1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Clubb, R.T.
Connolly, K.M.
Wojciak, J.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
5
546
550
10.1038/799
9665166
Site-specific DNA binding using a variation of the double stranded RNA binding motif.
1998
10.2210/pdb1bb8/pdb
pdb_00001bb8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8462.620
INTEGRASE
N-TERMINAL DNA BINDING DOMAIN
1
man
polymer
no
no
EKRRDNRGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKDIHD
EKRRDNRGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKDIHD
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
Enterococcus
Escherichia
Escherichia coli
sample
BL21
1351
Enterococcus faecalis
CYTOPLASM
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PLASMID
PET11A
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1998-11-25
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1998-04-29
REL
THREE AND FOUR-DIMENSIONAL HETERONUCLEAR NMR EXPERIMENTS
LEAST RESTRAINT VIOLATION
100
25
NOESY ETC.
6.0
300
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
DISTANCE GEOMETRY AND SIMULATED ANNEALING
H2O
BRUNGER
refinement
X-PLOR
3.843
structure solution
X-PLOR
500
Bruker
DRX
600
Bruker
DRX
GLU
3
n
1
GLU
3
A
LYS
4
n
2
LYS
4
A
ARG
5
n
3
ARG
5
A
ARG
6
n
4
ARG
6
A
ASP
7
n
5
ASP
7
A
ASN
8
n
6
ASN
8
A
ARG
9
n
7
ARG
9
A
GLY
10
n
8
GLY
10
A
ARG
11
n
9
ARG
11
A
ILE
12
n
10
ILE
12
A
LEU
13
n
11
LEU
13
A
LYS
14
n
12
LYS
14
A
THR
15
n
13
THR
15
A
GLY
16
n
14
GLY
16
A
GLU
17
n
15
GLU
17
A
SER
18
n
16
SER
18
A
GLN
19
n
17
GLN
19
A
ARG
20
n
18
ARG
20
A
LYS
21
n
19
LYS
21
A
ASP
22
n
20
ASP
22
A
GLY
23
n
21
GLY
23
A
ARG
24
n
22
ARG
24
A
TYR
25
n
23
TYR
25
A
LEU
26
n
24
LEU
26
A
TYR
27
n
25
TYR
27
A
LYS
28
n
26
LYS
28
A
TYR
29
n
27
TYR
29
A
ILE
30
n
28
ILE
30
A
ASP
31
n
29
ASP
31
A
SER
32
n
30
SER
32
A
PHE
33
n
31
PHE
33
A
GLY
34
n
32
GLY
34
A
GLU
35
n
33
GLU
35
A
PRO
36
n
34
PRO
36
A
GLN
37
n
35
GLN
37
A
PHE
38
n
36
PHE
38
A
VAL
39
n
37
VAL
39
A
TYR
40
n
38
TYR
40
A
SER
41
n
39
SER
41
A
TRP
42
n
40
TRP
42
A
LYS
43
n
41
LYS
43
A
LEU
44
n
42
LEU
44
A
VAL
45
n
43
VAL
45
A
ALA
46
n
44
ALA
46
A
THR
47
n
45
THR
47
A
ASP
48
n
46
ASP
48
A
ARG
49
n
47
ARG
49
A
VAL
50
n
48
VAL
50
A
PRO
51
n
49
PRO
51
A
ALA
52
n
50
ALA
52
A
GLY
53
n
51
GLY
53
A
LYS
54
n
52
LYS
54
A
ARG
55
n
53
ARG
55
A
ASP
56
n
54
ASP
56
A
CYS
57
n
55
CYS
57
A
ILE
58
n
56
ILE
58
A
SER
59
n
57
SER
59
A
LEU
60
n
58
LEU
60
A
ARG
61
n
59
ARG
61
A
GLU
62
n
60
GLU
62
A
LYS
63
n
61
LYS
63
A
ILE
64
n
62
ILE
64
A
ALA
65
n
63
ALA
65
A
GLU
66
n
64
GLU
66
A
LEU
67
n
65
LEU
67
A
GLN
68
n
66
GLN
68
A
LYS
69
n
67
LYS
69
A
ASP
70
n
68
ASP
70
A
ILE
71
n
69
ILE
71
A
HIS
72
n
70
HIS
72
A
ASP
73
n
71
ASP
73
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
A
H
OD2
VAL
ASP
45
48
1.42
2
A
A
O
H
LEU
ILE
60
64
1.45
2
A
A
OD1
H
ASP
ARG
7
11
1.48
2
A
A
HH11
OH
ARG
TYR
11
25
1.56
2
A
A
H
OD2
LEU
ASP
44
48
1.57
3
A
A
O
HE22
GLU
GLN
35
37
1.47
3
A
A
O
H
LEU
ILE
60
64
1.53
3
A
A
OD1
H
ASP
ARG
7
11
1.53
4
A
A
H
OD2
VAL
ASP
45
48
1.44
4
A
A
HH11
O
ARG
VAL
49
50
1.55
4
A
A
H
OE1
ASN
GLN
8
19
1.57
5
A
A
H
O
TYR
SER
25
41
1.54
6
A
A
O
H
LEU
ILE
60
64
1.50
7
A
A
OD2
HE21
ASP
GLN
31
37
1.42
8
A
A
H
HG
TRP
CYS
42
57
1.34
8
A
A
O
H
LYS
LEU
63
67
1.50
9
A
A
OD1
H
ASP
ARG
7
11
1.50
9
A
A
O
HE22
GLU
GLN
35
37
1.57
10
A
A
OD2
HE
ASP
ARG
22
24
1.42
11
A
A
O
HE22
GLU
GLN
35
37
1.56
12
A
A
O
HE22
GLU
GLN
35
37
1.51
12
A
A
OD1
H
ASP
ARG
7
11
1.58
12
A
A
O
H
PRO
LYS
51
54
1.60
13
A
A
O
H
ALA
LYS
52
54
1.50
13
A
A
OD2
HH22
ASP
ARG
7
11
1.56
14
A
A
HH21
HE1
ARG
TRP
24
42
1.33
15
A
A
OD1
H
ASP
ARG
7
11
1.52
15
A
A
O
HE22
GLU
GLN
35
37
1.53
15
A
A
O
HZ3
ILE
LYS
58
63
1.60
15
A
A
O
H
SER
LYS
59
63
1.60
16
A
A
O
HE22
GLU
GLN
35
37
1.45
17
A
A
O
H
LYS
LEU
63
67
1.54
18
A
A
H
OE2
ASP
GLU
31
35
1.49
19
A
A
O
HE22
GLU
GLN
35
37
1.49
19
A
A
OD1
H
ASP
GLY
7
10
1.56
19
A
A
O
H
LEU
ILE
60
64
1.60
20
A
A
HZ2
H
LYS
CYS
43
57
1.33
20
A
A
HZ2
O
LYS
CYS
43
57
1.53
20
A
A
H
OE1
ASN
GLN
8
19
1.53
20
A
A
H
OD2
VAL
ASP
45
48
1.57
20
A
A
OD1
H
ASP
GLY
7
10
1.58
21
A
A
HH11
O
ARG
VAL
49
50
1.50
21
A
A
O
H
LYS
LEU
63
67
1.51
21
A
A
H
OE1
ASN
GLN
8
19
1.54
22
A
A
O
HE22
GLU
GLN
35
37
1.46
22
A
A
O
H
PRO
LYS
51
54
1.52
22
A
A
H
OD2
VAL
ASP
45
48
1.56
23
A
A
OD2
HH22
ASP
ARG
22
24
1.54
24
A
A
O
HE22
GLU
GLN
35
37
1.36
25
A
A
HH11
HH21
ARG
ARG
20
24
1.20
25
A
A
HZ2
H
LYS
CYS
43
57
1.33
25
A
A
OD1
HE21
ASP
GLN
31
37
1.43
25
A
A
O
H
LYS
LEU
63
67
1.54
1
A
ARG
9
-101.30
-71.67
1
A
SER
32
-62.11
6.28
1
A
SER
41
-170.78
136.50
1
A
HIS
72
-151.65
37.14
2
A
LYS
4
-152.61
-113.92
2
A
SER
32
-59.79
-2.82
2
A
SER
41
-172.27
145.47
2
A
ALA
46
-55.15
-7.04
3
A
HIS
72
-156.52
15.84
4
A
ARG
9
-95.57
-77.38
4
A
SER
41
-171.66
146.19
4
A
HIS
72
-144.76
-59.98
5
A
SER
41
-171.26
143.60
5
A
ALA
52
-48.96
150.50
6
A
ARG
9
-104.77
-81.75
7
A
LYS
4
-155.28
-141.73
7
A
ASP
7
-81.57
-159.96
7
A
ARG
9
-92.18
-86.01
7
A
ASP
56
-49.53
162.33
8
A
ARG
5
-94.70
-148.03
8
A
SER
41
-174.31
146.31
9
A
SER
32
-60.55
1.46
10
A
ARG
9
-103.98
-80.13
10
A
SER
32
-66.20
6.06
10
A
SER
59
-57.97
174.77
10
A
HIS
72
-156.45
-42.13
11
A
LYS
4
-86.11
44.24
11
A
ASP
7
-137.56
-103.72
11
A
ASN
8
-66.46
-80.93
11
A
SER
32
-64.10
0.74
11
A
SER
41
-172.11
148.61
11
A
HIS
72
-158.18
13.52
12
A
SER
32
-58.90
0.30
12
A
ASP
48
-69.51
-174.43
13
A
ARG
9
-100.20
-73.39
13
A
PRO
51
-82.09
-112.88
13
A
ALA
52
-55.00
-149.76
13
A
HIS
72
-85.28
-127.39
14
A
SER
32
-59.87
-3.98
14
A
SER
41
-171.77
148.62
14
A
ALA
52
-45.36
151.60
14
A
ARG
55
-78.08
-99.10
15
A
ASP
7
-123.58
-169.57
15
A
SER
32
-60.73
3.33
15
A
GLN
68
-78.82
-72.57
16
A
SER
32
-59.28
-0.43
16
A
ALA
52
-45.33
159.55
16
A
ASP
56
-52.10
176.48
17
A
ASP
7
-130.98
-159.59
17
A
SER
32
-63.01
0.36
17
A
CYS
57
-172.46
-174.99
18
A
SER
32
-57.08
-3.94
19
A
ASN
8
-69.17
1.64
19
A
SER
32
-53.66
-8.59
19
A
HIS
72
-151.43
-56.28
20
A
SER
32
-64.09
0.59
20
A
ILE
71
-84.97
44.23
20
A
HIS
72
-156.90
41.69
21
A
ILE
71
-89.88
44.32
21
A
HIS
72
-153.59
37.41
22
A
ASP
7
-74.40
-167.36
22
A
ARG
9
-101.30
-87.13
22
A
SER
32
-58.20
-2.18
22
A
ASP
48
-69.40
-179.69
22
A
ASP
56
-43.78
154.81
22
A
HIS
72
-148.61
-33.34
23
A
ASP
7
-104.09
-167.66
23
A
SER
32
-60.35
5.71
24
A
ARG
9
-96.41
-75.79
24
A
SER
41
-172.34
137.74
25
A
ALA
52
-44.84
153.32
25
A
SER
59
-59.19
176.04
model building
X-PLOR
3.843
refinement
X-PLOR
3.843
phasing
X-PLOR
3.843
N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES
1
Y
N
A
LEU
60
A
LEU
58
HELX_P
A
ASP
70
A
ASP
68
1
1
11
INTEGRASE
INTEGRASE, DNA BINDING, TRANSPOSITION
TNR6_ENTFA
UNP
1
1
P22886
MSEKRRDNRGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKDIHDGIDVVGK
KMTLCQLYAKQNAQRPKVRKNTETGRKYLMDILKKDKLGVRSIDSIKPSDAKEWAIRMSENGYAYQTINNYKRSLKASFY
IAIQDDCVRKNPFDFQLKAVLDDDTVPKTVLTEEQEEKLLAFAKADKTYSKNYDEILILLKTGLRISEFGGLTLPDLDFE
NRLVNIDHQLLRDTEIGYYIETPKTKSGERQVPMVEEAYQAFKRVLANRKNDKRVEIDGYSDFLFLNRKNYPKVASDYNG
MMKGLVKKYNKYNEDKLPHITPHSLRHTFCTNYANAGMNPKALQYIMGHANIAMTLNYYAHATFDSAMAEMKRLNKEKQQ
ERLVA
3
73
1BB8
3
73
P22886
A
1
1
71
3
parallel
anti-parallel
A
SER
18
A
SER
16
A
GLN
19
A
GLN
17
A
TYR
25
A
TYR
23
A
ILE
30
A
ILE
28
A
PRO
36
A
PRO
34
A
SER
41
A
SER
39
1
P 1