1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kwan, A.H.Y.
Gell, D.A.
Verger, A.
Crossley, M.
Matthews, J.M.
Mackay, J.P.
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 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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
UK
structure
STRUE6
2005
0969-2126
11
803
813
10.1016/S0969-2126(03)00122-9
12842043
Engineering a Protein Scaffold from a PHD Finger
2003
10.2210/pdb1mm2/pdb
pdb_00001mm2
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
6689.790
Mi2-beta
Mi2-beta (residues 446-501)
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
Chromodomain helicase-DNA-binding protein 4
no
no
GPLGSDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK
GPLGSDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK
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
human
Homo
Escherichia
Escherichia coli
sample
CHD4
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PLASMID
pGEX-6P
database_2
pdbx_nmr_software
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
Data collection
Database references
Derived calculations
1
0
2003-07-22
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_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.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
1FP0 contains PHD domain from KAP-1
1F62 contains PHD domain from WSTF
1MM3 contains the 2nd PHD domain from Mi2b with C-terminal loop replaced by corresponding loop from WSTF
RCSB
Y
PDBJ
2002-09-02
REL
REL
ZN
ZINC ION
This structure was determined mostly using standard 2D homonuclear techniques
structures with the lowest energy
500
20
2D NOESY
2D TOCSY
DQF-COSY
N15-HSQC
7.5
ambient
298
K
Structure calculations were performed using the package ARIA1.1 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 1284 unambiguous NOE-derived distance constraints, 8 sets of ambiguous NOE-derived distance constraints and 39 additional dihedral angle restraints.
simulated annealing, molecular dynamics, torsion angle dynamics
1
lowest energy
1mM Mi2-PHD2 protein, 1mM DTT, 10mM sodium phosphate buffer (pH 7.5), 150mM NaCl, 95% H2O, 5% D2O
95% H2O/5% D2O
0.2mM N15-labelled Mi2-PHD2 protein, 1mM DTT, 10mM sodium phosphate buffer (pH 7.5), 150mM NaCl, 95% H2O, 5% D2O
95% H2O/5% D2O
Bruker
processing
XwinNMR
2.5
Bartels et al
data analysis
XEASY
1.3.13
Guntert et al
refinement
DYANA
1.5
Linge et al
structure solution
ARIA
1.1.2
600
Bruker
DRX
ZN
62
2
ZN
ZN
62
A
ZN
63
2
ZN
ZN
63
A
GLY
1
n
1
GLY
1
A
PRO
2
n
2
PRO
2
A
LEU
3
n
3
LEU
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
ASP
6
n
6
ASP
6
A
HIS
7
n
7
HIS
7
A
HIS
8
n
8
HIS
8
A
MET
9
n
9
MET
9
A
GLU
10
n
10
GLU
10
A
PHE
11
n
11
PHE
11
A
CYS
12
n
12
CYS
12
A
ARG
13
n
13
ARG
13
A
VAL
14
n
14
VAL
14
A
CYS
15
n
15
CYS
15
A
LYS
16
n
16
LYS
16
A
ASP
17
n
17
ASP
17
A
GLY
18
n
18
GLY
18
A
GLY
19
n
19
GLY
19
A
GLU
20
n
20
GLU
20
A
LEU
21
n
21
LEU
21
A
LEU
22
n
22
LEU
22
A
CYS
23
n
23
CYS
23
A
CYS
24
n
24
CYS
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
CYS
27
n
27
CYS
27
A
PRO
28
n
28
PRO
28
A
SER
29
n
29
SER
29
A
SER
30
n
30
SER
30
A
TYR
31
n
31
TYR
31
A
HIS
32
n
32
HIS
32
A
ILE
33
n
33
ILE
33
A
HIS
34
n
34
HIS
34
A
CYS
35
n
35
CYS
35
A
LEU
36
n
36
LEU
36
A
ASN
37
n
37
ASN
37
A
PRO
38
n
38
PRO
38
A
PRO
39
n
39
PRO
39
A
LEU
40
n
40
LEU
40
A
PRO
41
n
41
PRO
41
A
GLU
42
n
42
GLU
42
A
ILE
43
n
43
ILE
43
A
PRO
44
n
44
PRO
44
A
ASN
45
n
45
ASN
45
A
GLY
46
n
46
GLY
46
A
GLU
47
n
47
GLU
47
A
TRP
48
n
48
TRP
48
A
LEU
49
n
49
LEU
49
A
CYS
50
n
50
CYS
50
A
PRO
51
n
51
PRO
51
A
ARG
52
n
52
ARG
52
A
CYS
53
n
53
CYS
53
A
THR
54
n
54
THR
54
A
CYS
55
n
55
CYS
55
A
PRO
56
n
56
PRO
56
A
ALA
57
n
57
ALA
57
A
LEU
58
n
58
LEU
58
A
LYS
59
n
59
LYS
59
A
GLY
60
n
60
GLY
60
A
LYS
61
n
61
LYS
61
A
author_defined_assembly
1
monomeric
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
63
C
ZN
ZN
1_555
A
CYS
15
A
SG
CYS
15
1_555
108.5
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
63
C
ZN
ZN
1_555
A
HIS
32
A
ND1
HIS
32
1_555
109.0
A
CYS
15
A
SG
CYS
15
1_555
A
ZN
63
C
ZN
ZN
1_555
A
HIS
32
A
ND1
HIS
32
1_555
108.5
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
63
C
ZN
ZN
1_555
A
CYS
35
A
SG
CYS
35
1_555
111.3
A
CYS
15
A
SG
CYS
15
1_555
A
ZN
63
C
ZN
ZN
1_555
A
CYS
35
A
SG
CYS
35
1_555
109.4
A
HIS
32
A
ND1
HIS
32
1_555
A
ZN
63
C
ZN
ZN
1_555
A
CYS
35
A
SG
CYS
35
1_555
110.1
A
CYS
24
A
SG
CYS
24
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
27
A
SG
CYS
27
1_555
109.3
A
CYS
24
A
SG
CYS
24
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
50
A
SG
CYS
50
1_555
111.8
A
CYS
27
A
SG
CYS
27
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
50
A
SG
CYS
50
1_555
108.8
A
CYS
24
A
SG
CYS
24
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
53
A
SG
CYS
53
1_555
109.4
A
CYS
27
A
SG
CYS
27
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
53
A
SG
CYS
53
1_555
107.8
A
CYS
50
A
SG
CYS
50
1_555
A
ZN
62
B
ZN
ZN
1_555
A
CYS
53
A
SG
CYS
53
1_555
109.6
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
1
A
A
HG
ZN
CYS
ZN
12
63
1.06
1
A
A
HB2
HB3
CYS
CYS
24
50
1.28
1
A
A
HB2
HB3
ARG
LEU
52
58
1.30
2
A
A
HG
ZN
CYS
ZN
12
63
1.40
4
A
A
HG
ZN
CYS
ZN
12
63
1.06
5
A
A
HB2
HB3
CYS
CYS
24
50
1.34
6
A
A
HB2
HE
CYS
ARG
50
52
1.33
7
A
A
HG
ZN
CYS
ZN
12
63
1.26
8
A
A
HG
ZN
CYS
ZN
12
63
1.12
9
A
A
HG
ZN
CYS
ZN
12
63
1.06
11
A
A
HG
ZN
CYS
ZN
12
63
1.20
13
A
A
HG
ZN
CYS
ZN
12
63
1.13
16
A
A
HG
ZN
CYS
ZN
12
63
1.08
16
A
A
HD2
HH2
TYR
TRP
31
48
1.29
18
A
A
HG
ZN
CYS
ZN
12
63
1.15
18
A
A
HB2
HE
CYS
ARG
50
52
1.19
18
A
A
HD2
HH2
TYR
TRP
31
48
1.31
19
A
A
HG
ZN
CYS
ZN
12
63
1.02
19
A
A
HB2
HB3
CYS
CYS
24
50
1.23
19
A
A
HB2
H
HIS
HIS
7
8
1.35
20
A
A
HG
ZN
CYS
ZN
12
63
1.36
1
A
ASP
6
-171.67
-169.78
1
A
HIS
8
62.66
-131.40
1
A
VAL
14
-99.88
-62.07
1
A
PRO
28
-75.32
38.18
1
A
TYR
31
-117.20
-146.52
1
A
PRO
51
-69.91
10.41
1
A
PRO
56
-79.17
44.18
1
A
ALA
57
-162.72
-163.65
2
A
ASP
6
-89.40
-132.89
2
A
THR
26
-106.08
-61.58
2
A
TYR
31
-127.33
-161.51
2
A
HIS
32
-123.07
-130.25
2
A
HIS
34
-143.46
-3.14
2
A
CYS
50
-48.51
159.85
2
A
ALA
57
-109.16
46.33
3
A
PRO
28
-81.56
40.79
3
A
TYR
31
-131.44
-153.43
3
A
LEU
36
-125.72
-166.57
3
A
CYS
50
-46.92
159.32
3
A
PRO
51
-66.30
34.57
3
A
ARG
52
-141.75
-47.18
3
A
CYS
55
53.30
71.41
4
A
LEU
3
67.95
-74.55
4
A
SER
5
-95.65
48.98
4
A
CYS
12
48.16
-109.06
4
A
ARG
13
-179.06
-55.00
4
A
ASP
17
168.31
-138.72
4
A
HIS
32
-128.96
-125.08
4
A
LYS
59
-165.27
106.75
5
A
HIS
7
70.34
-67.36
5
A
PRO
28
-82.46
34.29
5
A
TYR
31
-130.87
-152.95
5
A
HIS
32
-134.38
-138.17
5
A
PRO
51
-66.99
13.76
5
A
ALA
57
-143.73
32.93
5
A
LYS
59
-147.06
29.54
6
A
HIS
8
68.68
-102.30
6
A
PRO
28
-88.22
48.33
6
A
TYR
31
-133.35
-159.64
6
A
LEU
36
-118.13
-166.21
6
A
PRO
51
-66.46
42.25
6
A
ARG
52
-151.29
-29.79
6
A
CYS
55
74.22
146.22
7
A
SER
5
-95.45
-68.51
7
A
HIS
8
62.79
-120.07
7
A
VAL
14
-138.22
-47.92
7
A
TYR
31
-128.80
-162.10
7
A
GLU
47
-99.73
59.98
7
A
PRO
51
-68.03
16.02
8
A
LEU
3
64.58
-164.88
8
A
SER
5
-140.79
-45.95
8
A
ASP
6
-172.79
-138.85
8
A
HIS
8
70.93
-175.84
8
A
THR
26
-121.57
-54.00
8
A
PRO
28
-78.36
48.42
8
A
TYR
31
-124.87
-156.15
8
A
LEU
36
-123.32
-166.45
8
A
THR
54
-63.25
-78.42
9
A
SER
5
-85.14
-76.91
9
A
ASP
6
-150.99
-91.63
9
A
HIS
8
55.97
-129.79
9
A
VAL
14
-103.51
-65.92
9
A
PRO
28
-74.87
38.26
9
A
TYR
31
-117.02
-152.41
9
A
HIS
32
-129.77
-160.46
9
A
CYS
50
-40.36
158.63
10
A
HIS
7
-152.07
-44.52
10
A
HIS
8
50.39
-137.46
10
A
THR
26
-120.93
-63.77
10
A
PRO
28
-96.36
30.84
10
A
LEU
36
-116.06
-158.54
10
A
PRO
51
-67.57
37.95
10
A
ARG
52
-146.66
-45.17
10
A
THR
54
-65.06
74.31
10
A
CYS
55
-175.90
133.22
11
A
ASP
6
-115.16
-148.78
11
A
HIS
7
61.26
-136.77
11
A
VAL
14
-144.36
-49.55
11
A
LYS
16
75.14
-0.97
11
A
THR
26
-124.48
-52.52
11
A
TYR
31
-125.70
-161.52
11
A
HIS
32
-134.35
-146.28
11
A
PRO
44
-67.38
93.97
11
A
PRO
51
-70.46
34.87
11
A
ARG
52
-140.38
-48.66
11
A
CYS
55
-160.92
85.99
11
A
LEU
58
-121.50
-51.39
11
A
LYS
59
-146.17
54.44
12
A
HIS
7
-147.62
11.14
12
A
PRO
28
-92.32
32.51
12
A
HIS
32
-126.07
-133.30
12
A
CYS
55
65.24
101.36
12
A
PRO
56
-66.83
-76.01
13
A
HIS
7
-167.47
-55.23
13
A
PRO
28
-89.03
33.06
13
A
TYR
31
-127.04
-154.31
13
A
LEU
36
-105.69
-164.16
13
A
LEU
49
69.08
130.39
14
A
TYR
31
-129.23
-155.33
14
A
CYS
50
-42.00
155.07
15
A
LEU
3
69.83
-69.68
15
A
ASP
6
-119.80
-72.72
15
A
HIS
7
56.05
-110.71
15
A
PRO
28
-95.27
40.47
15
A
TYR
31
-129.72
-166.51
15
A
HIS
32
-120.59
-127.73
15
A
PRO
51
-70.23
33.57
15
A
ARG
52
-137.56
-36.29
15
A
CYS
55
73.79
114.38
16
A
ASP
6
-96.19
-60.08
16
A
HIS
7
65.06
97.60
16
A
HIS
8
63.58
-124.64
16
A
ARG
13
-75.49
46.81
16
A
VAL
14
-136.63
-33.10
16
A
PRO
28
-78.51
39.62
16
A
TYR
31
-125.07
-154.01
16
A
LEU
36
-150.06
-67.18
16
A
CYS
50
-47.44
162.28
16
A
ALA
57
-104.34
63.23
16
A
LYS
59
69.37
-170.90
17
A
HIS
8
62.38
-99.74
17
A
ASP
17
-166.99
-154.64
17
A
TYR
31
-128.78
-152.23
17
A
HIS
32
-143.66
-157.03
17
A
LEU
36
-126.34
-157.81
18
A
SER
5
71.05
-50.17
18
A
VAL
14
-79.59
-73.16
18
A
TYR
31
-126.67
-159.06
18
A
PRO
51
-66.48
50.33
18
A
ARG
52
-166.21
-22.03
18
A
PRO
56
-50.12
109.30
19
A
HIS
7
-86.66
-124.89
19
A
HIS
8
69.46
-100.87
19
A
PHE
11
-124.15
-74.30
19
A
CYS
12
159.35
138.39
19
A
TYR
31
-126.01
-155.99
19
A
HIS
32
-128.67
-129.75
19
A
LEU
58
74.10
-45.81
19
A
LYS
59
69.65
-66.79
20
A
ASP
6
-167.88
-149.40
20
A
CYS
12
-62.86
-79.19
20
A
ARG
13
179.24
-48.88
20
A
THR
26
-122.45
-53.46
20
A
HIS
32
-126.77
-121.53
20
A
HIS
34
-155.92
8.32
20
A
CYS
50
-49.62
161.56
20
A
PRO
51
-66.86
39.42
20
A
ARG
52
-149.67
-39.02
Solution structure of the 2nd PHD domain from Mi2b
1
N
N
2
N
N
2
N
N
metalc
2.241
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
63
C
ZN
ZN
1_555
metalc
2.287
A
CYS
15
A
SG
CYS
15
1_555
A
ZN
63
C
ZN
ZN
1_555
metalc
2.318
A
CYS
24
A
SG
CYS
24
1_555
A
ZN
62
B
ZN
ZN
1_555
metalc
2.272
A
CYS
27
A
SG
CYS
27
1_555
A
ZN
62
B
ZN
ZN
1_555
metalc
1.961
A
HIS
32
A
ND1
HIS
32
1_555
A
ZN
63
C
ZN
ZN
1_555
metalc
2.327
A
CYS
35
A
SG
CYS
35
1_555
A
ZN
63
C
ZN
ZN
1_555
metalc
2.287
A
CYS
50
A
SG
CYS
50
1_555
A
ZN
62
B
ZN
ZN
1_555
metalc
2.279
A
CYS
53
A
SG
CYS
53
1_555
A
ZN
62
B
ZN
ZN
1_555
DNA BINDING PROTEIN
PHD, zinc finger, protein scaffold, DNA binding protein
CHD4_HUMAN
UNP
1
446
Q14839
DHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK
446
501
1MM2
6
61
Q14839
A
1
6
61
1
cloning artifact
GLY
1
1MM2
A
Q14839
UNP
1
1
cloning artifact
PRO
2
1MM2
A
Q14839
UNP
2
1
cloning artifact
LEU
3
1MM2
A
Q14839
UNP
3
1
cloning artifact
GLY
4
1MM2
A
Q14839
UNP
4
1
cloning artifact
SER
5
1MM2
A
Q14839
UNP
5
BINDING SITE FOR RESIDUE ZN A 62
A
ZN
62
Software
4
BINDING SITE FOR RESIDUE ZN A 63
A
ZN
63
Software
4
A
CYS
24
A
CYS
24
4
1_555
A
CYS
27
A
CYS
27
4
1_555
A
CYS
50
A
CYS
50
4
1_555
A
CYS
53
A
CYS
53
4
1_555
A
CYS
12
A
CYS
12
4
1_555
A
CYS
15
A
CYS
15
4
1_555
A
HIS
32
A
HIS
32
4
1_555
A
CYS
35
A
CYS
35
4
1_555