0.029593
-0.000001
-0.000001
0.000000
0.013007
0.000000
0.000000
0.000000
0.013237
0.00000
0.00000
0.00000
Jacobs, S.A.
Khorasanizadeh, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
33.792
76.883
75.548
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
H2 O
18.015
WATER
non-polymer
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
C8 H18 N2 O2
174.241
n
N-DIMETHYL-LYSINE
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
Science
SCIEAS
0038
0036-8075
295
2080
2083
10.1126/science.1069473
11859155
Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail.
2002
10.2210/pdb1kna/pdb
pdb_00001kna
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2001-10-10
BRUKER SMART 6000
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU
8586.468
HETEROCHROMATIN PROTEIN 1
Residues 23-76
K38M
1
man
polymer
1756.017
METHYLATED Histone H3
Residues 1-16
P16Y
1
syn
polymer
18.015
water
86
nat
water
HP1, NONHISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN
no
no
MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD
MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD
A
polypeptide(L)
no
yes
ARTKQTAR(MLY)STGGKAY
ARTKQTARKSTGGKAY
P
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
fruit fly
Drosophila
Escherichia
sample
7227
Drosophila melanogaster
562
Escherichia coli
BL21(De3)pLysS
Plasmid
pET11a
1
2.37
48.14
VAPOR DIFFUSION, SITTING DROP
6.0
Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K
283.0
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-03-20
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2001-12-18
REL
REL
HOH
water
Synthetic peptide Corresponding to residues 1-16 of Histone H3. K9 dimethylated. P16Y mutation.
sample
HOH
1
3
HOH
HOH
77
A
HOH
2
3
HOH
HOH
78
A
HOH
3
3
HOH
HOH
79
A
HOH
4
3
HOH
HOH
80
A
HOH
5
3
HOH
HOH
81
A
HOH
6
3
HOH
HOH
82
A
HOH
7
3
HOH
HOH
83
A
HOH
8
3
HOH
HOH
84
A
HOH
9
3
HOH
HOH
85
A
HOH
10
3
HOH
HOH
86
A
HOH
11
3
HOH
HOH
87
A
HOH
12
3
HOH
HOH
88
A
HOH
13
3
HOH
HOH
89
A
HOH
14
3
HOH
HOH
90
A
HOH
15
3
HOH
HOH
91
A
HOH
16
3
HOH
HOH
92
A
HOH
17
3
HOH
HOH
93
A
HOH
18
3
HOH
HOH
94
A
HOH
19
3
HOH
HOH
95
A
HOH
20
3
HOH
HOH
96
A
HOH
22
3
HOH
HOH
97
A
HOH
23
3
HOH
HOH
98
A
HOH
25
3
HOH
HOH
99
A
HOH
26
3
HOH
HOH
100
A
HOH
27
3
HOH
HOH
101
A
HOH
28
3
HOH
HOH
102
A
HOH
29
3
HOH
HOH
103
A
HOH
30
3
HOH
HOH
104
A
HOH
31
3
HOH
HOH
105
A
HOH
32
3
HOH
HOH
106
A
HOH
33
3
HOH
HOH
107
A
HOH
34
3
HOH
HOH
108
A
HOH
36
3
HOH
HOH
109
A
HOH
37
3
HOH
HOH
110
A
HOH
38
3
HOH
HOH
111
A
HOH
39
3
HOH
HOH
112
A
HOH
40
3
HOH
HOH
113
A
HOH
41
3
HOH
HOH
114
A
HOH
42
3
HOH
HOH
115
A
HOH
43
3
HOH
HOH
116
A
HOH
44
3
HOH
HOH
117
A
HOH
45
3
HOH
HOH
118
A
HOH
46
3
HOH
HOH
119
A
HOH
47
3
HOH
HOH
120
A
HOH
49
3
HOH
HOH
121
A
HOH
50
3
HOH
HOH
122
A
HOH
51
3
HOH
HOH
123
A
HOH
52
3
HOH
HOH
124
A
HOH
53
3
HOH
HOH
125
A
HOH
54
3
HOH
HOH
126
A
HOH
55
3
HOH
HOH
127
A
HOH
56
3
HOH
HOH
128
A
HOH
57
3
HOH
HOH
129
A
HOH
58
3
HOH
HOH
130
A
HOH
59
3
HOH
HOH
131
A
HOH
60
3
HOH
HOH
132
A
HOH
61
3
HOH
HOH
133
A
HOH
62
3
HOH
HOH
134
A
HOH
63
3
HOH
HOH
135
A
HOH
64
3
HOH
HOH
136
A
HOH
65
3
HOH
HOH
137
A
HOH
66
3
HOH
HOH
138
A
HOH
67
3
HOH
HOH
139
A
HOH
68
3
HOH
HOH
140
A
HOH
69
3
HOH
HOH
141
A
HOH
71
3
HOH
HOH
142
A
HOH
72
3
HOH
HOH
143
A
HOH
73
3
HOH
HOH
144
A
HOH
74
3
HOH
HOH
145
A
HOH
75
3
HOH
HOH
146
A
HOH
78
3
HOH
HOH
147
A
HOH
79
3
HOH
HOH
148
A
HOH
80
3
HOH
HOH
149
A
HOH
81
3
HOH
HOH
150
A
HOH
82
3
HOH
HOH
151
A
HOH
83
3
HOH
HOH
152
A
HOH
21
3
HOH
HOH
21
P
HOH
24
3
HOH
HOH
24
P
HOH
35
3
HOH
HOH
35
P
HOH
48
3
HOH
HOH
48
P
HOH
70
3
HOH
HOH
70
P
HOH
76
3
HOH
HOH
76
P
HOH
77
3
HOH
HOH
77
P
HOH
84
3
HOH
HOH
84
P
HOH
85
3
HOH
HOH
85
P
HOH
86
3
HOH
HOH
86
P
n
1
8
A
n
2
9
A
n
3
10
A
n
4
11
A
n
5
12
A
n
6
13
A
n
7
14
A
n
8
15
A
n
9
16
A
n
10
17
A
n
11
18
A
n
12
19
A
n
13
20
A
n
14
21
A
n
15
22
A
GLU
23
n
16
GLU
23
A
TYR
24
n
17
TYR
24
A
ALA
25
n
18
ALA
25
A
VAL
26
n
19
VAL
26
A
GLU
27
n
20
GLU
27
A
LYS
28
n
21
LYS
28
A
ILE
29
n
22
ILE
29
A
ILE
30
n
23
ILE
30
A
ASP
31
n
24
ASP
31
A
ARG
32
n
25
ARG
32
A
ARG
33
n
26
ARG
33
A
VAL
34
n
27
VAL
34
A
ARG
35
n
28
ARG
35
A
LYS
36
n
29
LYS
36
A
GLY
37
n
30
GLY
37
A
MET
38
n
31
MET
38
A
VAL
39
n
32
VAL
39
A
GLU
40
n
33
GLU
40
A
TYR
41
n
34
TYR
41
A
TYR
42
n
35
TYR
42
A
LEU
43
n
36
LEU
43
A
LYS
44
n
37
LYS
44
A
TRP
45
n
38
TRP
45
A
LYS
46
n
39
LYS
46
A
GLY
47
n
40
GLY
47
A
TYR
48
n
41
TYR
48
A
PRO
49
n
42
PRO
49
A
GLU
50
n
43
GLU
50
A
THR
51
n
44
THR
51
A
GLU
52
n
45
GLU
52
A
ASN
53
n
46
ASN
53
A
THR
54
n
47
THR
54
A
TRP
55
n
48
TRP
55
A
GLU
56
n
49
GLU
56
A
PRO
57
n
50
PRO
57
A
GLU
58
n
51
GLU
58
A
ASN
59
n
52
ASN
59
A
ASN
60
n
53
ASN
60
A
LEU
61
n
54
LEU
61
A
ASP
62
n
55
ASP
62
A
CYS
63
n
56
CYS
63
A
GLN
64
n
57
GLN
64
A
ASP
65
n
58
ASP
65
A
LEU
66
n
59
LEU
66
A
ILE
67
n
60
ILE
67
A
GLN
68
n
61
GLN
68
A
GLN
69
n
62
GLN
69
A
TYR
70
n
63
TYR
70
A
GLU
71
n
64
GLU
71
A
ALA
72
n
65
ALA
72
A
SER
73
n
66
SER
73
A
ARG
74
n
67
ARG
74
A
n
68
75
A
n
69
76
A
n
1
1
P
n
2
2
P
n
3
3
P
n
4
4
P
GLN
5
n
5
GLN
5
P
THR
6
n
6
THR
6
P
ALA
7
n
7
ALA
7
P
ARG
8
n
8
ARG
8
P
MLY
9
n
9
MLY
9
P
SER
10
n
10
SER
10
P
n
11
11
P
n
12
12
P
n
13
13
P
n
14
14
P
n
15
15
P
n
16
16
P
author_and_software_defined_assembly
PISA
2
dimeric
1030
-4
4040
P
MLY
9
N-DIMETHYL-LYSINE
B
MLY
9
LYS
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
THR
54
A
O
THR
47
A
N
LEU
43
A
N
LEU
36
A
O
GLU
40
A
O
GLU
33
A
N
ARG
33
A
N
ARG
26
A
N
TYR
24
A
N
TYR
17
P
O
ALA
7
B
O
ALA
7
P
O
THR
6
B
O
THR
6
A
N
ASP
62
A
N
ASP
55
1
A
HOH
146
C
HOH
1
A
CG
ASN
59
A
CG
ASN
52
0
Y
1
A
OD1
ASN
59
A
OD1
ASN
52
0
Y
1
A
ND2
ASN
59
A
ND2
ASN
52
0
Y
1
A
MET
8
A
MET
1
1
Y
1
A
LYS
9
A
LYS
2
1
Y
1
A
LYS
10
A
LYS
3
1
Y
1
A
HIS
11
A
HIS
4
1
Y
1
A
HIS
12
A
HIS
5
1
Y
1
A
HIS
13
A
HIS
6
1
Y
1
A
HIS
14
A
HIS
7
1
Y
1
A
HIS
15
A
HIS
8
1
Y
1
A
HIS
16
A
HIS
9
1
Y
1
A
ALA
17
A
ALA
10
1
Y
1
A
GLU
18
A
GLU
11
1
Y
1
A
GLU
19
A
GLU
12
1
Y
1
A
GLU
20
A
GLU
13
1
Y
1
A
GLU
21
A
GLU
14
1
Y
1
A
GLU
22
A
GLU
15
1
Y
1
A
LYS
75
A
LYS
68
1
Y
1
A
ASP
76
A
ASP
69
1
Y
1
P
ALA
1
B
ALA
1
1
Y
1
P
ARG
2
B
ARG
2
1
Y
1
P
THR
3
B
THR
3
1
Y
1
P
LYS
4
B
LYS
4
1
Y
1
P
THR
11
B
THR
11
1
Y
1
P
GLY
12
B
GLY
12
1
Y
1
P
GLY
13
B
GLY
13
1
Y
1
P
LYS
14
B
LYS
14
1
Y
1
P
ALA
15
B
ALA
15
1
Y
1
P
TYR
16
B
TYR
16
1
Y
1
A
A
O
O
HOH
HOH
147
147
1.27
1_555
3_555
1
A
A
OG
OG
SER
SER
73
73
1.74
1_555
4_565
26.3
5.6
-3.48
-2.11
0.00
0.00
0.00
0.259
0.026
0.228
2.10
28.63
654
6008
5354
10.90
99.80
RANDOM
117307.12
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
Engh & Huber
0.32
0.26
5.00
0.19
0.16
2.10
28.63
86
585
0
0
499
0.005
1.2
22.8
0.59
0.281
0.026
0.245
2.23
116
842
6
12.1
99.30
14.8
2.10
30.0
1KNA
6032
6032
2.0
0.0
0.079
1
61.6
20.1
99.8
2.10
2.23
10.5
842
0.279
99.3
data reduction
DENZO
data reduction
TRUNCATE
refinement
CNS
data scaling
CCP4
(TRUNCATE)
phasing
CNS
Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
1
N
N
2
N
N
3
N
N
3
N
N
A
PRO
49
A
PRO
42
HELX_P
A
ASN
53
A
ASN
46
5
1
5
A
CYS
63
A
CYS
56
HELX_P
A
ARG
74
A
ARG
67
1
2
12
covale
1.325
both
P
ARG
8
B
C
ARG
8
1_555
P
MLY
9
B
N
MLY
9
1_555
covale
1.329
both
P
MLY
9
B
C
MLY
9
1_555
P
SER
10
B
N
SER
10
1_555
STRUCTURAL PROTEIN
chromo, HP1, histone, dimethyllysine, methyllysine, H3, STRUCTURAL PROTEIN
HP1_DROME
UNP
1
17
P05205
AEEEEEEYAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD
H3_DROME
UNP
2
1
P02299
ARTKQTARKSTGGKAP
17
76
1KNA
8
76
P05205
A
1
1
69
1
16
1KNA
1
16
P02299
P
2
1
16
1
engineered mutation
MET
8
1KNA
A
P05205
UNP
8
1
1
engineered mutation
LYS
9
1KNA
A
P05205
UNP
9
2
1
engineered mutation
LYS
10
1KNA
A
P05205
UNP
10
3
1
expression tag
HIS
11
1KNA
A
P05205
UNP
11
4
1
expression tag
HIS
12
1KNA
A
P05205
UNP
12
5
1
expression tag
HIS
13
1KNA
A
P05205
UNP
13
6
1
expression tag
HIS
14
1KNA
A
P05205
UNP
14
7
1
expression tag
HIS
15
1KNA
A
P05205
UNP
15
8
1
expression tag
HIS
16
1KNA
A
P05205
UNP
16
9
1
LYS
engineered mutation
MET
38
1KNA
A
P05205
UNP
38
31
2
LYS
modified residue
MLY
9
1KNA
P
P02299
UNP
9
9
2
PRO
engineered mutation
TYR
16
1KNA
P
P02299
UNP
16
16
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
54
A
THR
47
A
PRO
57
A
PRO
50
A
MET
38
A
MET
31
A
TRP
45
A
TRP
38
A
TYR
24
A
TYR
17
A
ARG
35
A
ARG
28
P
THR
6
B
THR
6
P
ALA
7
B
ALA
7
A
LEU
61
A
LEU
54
A
ASP
62
A
ASP
55
20
C 2 2 21