
D
D
11
10
3.535
7.430
-0.645
-0.591
CC_DG13DA14:DT10DC11_DD
13
0.085
-0.146
33.326
-2.259
1.114
3.388
35.334
C
C
14
15
-11.237
D
D
10
9
3.382
-6.778
-0.427
-0.261
CC_DA14DT15:DA9DT10_DD
14
-1.793
2.973
34.653
0.617
0.427
2.679
37.445
C
C
15
16
23.143
D
D
9
8
2.972
14.492
-0.249
-0.222
CC_DT15DA16:DT8DA9_DD
15
-1.340
2.139
34.595
-2.060
0.229
4.266
35.692
C
C
16
17
-7.823
D
D
8
7
4.320
-4.778
0.098
0.009
CC_DA16DA17:DT7DT8_DD
16
-2.525
4.135
35.294
0.927
-0.642
3.184
36.038
C
C
17
18
4.953
D
D
7
6
3.228
3.058
0.043
-0.271
CC_DA17DC18:DG6DT7_DD
17
-2.490
4.033
35.829
-0.864
-0.417
3.085
38.985
C
C
18
19
18.878
D
D
6
5
3.236
12.379
-0.605
0.241
CC_DC18DA19:DT5DG6_DD
18
3.660
-5.581
36.865
-1.129
1.347
3.339
33.865
C
C
19
20
7.896
D
D
5
4
3.525
4.541
0.244
0.048
CC_DA19DA20:DT4DT5_DD
19
-8.329
14.481
32.546
-0.701
-1.856
3.082
32.820
C
C
20
21
5.433
D
D
4
3
3.143
3.065
-0.066
-0.542
CC_DA20DT21:DA3DT4_DD
20
-0.976
1.730
32.666
-1.461
-0.042
3.075
38.229
C
C
21
22
-0.026
D
D
3
2
3.086
-0.017
-0.115
-0.157
CC_DT21DT22:DA2DA3_DD
21
2.165
-3.307
38.170
-0.238
0.433
2.920
36.357
C
C
22
23
11.174
D
D
2
1
3.047
6.924
0.080
-0.387
CC_DT22DT23:DA1DA2_DD
22
2.995
-4.833
35.591
-1.510
0.256
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-06-26
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2002-02-19
REL
REL
This structure was determined using standard 2D and 3D homo- and heteronuclearnuclear techniques.
13C-15N labeled protein was used and unlabeled nucleotide.
IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES.
structures with the lowest energy
100
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
2D NOESY
10mM KPi, 20mM KCl
6.0
ambient
315
K
The structure of the complex was calculated as follows. First the structure of the dimeric lac HP62-V52C was calculated using only protein NMR restraints. The 50 best structures were selected and docked onto the natural lac operator B-DNA using simulated annealing. Distance and planarity restraints for the DNA were incorporated in order to keep DNA close to B-DNA but allowing a bend necessary to accommodate the two headpiece molecules on the DNA.
SIMULATED ANNEALING FOLLOWED BY RESTRAINED MDR
1
closest to the average
2mM Lac-HP62-V52C U-15N,13C, 10mM KPi, 20mM KCl, 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.1
Delaglio
processing
NMRPipe
1.0
Johnson
data analysis
NMRView
5.0.4
Brunger
structure solution
CNS
1.1
Brunger
refinement
CNS
1.1
750
Bruker
DRX
600
Bruker
DRX
G
1
n
1
DG
1
C
A
2
n
2
DA
2
C
A
3
n
3
DA
3
C
T
4
n
4
DT
4
C
T
5
n
5
DT
5
C
G
6
n
6
DG
6
C
T
7
n
7
DT
7
C
G
8
n
8
DG
8
C
A
9
n
9
DA
9
C
G
10
n
10
DG
10
C
C
11
n
11
DC
11
C
G
12
n
12
DG
12
C
G
13
n
13
DG
13
C
A
14
n
14
DA
14
C
T
15
n
15
DT
15
C
A
16
n
16
DA
16
C
A
17
n
17
DA
17
C
C
18
n
18
DC
18
C
A
19
n
19
DA
19
C
A
20
n
20
DA
20
C
T
21
n
21
DT
21
C
T
22
n
22
DT
22
C
T
23
n
23
DT
23
C
A
1
n
1
DA
1
D
A
2
n
2
DA
2
D
A
3
n
3
DA
3
D
T
4
n
4
DT
4
D
T
5
n
5
DT
5
D
G
6
n
6
DG
6
D
T
7
n
7
DT
7
D
T
8
n
8
DT
8
D
A
9
n
9
DA
9
D
T
10
n
10
DT
10
D
C
11
n
11
DC
11
D
C
12
n
12
DC
12
D
G
13
n
13
DG
13
D
C
14
n
14
DC
14
D
T
15
n
15
DT
15
D
C
16
n
16
DC
16
D
A
17
n
17
DA
17
D
C
18
n
18
DC
18
D
A
19
n
19
DA
19
D
A
20
n
20
DA
20
D
T
21
n
21
DT
21
D
T
22
n
22
DT
22
D
C
23
n
23
DC
23
D
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
PRO
3
n
3
PRO
3
A
VAL
4
n
4
VAL
4
A
THR
5
n
5
THR
5
A
LEU
6
n
6
LEU
6
A
TYR
7
n
7
TYR
7
A
ASP
8
n
8
ASP
8
A
VAL
9
n
9
VAL
9
A
ALA
10
n
10
ALA
10
A
GLU
11
n
11
GLU
11
A
TYR
12
n
12
TYR
12
A
ALA
13
n
13
ALA
13
A
GLY
14
n
14
GLY
14
A
VAL
15
n
15
VAL
15
A
SER
16
n
16
SER
16
A
TYR
17
n
17
TYR
17
A
GLN
18
n
18
GLN
18
A
THR
19
n
19
THR
19
A
VAL
20
n
20
VAL
20
A
SER
21
n
21
SER
21
A
ARG
22
n
22
ARG
22
A
VAL
23
n
23
VAL
23
A
VAL
24
n
24
VAL
24
A
ASN
25
n
25
ASN
25
A
GLN
26
n
26
GLN
26
A
ALA
27
n
27
ALA
27
A
SER
28
n
28
SER
28
A
HIS
29
n
29
HIS
29
A
VAL
30
n
30
VAL
30
A
SER
31
n
31
SER
31
A
ALA
32
n
32
ALA
32
A
LYS
33
n
33
LYS
33
A
THR
34
n
34
THR
34
A
ARG
35
n
35
ARG
35
A
GLU
36
n
36
GLU
36
A
LYS
37
n
37
LYS
37
A
VAL
38
n
38
VAL
38
A
GLU
39
n
39
GLU
39
A
ALA
40
n
40
ALA
40
A
ALA
41
n
41
ALA
41
A
MET
42
n
42
MET
42
A
ALA
43
n
43
ALA
43
A
GLU
44
n
44
GLU
44
A
LEU
45
n
45
LEU
45
A
ASN
46
n
46
ASN
46
A
TYR
47
n
47
TYR
47
A
ILE
48
n
48
ILE
48
A
PRO
49
n
49
PRO
49
A
ASN
50
n
50
ASN
50
A
ARG
51
n
51
ARG
51
A
CYS
52
n
52
CYS
52
A
ALA
53
n
53
ALA
53
A
GLN
54
n
54
GLN
54
A
GLN
55
n
55
GLN
55
A
LEU
56
n
56
LEU
56
A
ALA
57
n
57
ALA
57
A
GLY
58
n
58
GLY
58
A
LYS
59
n
59
LYS
59
A
GLN
60
n
60
GLN
60
A
SER
61
n
61
SER
61
A
LEU
62
n
62
LEU
62
A
MET
1
n
1
MET
1
B
LYS
2
n
2
LYS
2
B
PRO
3
n
3
PRO
3
B
VAL
4
n
4
VAL
4
B
THR
5
n
5
THR
5
B
LEU
6
n
6
LEU
6
B
TYR
7
n
7
TYR
7
B
ASP
8
n
8
ASP
8
B
VAL
9
n
9
VAL
9
B
ALA
10
n
10
ALA
10
B
GLU
11
n
11
GLU
11
B
TYR
12
n
12
TYR
12
B
ALA
13
n
13
ALA
13
B
GLY
14
n
14
GLY
14
B
VAL
15
n
15
VAL
15
B
SER
16
n
16
SER
16
B
TYR
17
n
17
TYR
17
B
GLN
18
n
18
GLN
18
B
THR
19
n
19
THR
19
B
VAL
20
n
20
VAL
20
B
SER
21
n
21
SER
21
B
ARG
22
n
22
ARG
22
B
VAL
23
n
23
VAL
23
B
VAL
24
n
24
VAL
24
B
ASN
25
n
25
ASN
25
B
GLN
26
n
26
GLN
26
B
ALA
27
n
27
ALA
27
B
SER
28
n
28
SER
28
B
HIS
29
n
29
HIS
29
B
VAL
30
n
30
VAL
30
B
SER
31
n
31
SER
31
B
ALA
32
n
32
ALA
32
B
LYS
33
n
33
LYS
33
B
THR
34
n
34
THR
34
B
ARG
35
n
35
ARG
35
B
GLU
36
n
36
GLU
36
B
LYS
37
n
37
LYS
37
B
VAL
38
n
38
VAL
38
B
GLU
39
n
39
GLU
39
B
ALA
40
n
40
ALA
40
B
ALA
41
n
41
ALA
41
B
MET
42
n
42
MET
42
B
ALA
43
n
43
ALA
43
B
GLU
44
n
44
GLU
44
B
LEU
45
n
45
LEU
45
B
ASN
46
n
46
ASN
46
B
TYR
47
n
47
TYR
47
B
ILE
48
n
48
ILE
48
B
PRO
49
n
49
PRO
49
B
ASN
50
n
50
ASN
50
B
ARG
51
n
51
ARG
51
B
CYS
52
n
52
CYS
52
B
ALA
53
n
53
ALA
53
B
GLN
54
n
54
GLN
54
B
GLN
55
n
55
GLN
55
B
LEU
56
n
56
LEU
56
B
ALA
57
n
57
ALA
57
B
GLY
58
n
58
GLY
58
B
LYS
59
n
59
LYS
59
B
GLN
60
n
60
GLN
60
B
SER
61
n
61
SER
61
B
LEU
62
n
62
LEU
62
B
author_defined_assembly
4
tetrameric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
C
D
H21
O2
DG
DC
10
14
1.53
1
C
D
H21
O2
DG
DC
13
11
1.58
1
C
D
H61
O4
DA
DT
19
5
1.60
2
C
D
H21
O2
DG
DC
10
14
1.55
2
C
D
H21
O2
DG
DC
6
18
1.57
2
C
D
H21
O2
DG
DC
13
11
1.59
2
C
D
H21
O2
DG
DC
1
23
1.59
2
C
D
O2
H21
DC
DG
18
6
1.60
3
A
A
HG
HB2
LEU
TYR
6
17
1.33
3
C
D
H21
O2
DG
DC
10
14
1.56
3
C
D
H21
O2
DG
DC
13
11
1.56
3
C
D
H21
O2
DG
DC
8
16
1.58
3
C
D
H21
O2
DG
DC
1
23
1.58
4
C
B
H22
HB2
DG
ALA
13
57
1.24
4
C
D
H21
O2
DG
DC
10
14
1.55
4
C
D
H21
O2
DG
DC
13
11
1.57
5
C
B
H22
HB1
DG
ALA
13
57
1.28
5
C
D
H21
O2
DG
DC
1
23
1.54
5
C
D
H21
O2
DG
DC
10
14
1.55
5
C
D
H21
O2
DG
DC
13
11
1.56
5
C
D
H21
O2
DG
DC
6
18
1.59
6
C
D
H21
O2
DG
DC
10
14
1.56
6
C
D
H21
O2
DG
DC
8
16
1.58
6
C
D
H21
O2
DG
DC
6
18
1.59
7
A
A
HB
HA
VAL
TYR
4
47
1.24
7
C
D
O2
H21
DC
DG
18
6
1.56
7
C
D
H21
O2
DG
DC
10
14
1.56
7
C
D
H21
O2
DG
DC
6
18
1.58
8
C
D
H21
O2
DG
DC
10
14
1.52
8
C
D
H21
O2
DG
DC
13
11
1.55
8
C
B
N7
HH
DA
TYR
14
17
1.55
8
B
B
HG1
OD2
THR
ASP
5
8
1.57
8
C
D
H21
O2
DG
DC
1
23
1.59
8
C
D
H21
O2
DG
DC
6
18
1.60
9
C
B
H22
HB3
DG
ALA
13
57
1.22
9
A
A
HG
HB2
LEU
TYR
6
17
1.33
9
C
D
H21
O2
DG
DC
10
14
1.58
10
B
B
HA
HB2
ARG
GLN
22
26
1.26
10
C
D
H21
O2
DG
DC
13
11
1.52
10
C
D
H21
O2
DG
DC
10
14
1.58
10
C
D
H21
O2
DG
DC
6
18
1.58
11
B
B
HA
HA
VAL
ALA
23
27
1.29
11
C
D
H21
O2
DG
DC
13
11
1.52
11
C
D
H21
O2
DG
DC
10
14
1.55
11
C
D
H21
O2
DG
DC
6
18
1.58
12
A
A
HA
HB2
GLN
LYS
55
59
1.19
12
C
B
H22
HB2
DG
ALA
13
57
1.22
12
C
D
H21
O2
DG
DC
10
14
1.56
12
C
D
H21
O2
DG
DC
6
18
1.58
12
C
D
H21
O2
DG
DC
13
11
1.60
13
C
D
H21
O2
DG
DC
6
18
1.57
13
C
D
H21
O2
DG
DC
10
14
1.58
13
C
D
H21
O2
DG
DC
13
11
1.58
14
C
B
H22
HB1
DG
ALA
13
57
1.27
14
C
D
H21
O2
DG
DC
10
14
1.53
14
C
D
O2
H21
DC
DG
18
6
1.56
14
C
D
H21
O2
DG
DC
6
18
1.56
14
C
D
H21
O2
DG
DC
13
11
1.58
14
C
B
N7
HH
DA
TYR
14
17
1.58
15
C
B
H22
HB1
DG
ALA
13
57
1.27
15
C
D
H21
O2
DG
DC
13
11
1.54
15
C
D
H21
O2
DG
DC
10
14
1.55
15
C
B
N7
HH
DA
TYR
14
17
1.58
15
C
D
H21
O2
DG
DC
6
18
1.58
15
C
D
H21
O2
DG
DC
1
23
1.58
16
B
B
HB
H
VAL
ILE
4
48
1.34
16
C
D
H21
O2
DG
DC
10
14
1.56
16
C
D
H21
O2
DG
DC
6
18
1.57
16
C
D
H61
O4
DA
DT
19
5
1.59
16
C
D
H21
O2
DG
DC
13
11
1.59
16
C
D
H21
O2
DG
DC
1
23
1.60
17
C
D
H21
O2
DG
DC
13
11
1.56
17
C
D
H21
O2
DG
DC
10
14
1.57
18
A
A
HG3
HG21
ARG
VAL
22
30
1.34
18
C
D
H21
O2
DG
DC
10
14
1.53
18
C
D
H21
O2
DG
DC
13
11
1.55
18
C
D
H21
O2
DG
DC
6
18
1.58
19
C
B
H2'
HE1
DG
TYR
13
7
1.33
19
C
D
H21
O2
DG
DC
13
11
1.53
19
C
D
H21
O2
DG
DC
10
14
1.54
20
B
B
HA
HB2
ARG
GLN
22
26
1.26
20
C
D
H21
O2
DG
DC
13
11
1.52
20
C
D
H21
O2
DG
DC
10
14
1.58
20
C
D
H21
O2
DG
DC
6
18
1.58
16
2.04
0.30
108.30
110.34
C
C
C
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
A
VAL
15
-123.56
-166.54
1
A
GLN
26
62.49
64.59
1
A
ALA
27
-121.75
-84.22
1
A
ASN
46
63.63
64.98
1
A
LYS
59
69.62
104.62
1
B
ASN
25
-123.52
-73.26
1
B
PRO
49
-38.67
138.81
1
B
ASN
50
-62.59
97.13
1
B
LYS
59
-153.77
65.90
2
A
ALA
27
-95.15
-137.15
2
A
ASN
46
68.34
63.02
2
B
ASN
25
-98.20
-75.08
2
B
ALA
27
-50.77
95.20
2
B
SER
31
-86.77
41.26
2
B
ALA
32
67.84
-61.45
2
B
ASN
46
67.36
65.73
2
B
ASN
50
-58.17
95.73
2
B
LYS
59
62.83
89.50
3
A
VAL
15
-124.12
-166.15
3
A
ALA
27
-94.14
-141.58
3
A
ASN
46
66.65
64.83
3
A
LYS
59
39.81
-138.83
3
B
LYS
2
62.09
70.56
3
B
ASN
25
-64.29
-74.91
3
B
GLN
26
-146.35
16.33
3
B
TYR
47
-59.27
108.77
3
B
PRO
49
-30.44
119.13
3
B
ASN
50
-67.19
88.34
3
B
ALA
57
-69.64
-80.29
3
B
LYS
59
70.40
120.81
4
A
ALA
27
-85.89
30.17
4
A
SER
28
60.59
-172.82
4
A
ASN
46
67.75
63.50
4
B
ASN
25
-128.45
-72.18
4
B
PRO
49
-28.21
122.51
4
B
ALA
57
-73.61
44.12
4
B
SER
61
-88.73
41.04
5
A
ALA
27
-103.02
-148.58
5
A
ASN
46
64.51
67.18
5
A
GLN
60
-66.60
90.94
5
B
ASN
25
-72.55
-73.74
5
B
GLN
26
-167.23
41.06
5
B
ALA
27
64.61
-117.15
5
B
SER
28
58.94
120.23
5
B
TYR
47
-52.66
108.99
5
B
PRO
49
-30.86
130.49
5
B
LEU
56
-70.63
-70.60
6
A
LYS
2
-159.93
81.71
6
A
GLN
26
-129.10
-53.38
6
A
SER
31
-74.07
-89.14
6
A
ALA
32
-160.24
-62.02
6
A
ASN
46
63.48
70.60
6
A
SER
61
66.50
-168.96
6
B
ASN
25
-79.08
-85.91
6
B
ALA
27
-28.82
96.55
6
B
ASN
46
61.65
63.32
6
B
ASN
50
-60.14
99.71
6
B
LYS
59
67.53
162.34
7
A
VAL
15
-129.29
-165.54
7
A
ALA
27
-106.82
-153.07
7
A
ASN
46
69.50
62.27
7
A
LYS
59
32.95
-106.25
7
B
ASN
25
-123.17
-70.55
7
B
PRO
49
-39.35
129.66
7
B
ASN
50
-54.74
99.73
7
B
GLN
60
-100.24
72.33
8
A
LYS
2
70.68
119.19
8
A
GLN
26
62.17
63.40
8
A
ALA
27
-106.63
-166.52
8
A
HIS
29
67.99
-60.52
8
A
LYS
59
72.28
106.42
8
A
GLN
60
69.29
109.47
8
B
ASN
25
-126.40
-72.34
8
B
PRO
49
-35.20
123.05
8
B
ASN
50
-55.49
97.45
8
B
ALA
57
-71.76
34.45
8
B
SER
61
-94.23
57.28
9
A
VAL
15
-127.10
-166.48
9
A
ALA
27
-91.88
-159.06
9
A
ASN
46
67.42
65.63
9
A
GLN
60
72.69
127.55
9
B
GLN
26
-144.38
-109.51
9
B
ALA
27
-161.01
22.29
9
B
PRO
49
-32.03
127.51
9
B
ASN
50
-52.56
99.55
9
B
GLN
60
54.83
-112.98
10
A
VAL
15
-118.96
-166.48
10
A
ALA
27
-65.56
81.32
10
A
SER
31
-70.81
-84.05
10
A
ALA
32
-168.02
-54.72
10
A
ASN
46
63.85
67.01
10
B
ASN
25
-146.95
-34.47
10
B
SER
28
71.93
179.66
10
B
HIS
29
37.92
36.35
10
B
PRO
49
-31.61
131.78
10
B
ASN
50
-60.36
84.59
10
B
LYS
59
64.30
92.66
11
A
LYS
2
-173.54
-56.53
11
A
SER
28
64.66
-171.52
11
A
LYS
59
69.70
-52.90
11
B
ASN
25
-75.47
-80.29
11
B
SER
31
-76.69
37.47
11
B
ALA
32
68.11
-57.64
11
B
ASN
46
61.37
67.16
11
B
PRO
49
-35.41
130.06
11
B
ASN
50
-44.98
108.83
12
A
VAL
15
-121.65
-167.63
12
A
ALA
27
-116.67
-152.20
12
A
ASN
46
63.97
61.93
12
B
LYS
2
60.30
83.58
12
B
ASN
25
-73.13
-86.39
12
B
GLN
26
-153.18
44.79
12
B
ALA
27
60.11
-135.54
12
B
SER
28
65.23
137.87
12
B
ASN
46
68.82
61.29
12
B
TYR
47
-55.00
108.37
12
B
PRO
49
-27.24
126.75
12
B
SER
61
65.49
104.01
13
A
VAL
15
-123.71
-164.24
13
A
SER
28
60.76
-174.60
13
A
ASN
46
62.16
66.84
13
A
LYS
59
70.34
-58.70
13
B
ASN
25
-77.52
-74.88
13
B
GLN
26
-169.03
47.08
13
B
ALA
27
57.87
-129.21
13
B
SER
28
70.74
124.20
13
B
PRO
49
-34.27
125.45
13
B
LYS
59
69.15
-73.06
13
B
GLN
60
-133.26
-46.04
13
B
SER
61
-148.65
-17.93
14
A
VAL
15
-124.47
-162.37
14
A
ALA
27
-103.72
-155.90
14
A
ASN
46
62.92
67.28
14
A
LYS
59
68.19
112.82
14
B
LYS
2
53.28
75.19
14
B
ASN
25
-119.52
-85.16
14
B
ALA
27
-68.69
57.25
14
B
PRO
49
-33.43
127.88
14
B
ASN
50
-55.21
91.67
15
A
ASN
46
59.20
77.06
15
A
GLN
60
62.93
66.80
15
B
ASN
25
-77.73
-73.24
15
B
GLN
26
-168.27
44.45
15
B
ALA
27
62.03
-130.63
15
B
SER
28
67.31
148.28
15
B
SER
31
-84.39
35.74
15
B
ALA
32
69.27
-53.66
15
B
PRO
49
-35.84
127.07
15
B
ASN
50
-52.76
99.54
15
B
LEU
56
-66.46
-70.54
16
A
LYS
2
53.66
71.74
16
A
VAL
15
-124.63
-166.52
16
A
GLN
26
57.79
76.13
16
A
SER
28
59.26
-166.09
16
A
ASN
46
67.00
65.92
16
A
GLN
60
-93.38
30.57
16
B
LYS
2
-160.36
114.07
16
B
ASN
25
-80.24
-78.66
16
B
GLN
26
-162.03
50.84
16
B
ALA
27
58.09
-126.58
16
B
SER
28
63.52
128.32
16
B
ASN
46
61.29
63.07
16
B
PRO
49
-36.60
125.23
16
B
ASN
50
-47.37
99.45
17
A
ALA
27
-93.90
-144.19
17
A
ASN
46
66.02
69.48
17
A
LYS
59
34.22
-104.40
17
A
SER
61
66.67
-95.75
17
B
LYS
2
59.77
76.60
17
B
ASN
25
-122.51
-68.73
17
B
ASN
46
76.78
57.32
17
B
PRO
49
-33.52
118.64
18
A
ALA
27
-102.79
-144.49
18
A
ASN
46
60.93
62.51
18
A
PRO
49
-65.56
95.55
18
B
ASN
25
-77.84
-79.78
18
B
GLN
26
-152.79
43.31
18
B
ALA
27
52.63
-120.64
18
B
SER
28
67.68
133.62
18
B
HIS
29
67.83
-61.07
18
B
TYR
47
-52.60
106.78
18
B
PRO
49
-30.40
115.81
18
B
SER
61
-164.91
-52.65
19
A
ALA
27
-93.81
-155.32
19
A
GLN
60
-98.56
39.48
19
B
ASN
25
-125.00
-83.87
19
B
HIS
29
69.63
-58.52
19
B
VAL
30
-57.58
102.75
19
B
PRO
49
-29.71
128.55
19
B
ASN
50
-68.52
75.55
19
B
LEU
56
-65.97
-70.25
19
B
GLN
60
-99.08
57.82
20
A
VAL
15
-118.96
-166.48
20
A
ALA
27
-65.56
81.32
20
A
SER
31
-70.81
-84.05
20
A
ALA
32
-168.02
-54.72
20
A
ASN
46
63.85
67.01
20
B
ASN
25
-146.95
-34.47
20
B
SER
28
71.93
179.66
20
B
HIS
29
37.92
36.35
20
B
PRO
49
-31.61
131.78
20
B
ASN
50
-60.36
84.59
20
B
LYS
59
64.30
92.66
SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1
1
N
N
2
N
N
3
N
N
3
N
N
A
THR
5
C
THR
5
HELX_P
A
GLY
14
C
GLY
14
1
1
10
A
SER
16
C
SER
16
HELX_P
A
GLN
26
C
GLN
26
1
2
11
A
SER
31
C
SER
31
HELX_P
A
LEU
45
C
LEU
45
1
3
15
A
ASN
50
C
ASN
50
HELX_P
A
GLY
58
C
GLY
58
1
4
9
B
THR
5
D
THR
5
HELX_P
B
GLY
14
D
GLY
14
1
5
10
B
SER
16
D
SER
16
HELX_P
B
ASN
25
D
ASN
25
1
6
10
B
SER
31
D
SER
31
HELX_P
B
LEU
45
D
LEU
45
1
7
15
B
ASN
50
D
ASN
50
HELX_P
B
GLY
58
D
GLY
58
1
8
9
disulf
2.031
A
CYS
52
C
SG
CYS
52
1_555
B
CYS
52
D
SG
CYS
52
1_555
hydrog
WATSON-CRICK
C
DG
1
A
N1
DG
1
1_555
D
DC
23
B
N3
DC
23
1_555
hydrog
WATSON-CRICK
C
DG
1
A
N2
DG
1
1_555
D
DC
23
B
O2
DC
23
1_555
hydrog
WATSON-CRICK
C
DG
1
A
O6
DG
1
1_555
D
DC
23
B
N4
DC
23
1_555
hydrog
WATSON-CRICK
C
DA
2
A
N1
DA
2
1_555
D
DT
22
B
N3
DT
22
1_555
hydrog
WATSON-CRICK
C
DA
2
A
N6
DA
2
1_555
D
DT
22
B
O4
DT
22
1_555
hydrog
WATSON-CRICK
C
DA
3
A
N1
DA
3
1_555
D
DT
21
B
N3
DT
21
1_555
hydrog
WATSON-CRICK
C
DA
3
A
N6
DA
3
1_555
D
DT
21
B
O4
DT
21
1_555
hydrog
WATSON-CRICK
C
DT
4
A
N3
DT
4
1_555
D
DA
20
B
N1
DA
20
1_555
hydrog
WATSON-CRICK
C
DT
4
A
O4
DT
4
1_555
D
DA
20
B
N6
DA
20
1_555
hydrog
WATSON-CRICK
C
DT
5
A
N3
DT
5
1_555
D
DA
19
B
N1
DA
19
1_555
hydrog
WATSON-CRICK
C
DT
5
A
O4
DT
5
1_555
D
DA
19
B
N6
DA
19
1_555
hydrog
WATSON-CRICK
C
DG
6
A
N1
DG
6
1_555
D
DC
18
B
N3
DC
18
1_555
hydrog
WATSON-CRICK
C
DG
6
A
N2
DG
6
1_555
D
DC
18
B
O2
DC
18
1_555
hydrog
WATSON-CRICK
C
DG
6
A
O6
DG
6
1_555
D
DC
18
B
N4
DC
18
1_555
hydrog
WATSON-CRICK
C
DT
7
A
N3
DT
7
1_555
D
DA
17
B
N1
DA
17
1_555
hydrog
WATSON-CRICK
C
DT
7
A
O4
DT
7
1_555
D
DA
17
B
N6
DA
17
1_555
hydrog
WATSON-CRICK
C
DG
8
A
N1
DG
8
1_555
D
DC
16
B
N3
DC
16
1_555
hydrog
WATSON-CRICK
C
DG
8
A
N2
DG
8
1_555
D
DC
16
B
O2
DC
16
1_555
hydrog
WATSON-CRICK
C
DG
8
A
O6
DG
8
1_555
D
DC
16
B
N4
DC
16
1_555
hydrog
WATSON-CRICK
C
DA
9
A
N1
DA
9
1_555
D
DT
15
B
N3
DT
15
1_555
hydrog
WATSON-CRICK
C
DA
9
A
N6
DA
9
1_555
D
DT
15
B
O4
DT
15
1_555
hydrog
WATSON-CRICK
C
DG
10
A
N1
DG
10
1_555
D
DC
14
B
N3
DC
14
1_555
hydrog
WATSON-CRICK
C
DG
10
A
N2
DG
10
1_555
D
DC
14
B
O2
DC
14
1_555
hydrog
WATSON-CRICK
C
DG
10
A
O6
DG
10
1_555
D
DC
14
B
N4
DC
14
1_555
hydrog
WATSON-CRICK
C
DC
11
A
N3
DC
11
1_555
D
DG
13
B
N1
DG
13
1_555
hydrog
WATSON-CRICK
C
DC
11
A
N4
DC
11
1_555
D
DG
13
B
O6
DG
13
1_555
hydrog
WATSON-CRICK
C
DC
11
A
O2
DC
11
1_555
D
DG
13
B
N2
DG
13
1_555
hydrog
WATSON-CRICK
C
DG
12
A
N1
DG
12
1_555
D
DC
12
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
C
DG
12
A
N2
DG
12
1_555
D
DC
12
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
C
DG
12
A
O6
DG
12
1_555
D
DC
12
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
C
DG
13
A
N1
DG
13
1_555
D
DC
11
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
C
DG
13
A
N2
DG
13
1_555
D
DC
11
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
C
DG
13
A
O6
DG
13
1_555
D
DC
11
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
C
DA
14
A
N1
DA
14
1_555
D
DT
10
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
C
DA
14
A
N6
DA
14
1_555
D
DT
10
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
C
DT
15
A
N3
DT
15
1_555
D
DA
9
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
C
DT
15
A
O4
DT
15
1_555
D
DA
9
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
C
DA
16
A
N1
DA
16
1_555
D
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
C
DA
16
A
N6
DA
16
1_555
D
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
C
DA
17
A
N1
DA
17
1_555
D
DT
7
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
C
DA
17
A
N6
DA
17
1_555
D
DT
7
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
C
DC
18
A
N3
DC
18
1_555
D
DG
6
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
18
A
N4
DC
18
1_555
D
DG
6
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
18
A
O2
DC
18
1_555
D
DG
6
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
C
DA
19
A
N1
DA
19
1_555
D
DT
5
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
C
DA
19
A
N6
DA
19
1_555
D
DT
5
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
C
DA
20
A
N1
DA
20
1_555
D
DT
4
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
C
DA
20
A
N6
DA
20
1_555
D
DT
4
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
C
DT
21
A
N3
DT
21
1_555
D
DA
3
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
C
DT
21
A
O4
DT
21
1_555
D
DA
3
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
C
DT
22
A
N3
DT
22
1_555
D
DA
2
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
C
DT
22
A
O4
DT
22
1_555
D
DA
2
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
C
DT
23
A
N3
DT
23
1_555
D
DA
1
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
C
DT
23
A
O4
DT
23
1_555
D
DA
1
B
N6
DA
1
1_555
TRANSCRIPTION REGULATOR/DNA
TRANSCRIPTION REGULATION, LAC OPERON, LAC REPRESSOR, NATURAL LAC OPERATOR, ASYMMETRIC DNA-BINDING, HTH, TRANSCRIPTION REGULATOR-DNA COMPLEX
LACI_ECOLI
UNP
3
1
P03023
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIV
AAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSII
FSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPT
AMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLP
VSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ
1L1M
PDB
1
1L1M
1L1M
PDB
2
1L1M
1
62
1L1M
1
62
P03023
A
1
1
62
1
62
1L1M
1
62
P03023
B
1
1
62
1
23
1L1M
1
23
1L1M
C
2
1
23
1
23
1L1M
1
23
1L1M
D
3
1
23
1
VAL
engineered mutation
CYS
52
1L1M
A
P03023
UNP
52
52
2
VAL
engineered mutation
CYS
52
1L1M
B
P03023
UNP
52
52