1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Song, J.
Patel, D.J.
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 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 H21 N2 O2 1
189.275
n
N-TRIMETHYLLYSINE
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
Mol.Cell
MOCEFL
2168
1097-2765
49
571
582
10.1016/j.molcel.2012.11.026
23273982
An H3K36 Methylation-Engaging Tudor Motif of Polycomb-like Proteins Mediates PRC2 Complex Targeting.
2013
8737.847
PHD finger protein 1
1
man
polymer
1259.500
H3K36me3 peptide
1
syn
polymer
Protein PHF1, Polycomb-like protein 1, hPCl1
no
no
SRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
SRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
A
polypeptide(L)
no
yes
ATGGV(M3L)KPHRY
ATGGVKKPHRY
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
human
sample
PHF1, PCL1
9606
Homo sapiens
562
Escherichia coli
plasmid
PRSF-Duet
repository
Initial release
Database references
1
0
2013-01-16
1
1
2013-02-27
BMRB
Y
RCSB
2012-10-30
REL
REL
REL
structures with the lowest energy
100
20
3D 1H-13C NOESY aliphatic
3D 1H-13C NOESY aromatic
2D 1H-15N HSQC
3D HNCACB
3D HBHA(CO)NH
3D CBCA(CO)NH
3D HCCH-TOCSY
2D 1H-1H NOESY
3D 1H-15N NOESY
0.3-0.5
mM
[U-100% 13C; U-100% 15N]
0.6-1.0
mM
50
7.0
ambient
298
K
simulated annealing, molecular dynamics
1
lowest energy
0.3-0.5 mM [U-100% 13C; U-100% 15N] PHF1 tudor, 0.6-1.0 mM H3K36me3 peptide, 90% H2O/10% D2O
90% H2O/10% D2O
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR_NIH
900
Bruker
DMX
Bruker DMX
700
Bruker
DMX
Bruker DMX
600
Bruker
DMX
Bruker DMX
SER
5
n
1
SER
5
A
ARG
6
n
2
ARG
6
A
LEU
7
n
3
LEU
7
A
SER
8
n
4
SER
8
A
ARG
9
n
5
ARG
9
A
SER
10
n
6
SER
10
A
GLY
11
n
7
GLY
11
A
ALA
12
n
8
ALA
12
A
SER
13
n
9
SER
13
A
SER
14
n
10
SER
14
A
LEU
15
n
11
LEU
15
A
TRP
16
n
12
TRP
16
A
ASP
17
n
13
ASP
17
A
PRO
18
n
14
PRO
18
A
ALA
19
n
15
ALA
19
A
SER
20
n
16
SER
20
A
PRO
21
n
17
PRO
21
A
ALA
22
n
18
ALA
22
A
PRO
23
n
19
PRO
23
A
THR
24
n
20
THR
24
A
SER
25
n
21
SER
25
A
GLY
26
n
22
GLY
26
A
PRO
27
n
23
PRO
27
A
ARG
28
n
24
ARG
28
A
PRO
29
n
25
PRO
29
A
ARG
30
n
26
ARG
30
A
LEU
31
n
27
LEU
31
A
TRP
32
n
28
TRP
32
A
GLU
33
n
29
GLU
33
A
GLY
34
n
30
GLY
34
A
GLN
35
n
31
GLN
35
A
ASP
36
n
32
ASP
36
A
VAL
37
n
33
VAL
37
A
LEU
38
n
34
LEU
38
A
ALA
39
n
35
ALA
39
A
ARG
40
n
36
ARG
40
A
TRP
41
n
37
TRP
41
A
THR
42
n
38
THR
42
A
ASP
43
n
39
ASP
43
A
GLY
44
n
40
GLY
44
A
LEU
45
n
41
LEU
45
A
LEU
46
n
42
LEU
46
A
TYR
47
n
43
TYR
47
A
LEU
48
n
44
LEU
48
A
GLY
49
n
45
GLY
49
A
THR
50
n
46
THR
50
A
ILE
51
n
47
ILE
51
A
LYS
52
n
48
LYS
52
A
LYS
53
n
49
LYS
53
A
VAL
54
n
50
VAL
54
A
ASP
55
n
51
ASP
55
A
SER
56
n
52
SER
56
A
ALA
57
n
53
ALA
57
A
ARG
58
n
54
ARG
58
A
GLU
59
n
55
GLU
59
A
VAL
60
n
56
VAL
60
A
CYS
61
n
57
CYS
61
A
LEU
62
n
58
LEU
62
A
VAL
63
n
59
VAL
63
A
GLN
64
n
60
GLN
64
A
PHE
65
n
61
PHE
65
A
GLU
66
n
62
GLU
66
A
ASP
67
n
63
ASP
67
A
ASP
68
n
64
ASP
68
A
SER
69
n
65
SER
69
A
GLN
70
n
66
GLN
70
A
PHE
71
n
67
PHE
71
A
LEU
72
n
68
LEU
72
A
VAL
73
n
69
VAL
73
A
LEU
74
n
70
LEU
74
A
TRP
75
n
71
TRP
75
A
LYS
76
n
72
LYS
76
A
ASP
77
n
73
ASP
77
A
ILE
78
n
74
ILE
78
A
SER
79
n
75
SER
79
A
PRO
80
n
76
PRO
80
A
ALA
81
n
77
ALA
81
A
ALA
82
n
78
ALA
82
A
LEU
83
n
79
LEU
83
A
ALA
331
n
1
ALA
331
B
THR
332
n
2
THR
332
B
GLY
333
n
3
GLY
333
B
GLY
334
n
4
GLY
334
B
VAL
335
n
5
VAL
335
B
M3L
336
n
6
M3L
336
B
LYS
337
n
7
LYS
337
B
PRO
338
n
8
PRO
338
B
HIS
339
n
9
HIS
339
B
ARG
340
n
10
ARG
340
B
TYR
341
n
11
TYR
341
B
author_defined_assembly
2
dimeric
B
M3L
336
N-TRIMETHYLLYSINE
B
M3L
6
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
N
VAL
37
A
N
VAL
33
A
O
GLY
49
A
O
GLY
45
A
N
THR
50
A
N
THR
46
A
O
GLN
64
A
O
GLN
60
A
N
CYS
61
A
N
CYS
57
A
O
VAL
73
A
O
VAL
69
1
A
O
LEU
83
A
O
LEU
79
1
Y
1
B
O
TYR
341
B
O
TYR
11
1
Y
2
A
O
LEU
83
A
O
LEU
79
1
Y
2
B
O
TYR
341
B
O
TYR
11
1
Y
3
A
O
LEU
83
A
O
LEU
79
1
Y
3
B
O
TYR
341
B
O
TYR
11
1
Y
4
A
O
LEU
83
A
O
LEU
79
1
Y
4
B
O
TYR
341
B
O
TYR
11
1
Y
5
A
O
LEU
83
A
O
LEU
79
1
Y
5
B
O
TYR
341
B
O
TYR
11
1
Y
6
A
O
LEU
83
A
O
LEU
79
1
Y
6
B
O
TYR
341
B
O
TYR
11
1
Y
7
A
O
LEU
83
A
O
LEU
79
1
Y
7
B
O
TYR
341
B
O
TYR
11
1
Y
8
A
O
LEU
83
A
O
LEU
79
1
Y
8
B
O
TYR
341
B
O
TYR
11
1
Y
9
A
O
LEU
83
A
O
LEU
79
1
Y
9
B
O
TYR
341
B
O
TYR
11
1
Y
10
A
O
LEU
83
A
O
LEU
79
1
Y
10
B
O
TYR
341
B
O
TYR
11
1
Y
11
A
O
LEU
83
A
O
LEU
79
1
Y
11
B
O
TYR
341
B
O
TYR
11
1
Y
12
A
O
LEU
83
A
O
LEU
79
1
Y
12
B
O
TYR
341
B
O
TYR
11
1
Y
13
A
O
LEU
83
A
O
LEU
79
1
Y
13
B
O
TYR
341
B
O
TYR
11
1
Y
14
A
O
LEU
83
A
O
LEU
79
1
Y
14
B
O
TYR
341
B
O
TYR
11
1
Y
15
A
O
LEU
83
A
O
LEU
79
1
Y
15
B
O
TYR
341
B
O
TYR
11
1
Y
16
A
O
LEU
83
A
O
LEU
79
1
Y
16
B
O
TYR
341
B
O
TYR
11
1
Y
17
A
O
LEU
83
A
O
LEU
79
1
Y
17
B
O
TYR
341
B
O
TYR
11
1
Y
18
A
O
LEU
83
A
O
LEU
79
1
Y
18
B
O
TYR
341
B
O
TYR
11
1
Y
19
A
O
LEU
83
A
O
LEU
79
1
Y
19
B
O
TYR
341
B
O
TYR
11
1
Y
20
A
O
LEU
83
A
O
LEU
79
1
Y
20
B
O
TYR
341
B
O
TYR
11
1
Y
1
A
A
HG
HE1
CYS
TRP
61
75
1.26
4
A
A
HG
HE1
CYS
TRP
61
75
1.23
5
A
A
HG
HE1
CYS
TRP
61
75
1.34
6
A
B
OE1
HZ2
GLU
LYS
66
337
1.55
8
A
A
HG
HE1
CYS
TRP
61
75
1.29
13
A
A
HG
HE1
CYS
TRP
61
75
1.30
15
A
B
OE1
HZ2
GLU
LYS
66
337
1.54
17
A
B
OE1
HZ3
GLU
LYS
66
337
1.53
18
A
B
OE2
HZ1
GLU
LYS
66
337
1.52
20
A
B
OE1
HZ1
GLU
LYS
66
337
1.54
1
A
SER
10
63.34
120.97
1
A
SER
14
55.17
101.09
1
A
ASP
67
-87.54
34.72
1
A
ALA
82
-141.24
-45.26
1
B
VAL
335
-93.69
-125.12
1
B
PRO
338
-67.39
-148.66
1
B
ARG
340
-154.32
-36.11
2
A
ARG
6
58.97
108.50
2
A
ALA
12
62.74
121.24
2
A
SER
14
-139.03
-42.66
2
A
ALA
22
54.64
98.36
2
A
PRO
27
-76.28
-81.93
2
A
ARG
28
-162.76
-52.11
2
A
ARG
30
-134.52
-35.23
2
A
ASP
67
-87.62
34.17
2
A
ALA
82
-131.75
-42.55
2
B
M3L
336
53.74
169.09
2
B
PRO
338
-78.83
-164.23
2
B
ARG
340
-146.08
-54.48
3
A
LEU
7
-134.58
-43.93
3
A
LEU
15
70.08
-53.56
3
A
THR
24
-147.92
-43.92
3
A
PRO
27
-80.50
32.97
3
A
ASP
67
-91.29
36.69
3
A
ALA
82
68.19
-58.92
3
B
THR
332
61.62
118.62
3
B
VAL
335
46.91
-179.27
3
B
ARG
340
-96.49
58.99
4
A
LEU
7
69.62
-58.97
4
A
SER
8
56.15
109.14
4
A
SER
13
-137.10
-40.13
4
A
LEU
15
71.24
-15.72
4
A
ARG
30
-144.77
-37.45
4
A
ASP
67
-88.45
33.16
4
B
THR
332
62.02
119.46
4
B
PRO
338
-63.53
-154.49
4
B
ARG
340
-147.25
-41.05
5
A
LEU
7
-131.03
-43.79
5
A
SER
14
62.42
123.84
5
A
SER
20
63.43
158.04
5
A
ARG
30
-164.27
-37.93
5
A
ASP
67
-90.28
34.88
5
B
PRO
338
-76.06
-158.43
5
B
ARG
340
-96.84
59.96
6
A
SER
13
-125.43
-50.79
6
A
SER
14
57.28
177.66
6
A
ASP
67
-91.13
33.82
7
A
ARG
28
56.02
80.29
7
A
ARG
30
69.81
-29.40
7
A
ASP
67
-90.61
35.68
7
B
M3L
336
56.06
132.95
8
A
SER
20
-146.43
-52.83
8
A
ASP
67
-87.94
33.68
8
B
VAL
335
-158.06
-71.52
8
B
M3L
336
52.53
160.23
8
B
PRO
338
-81.23
-154.91
8
B
HIS
339
-63.86
-162.72
9
A
ARG
6
62.18
119.58
9
A
SER
13
-143.53
-48.68
9
A
ALA
22
-138.90
-50.56
9
A
SER
25
63.37
130.06
9
A
ASP
67
-90.94
32.97
9
A
ALA
82
-132.09
-42.04
9
B
VAL
335
-104.62
-64.88
9
B
M3L
336
59.57
153.23
9
B
PRO
338
-83.82
-155.04
10
A
LEU
7
63.43
125.54
10
A
SER
8
63.37
145.08
10
A
LEU
15
-135.09
-45.82
10
A
THR
24
63.52
126.69
10
A
ARG
28
-142.91
-49.36
10
A
ASP
67
-94.48
39.71
10
A
ALA
81
-78.43
-155.44
10
A
ALA
82
72.82
-8.68
11
A
THR
24
54.36
103.83
11
A
ARG
30
72.53
-47.62
11
A
ASP
67
-88.55
32.95
12
A
LEU
15
-138.48
-51.08
12
A
PRO
18
-78.01
47.32
12
A
ARG
30
-120.04
-68.47
12
A
ASP
67
-90.17
32.98
12
A
ALA
82
67.54
133.76
12
B
VAL
335
-120.64
-50.64
12
B
M3L
336
55.80
160.36
12
B
PRO
338
-79.09
-158.17
12
B
ARG
340
42.08
103.97
13
A
ARG
6
71.01
-47.00
13
A
LEU
7
63.95
163.28
13
A
LEU
15
-141.61
-55.19
13
A
SER
20
63.05
117.88
13
A
ALA
22
64.46
136.86
13
A
ASP
67
-88.84
34.66
13
B
THR
332
61.47
114.40
13
B
M3L
336
56.75
136.60
13
B
PRO
338
-76.40
-163.44
13
B
ARG
340
56.21
-69.16
14
A
SER
8
64.27
157.79
14
A
SER
10
-136.96
-42.79
14
A
SER
13
56.02
104.14
14
A
SER
14
-142.27
-9.27
14
A
SER
20
61.71
101.59
14
A
ARG
30
-146.18
-44.14
14
A
ASP
67
-88.87
34.73
14
B
VAL
335
-101.44
-79.00
14
B
ARG
340
56.70
78.72
15
A
SER
8
69.37
-53.27
15
A
LEU
15
-138.39
-45.83
15
A
SER
20
62.26
158.95
15
A
ASP
67
-90.60
34.08
15
B
M3L
336
57.74
129.68
15
B
PRO
338
-78.30
-162.69
15
B
ARG
340
67.05
-61.65
16
A
SER
8
-135.12
-44.92
16
A
ARG
9
-132.69
-47.94
16
A
SER
10
-134.72
-43.64
16
A
SER
13
-131.25
-44.47
16
A
SER
25
61.38
126.75
16
A
ARG
30
-122.41
-63.00
16
A
ASP
67
-85.21
33.07
16
A
ALA
82
68.71
-32.42
16
B
M3L
336
55.18
165.53
17
A
SER
10
55.90
103.16
17
A
ALA
12
-135.23
-45.14
17
A
ALA
22
-136.56
-51.17
17
A
ASP
67
-91.60
36.50
17
B
M3L
336
53.71
156.19
17
B
ARG
340
68.66
-56.10
18
A
SER
14
60.16
114.28
18
A
PRO
18
-71.59
-93.78
18
A
PRO
23
-78.11
40.58
18
A
THR
24
63.20
176.83
18
A
SER
25
67.35
146.48
18
A
ARG
30
-172.52
-166.64
18
A
ASP
67
-87.31
32.32
18
B
THR
332
-136.54
-42.50
18
B
VAL
335
-138.38
-33.96
18
B
M3L
336
54.71
-175.22
18
B
PRO
338
-76.67
-157.33
18
B
ARG
340
48.64
112.10
19
A
SER
8
-93.49
57.68
19
A
SER
14
58.71
107.47
19
A
LEU
15
-133.02
-48.28
19
A
ARG
28
-132.62
-48.48
19
A
ARG
30
76.78
-19.27
19
A
ASP
67
-90.34
32.30
19
A
ALA
82
64.74
128.98
19
B
VAL
335
46.78
-87.69
19
B
M3L
336
57.01
157.27
19
B
LYS
337
-145.26
49.89
19
B
PRO
338
-77.39
-162.58
19
B
ARG
340
38.40
102.85
20
A
ARG
6
63.32
132.41
20
A
ALA
22
58.93
111.50
20
A
THR
42
-79.46
20.12
20
A
ASP
67
-87.79
32.68
20
B
M3L
336
53.77
161.66
PHD finger protein 1, H3K36me3 peptide
The solution structure of human PHF1 in complex with H3K36me3
1
N
N
2
N
N
covale
1.349
B
VAL
335
B
C
VAL
5
1_555
B
M3L
336
B
N
M3L
6
1_555
covale
1.337
B
M3L
336
B
C
M3L
6
1_555
B
LYS
337
B
N
LYS
7
1_555
PEPTIDE BINDING PROTEIN
Tudor Domain, H3K36me3 binding, PEPTIDE BINDING PROTEIN
PHF1_HUMAN
UNP
1
6
O43189
RLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
2M0O
PDB
2
2M0O
6
83
2M0O
6
83
O43189
A
1
2
79
331
341
2M0O
331
341
2M0O
B
2
1
11
1
EXPRESSION TAG
SER
5
2M0O
A
O43189
UNP
1
4
anti-parallel
anti-parallel
anti-parallel
A
ASP
36
A
ASP
32
A
LEU
38
A
LEU
34
A
LEU
48
A
LEU
44
A
ASP
55
A
ASP
51
A
VAL
60
A
VAL
56
A
PHE
65
A
PHE
61
A
GLN
70
A
GLN
66
A
LEU
74
A
LEU
70