1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Capili, A.D.
Schultz, D.C.
Rauscher III, F.J.
Borden, K.L.B.
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
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
UK
EMBO J.
EMJODG
0897
0261-4189
20
165
177
10.1093/emboj/20.1.165
11226167
Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
2001
10.2210/pdb1fp0/pdb
pdb_00001fp0
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9939.204
KAP-1 COREPRESSOR
PHD DOMAIN
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA, NUCLEAR COREPRESSOR, KAP-1, KRAB-ASSOCIATED PROTEIN 1
no
no
MRGSHHHHHHGSDIIDEFGTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDV
DLQACKLN
MRGSHHHHHHGSDIIDEFGTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDV
DLQACKLN
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
PLASMID
PQE50
database_2
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2001-01-24
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2000-08-29
REL
ZN
ZINC ION
First 17 residues (MRGSHHHHHHGSDIIDE) and last 9 residues (VDLQACKLN)
do not belong to the natural protein molecule, residues 618 to 679
corresponds to KAP-1, structured region corresponds to residues
627-670 which contain the PHD domain
1
7.50
AMBIENT
303
K
distance geometry and simulated annealing
1
closest to the average
1.5-3.0 mM 15N-labelled or unlabelled KAP-1 PHD,
20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5
90% H2O/10% D2O
1.5-3.0 mM unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5
100% D2O
Brunger
refinement
X-PLOR
3.851
500
Bruker
DRX
ZN
89
2
ZN
ZN
89
A
ZN
90
2
ZN
ZN
90
A
MET
1
n
1
MET
1
A
ARG
2
n
2
ARG
2
A
GLY
3
n
3
GLY
3
A
SER
4
n
4
SER
4
A
HIS
5
n
5
HIS
5
A
HIS
6
n
6
HIS
6
A
HIS
7
n
7
HIS
7
A
HIS
8
n
8
HIS
8
A
HIS
9
n
9
HIS
9
A
HIS
10
n
10
HIS
10
A
GLY
11
n
11
GLY
11
A
SER
12
n
12
SER
12
A
ASP
13
n
13
ASP
13
A
ILE
14
n
14
ILE
14
A
ILE
15
n
15
ILE
15
A
ASP
16
n
16
ASP
16
A
GLU
17
n
17
GLU
17
A
PHE
18
n
18
PHE
18
A
GLY
19
n
19
GLY
19
A
THR
20
n
20
THR
20
A
LEU
21
n
21
LEU
21
A
ASP
22
n
22
ASP
22
A
ASP
23
n
23
ASP
23
A
SER
24
n
24
SER
24
A
ALA
25
n
25
ALA
25
A
THR
26
n
26
THR
26
A
ILE
27
n
27
ILE
27
A
CYS
28
n
28
CYS
28
A
ARG
29
n
29
ARG
29
A
VAL
30
n
30
VAL
30
A
CYS
31
n
31
CYS
31
A
GLN
32
n
32
GLN
32
A
LYS
33
n
33
LYS
33
A
PRO
34
n
34
PRO
34
A
GLY
35
n
35
GLY
35
A
ASP
36
n
36
ASP
36
A
LEU
37
n
37
LEU
37
A
VAL
38
n
38
VAL
38
A
MET
39
n
39
MET
39
A
CYS
40
n
40
CYS
40
A
ASN
41
n
41
ASN
41
A
GLN
42
n
42
GLN
42
A
CYS
43
n
43
CYS
43
A
GLU
44
n
44
GLU
44
A
PHE
45
n
45
PHE
45
A
CYS
46
n
46
CYS
46
A
PHE
47
n
47
PHE
47
A
HIS
48
n
48
HIS
48
A
LEU
49
n
49
LEU
49
A
ASP
50
n
50
ASP
50
A
CYS
51
n
51
CYS
51
A
HIS
52
n
52
HIS
52
A
LEU
53
n
53
LEU
53
A
PRO
54
n
54
PRO
54
A
ALA
55
n
55
ALA
55
A
LEU
56
n
56
LEU
56
A
GLN
57
n
57
GLN
57
A
ASP
58
n
58
ASP
58
A
VAL
59
n
59
VAL
59
A
PRO
60
n
60
PRO
60
A
GLY
61
n
61
GLY
61
A
GLU
62
n
62
GLU
62
A
GLU
63
n
63
GLU
63
A
TRP
64
n
64
TRP
64
A
SER
65
n
65
SER
65
A
CYS
66
n
66
CYS
66
A
SER
67
n
67
SER
67
A
LEU
68
n
68
LEU
68
A
CYS
69
n
69
CYS
69
A
HIS
70
n
70
HIS
70
A
VAL
71
n
71
VAL
71
A
LEU
72
n
72
LEU
72
A
PRO
73
n
73
PRO
73
A
ASP
74
n
74
ASP
74
A
LEU
75
n
75
LEU
75
A
LYS
76
n
76
LYS
76
A
GLU
77
n
77
GLU
77
A
GLU
78
n
78
GLU
78
A
ASP
79
n
79
ASP
79
A
VAL
80
n
80
VAL
80
A
ASP
81
n
81
ASP
81
A
LEU
82
n
82
LEU
82
A
GLN
83
n
83
GLN
83
A
ALA
84
n
84
ALA
84
A
CYS
85
n
85
CYS
85
A
LYS
86
n
86
LYS
86
A
LEU
87
n
87
LEU
87
A
ASN
88
n
88
ASN
88
A
author_defined_assembly
1
monomeric
A
CYS
28
A
SG
CYS
28
1_555
A
ZN
90
C
ZN
ZN
1_555
A
CYS
31
A
SG
CYS
31
1_555
112.0
A
CYS
28
A
SG
CYS
28
1_555
A
ZN
90
C
ZN
ZN
1_555
A
HIS
48
A
ND1
HIS
48
1_555
109.9
A
CYS
31
A
SG
CYS
31
1_555
A
ZN
90
C
ZN
ZN
1_555
A
HIS
48
A
ND1
HIS
48
1_555
108.3
A
CYS
28
A
SG
CYS
28
1_555
A
ZN
90
C
ZN
ZN
1_555
A
CYS
51
A
SG
CYS
51
1_555
110.9
A
CYS
31
A
SG
CYS
31
1_555
A
ZN
90
C
ZN
ZN
1_555
A
CYS
51
A
SG
CYS
51
1_555
108.6
A
HIS
48
A
ND1
HIS
48
1_555
A
ZN
90
C
ZN
ZN
1_555
A
CYS
51
A
SG
CYS
51
1_555
107.0
A
CYS
40
A
SG
CYS
40
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
106.4
A
CYS
40
A
SG
CYS
40
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
66
A
SG
CYS
66
1_555
111.0
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
66
A
SG
CYS
66
1_555
110.2
A
CYS
40
A
SG
CYS
40
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
69
A
SG
CYS
69
1_555
109.5
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
69
A
SG
CYS
69
1_555
109.1
A
CYS
66
A
SG
CYS
66
1_555
A
ZN
89
B
ZN
ZN
1_555
A
CYS
69
A
SG
CYS
69
1_555
110.6
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
VAL
38
A
O
VAL
38
A
N
PHE
47
A
N
PHE
47
1
A
A
O
H
LEU
ALA
53
55
1.53
1
A
ARG
2
0.279
SIDE CHAIN
1
A
ARG
29
0.317
SIDE CHAIN
1
A
SER
4
-163.05
30.42
1
A
HIS
8
55.89
175.68
1
A
HIS
9
-146.37
-143.53
1
A
HIS
10
-41.93
-82.44
1
A
ASP
13
178.08
-50.47
1
A
ILE
14
80.02
-24.91
1
A
ILE
15
57.47
121.06
1
A
THR
20
38.56
34.63
1
A
LEU
21
-139.57
-71.38
1
A
ASP
22
-81.86
-150.67
1
A
ASP
23
55.51
19.81
1
A
SER
24
178.03
178.38
1
A
ALA
25
70.64
-135.38
1
A
THR
26
-39.89
170.30
1
A
CYS
31
-160.21
-41.12
1
A
LYS
33
-140.88
-66.55
1
A
ASP
36
44.28
104.18
1
A
LEU
37
-168.35
105.86
1
A
ASN
41
-69.34
5.58
1
A
CYS
43
-153.92
-84.51
1
A
GLU
44
-175.95
33.37
1
A
PHE
47
-139.06
-157.40
1
A
LEU
49
-69.49
9.08
1
A
HIS
52
-88.79
-87.31
1
A
PRO
54
-63.22
63.90
1
A
ALA
55
177.18
42.52
1
A
GLU
62
58.73
-108.90
1
A
GLU
63
-99.66
-151.36
1
A
TRP
64
-74.91
-102.24
1
A
SER
65
172.62
37.42
1
A
CYS
66
57.50
163.62
1
A
SER
67
-135.06
-141.70
1
A
VAL
71
-111.23
52.71
1
A
CYS
85
-59.14
-144.70
SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR
1
N
N
2
N
N
2
N
N
metalc
2.344
A
CYS
28
A
SG
CYS
28
1_555
A
ZN
90
C
ZN
ZN
1_555
metalc
2.312
A
CYS
31
A
SG
CYS
31
1_555
A
ZN
90
C
ZN
ZN
1_555
metalc
2.276
A
CYS
40
A
SG
CYS
40
1_555
A
ZN
89
B
ZN
ZN
1_555
metalc
2.297
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
89
B
ZN
ZN
1_555
metalc
1.977
A
HIS
48
A
ND1
HIS
48
1_555
A
ZN
90
C
ZN
ZN
1_555
metalc
2.293
A
CYS
51
A
SG
CYS
51
1_555
A
ZN
90
C
ZN
ZN
1_555
metalc
2.317
A
CYS
66
A
SG
CYS
66
1_555
A
ZN
89
B
ZN
ZN
1_555
metalc
2.299
A
CYS
69
A
SG
CYS
69
1_555
A
ZN
89
B
ZN
ZN
1_555
TRANSCRIPTION
PHD domain, C3HC4 type zinc binding domain, NMR-structure, TRANSCRIPTION
TIF1B_HUMAN
UNP
1
619
Q13263
GTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEED
619
679
1FP0
19
79
Q13263
A
1
19
79
1
expression tag
MET
1
1FP0
A
Q13263
UNP
1
1
expression tag
ARG
2
1FP0
A
Q13263
UNP
2
1
expression tag
GLY
3
1FP0
A
Q13263
UNP
3
1
expression tag
SER
4
1FP0
A
Q13263
UNP
4
1
expression tag
HIS
5
1FP0
A
Q13263
UNP
5
1
expression tag
HIS
6
1FP0
A
Q13263
UNP
6
1
expression tag
HIS
7
1FP0
A
Q13263
UNP
7
1
expression tag
HIS
8
1FP0
A
Q13263
UNP
8
1
expression tag
HIS
9
1FP0
A
Q13263
UNP
9
1
expression tag
HIS
10
1FP0
A
Q13263
UNP
10
1
expression tag
GLY
11
1FP0
A
Q13263
UNP
11
1
expression tag
SER
12
1FP0
A
Q13263
UNP
12
1
expression tag
ASP
13
1FP0
A
Q13263
UNP
13
1
expression tag
ILE
14
1FP0
A
Q13263
UNP
14
1
expression tag
ILE
15
1FP0
A
Q13263
UNP
15
1
expression tag
ASP
16
1FP0
A
Q13263
UNP
16
1
expression tag
GLU
17
1FP0
A
Q13263
UNP
17
1
expression tag
PHE
18
1FP0
A
Q13263
UNP
18
1
cloning artifact
VAL
80
1FP0
A
Q13263
UNP
80
1
cloning artifact
ASP
81
1FP0
A
Q13263
UNP
81
1
cloning artifact
LEU
82
1FP0
A
Q13263
UNP
82
1
cloning artifact
GLN
83
1FP0
A
Q13263
UNP
83
1
cloning artifact
ALA
84
1FP0
A
Q13263
UNP
84
1
cloning artifact
CYS
85
1FP0
A
Q13263
UNP
85
1
cloning artifact
LYS
86
1FP0
A
Q13263
UNP
86
1
cloning artifact
LEU
87
1FP0
A
Q13263
UNP
87
1
cloning artifact
ASN
88
1FP0
A
Q13263
UNP
88
3
anti-parallel
A
VAL
38
A
VAL
38
A
CYS
40
A
CYS
40
A
PHE
45
A
PHE
45
A
PHE
47
A
PHE
47
A
TRP
64
A
TRP
64
A
SER
67
A
SER
67
BINDING SITE FOR RESIDUE ZN A 89
A
ZN
89
Software
5
BINDING SITE FOR RESIDUE ZN A 90
A
ZN
90
Software
6
A
CYS
40
A
CYS
40
5
1_555
A
GLN
42
A
GLN
42
5
1_555
A
CYS
43
A
CYS
43
5
1_555
A
CYS
66
A
CYS
66
5
1_555
A
CYS
69
A
CYS
69
5
1_555
A
CYS
28
A
CYS
28
6
1_555
A
VAL
30
A
VAL
30
6
1_555
A
CYS
31
A
CYS
31
6
1_555
A
PHE
47
A
PHE
47
6
1_555
A
HIS
48
A
HIS
48
6
1_555
A
CYS
51
A
CYS
51
6
1_555
1
P 1