1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Pires, J.R.
Taha-Nejad, F.
Toepert, F.
Ast, T.
Hoffmuller, U.
Schneider-Mergener, J.
Kuhne, R.
Macias, M.J.
Oschkinat, H.
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
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
H2 N
16.023
AMINO GROUP
non-polymer
C8 H18
114.229
N-OCTANE
non-polymer
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
314
1147
1156
10.1006/jmbi.2000.5199
11743730
Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope.
2001
10.2210/pdb1k9q/pdb
pdb_00001k9q
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
4682.166
65 kDa Yes-associated protein
Wild type WW domain
1
syn
polymer
527.593
WW domain binding protein-1
residues 149-153
P3G
1
syn
polymer
114.229
N-OCTANE
1
syn
non-polymer
YAP65
WBP-1
no
no
FEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRK
FEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRK
A
polypeptide(L)
no
yes
GPPPY(NH2)
GPPPYX
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
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Other
Other
Data collection
Database references
Derived calculations
1
0
2001-12-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2012-12-12
1
4
2013-03-13
1
5
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1JMQ contains YAP65 (L30K mutant) WW domain in Complexed with GTPPPPYTVG peptide
1E0M contains Prototype Ww Domain
1EG3 contains Dystrophin Ww Domain Fragment
1EG4 contains Dystrophin Ww Domain Fragment In Complexed With beta-Dystroglycan Peptide
1I5H contains Rnedd4 Wwiii Domain-Renac Bp2 Peptide Complex
1K9R contains YAP65 WW domain complexed with Acetyl-PLPPY
RCSB
Y
PDBJ
2001-10-30
REL
REL
OCT
N-OCTANE
This sequence was synthetically obtained, by semiautomated spot synthesis in a cellulose support.
sample
This sequence was synthetically obtained by spot synthesis in a cellulose support.
9606
Homo sapiens
sample
structures with the lowest energy
200
20
2D NOESY
2D NOESY
100mM NaCl
6
1
atm
288
K
100mM NaCl
6
1
atm
288
K
2000K, 200 runs, Force constants for NOE 50kcal mol-1 rad-2, 422 restraints
Simulated anneling
1
lowest energy
phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM
H2O (10% D2O)
phosphate buffer 10mM, NaCl 100mM, DTT 0.1mM, EDTA 0.1mM, pH 6, WW domain 1.2mM, ligand 2.4mM
D2O
Bruker
processing
XwinNMR
2.6
Kraulis, P.J.
data analysis
ANSIG
3.3
Brunger, A.T.
refinement
X-PLOR
3.1
600
Bruker
DRX
750
Bruker
DMX
OCT
2
3
OCT
OCT
2
B
PHE
5
n
1
PHE
5
A
GLU
6
n
2
GLU
6
A
ILE
7
n
3
ILE
7
A
PRO
8
n
4
PRO
8
A
ASP
9
n
5
ASP
9
A
ASP
10
n
6
ASP
10
A
VAL
11
n
7
VAL
11
A
PRO
12
n
8
PRO
12
A
LEU
13
n
9
LEU
13
A
PRO
14
n
10
PRO
14
A
ALA
15
n
11
ALA
15
A
GLY
16
n
12
GLY
16
A
TRP
17
n
13
TRP
17
A
GLU
18
n
14
GLU
18
A
MET
19
n
15
MET
19
A
ALA
20
n
16
ALA
20
A
LYS
21
n
17
LYS
21
A
THR
22
n
18
THR
22
A
SER
23
n
19
SER
23
A
SER
24
n
20
SER
24
A
GLY
25
n
21
GLY
25
A
GLN
26
n
22
GLN
26
A
ARG
27
n
23
ARG
27
A
TYR
28
n
24
TYR
28
A
PHE
29
n
25
PHE
29
A
LEU
30
n
26
LEU
30
A
ASN
31
n
27
ASN
31
A
HIS
32
n
28
HIS
32
A
ILE
33
n
29
ILE
33
A
ASP
34
n
30
ASP
34
A
GLN
35
n
31
GLN
35
A
THR
36
n
32
THR
36
A
THR
37
n
33
THR
37
A
THR
38
n
34
THR
38
A
TRP
39
n
35
TRP
39
A
GLN
40
n
36
GLN
40
A
ASP
41
n
37
ASP
41
A
PRO
42
n
38
PRO
42
A
ARG
43
n
39
ARG
43
A
LYS
44
n
40
LYS
44
A
GLY
3
n
1
GLY
3
B
PRO
4
n
2
PRO
4
B
PRO
5
n
3
PRO
5
B
PRO
6
n
4
PRO
6
B
TYR
7
n
5
TYR
7
B
NH2
8
n
6
NH2
8
B
author_defined_assembly
2
dimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ALA
20
A
N
ALA
16
A
O
TYR
28
A
O
TYR
24
A
N
PHE
29
A
N
PHE
25
A
O
THR
38
A
O
THR
34
11
A
A
OG
HE21
SER
GLN
23
26
1.57
11
A
A
H
O
ASN
THR
31
36
1.58
12
A
A
H
O
ASN
THR
31
36
1.59
16
A
A
O
HH11
PRO
ARG
42
43
1.58
1
A
ILE
7
-167.65
71.34
1
A
PRO
12
-71.88
-159.13
1
A
ALA
20
-172.73
149.16
1
A
SER
23
-176.11
-154.70
1
A
SER
24
-66.68
74.58
1
A
ARG
27
-63.97
74.27
1
A
GLN
35
54.94
72.02
1
A
TRP
39
-63.70
-160.83
1
A
ASP
41
-177.54
-59.90
2
A
GLU
6
54.35
99.21
2
A
LEU
13
54.64
176.96
2
A
SER
23
178.56
-85.68
2
A
SER
24
-128.30
-80.52
2
A
ARG
27
-64.93
72.41
2
A
GLN
35
53.93
75.30
2
A
TRP
39
-109.36
-66.99
3
A
GLU
6
-79.19
-72.89
3
A
PRO
12
-73.62
-159.59
3
A
SER
23
-176.82
59.98
3
A
SER
24
48.09
90.01
3
A
ARG
27
-65.16
73.57
3
A
TRP
39
-63.54
-149.63
3
A
ASP
41
-175.99
-60.13
4
A
ILE
7
-52.84
108.45
4
A
ASP
9
-113.84
77.63
4
A
ASP
10
-174.39
-60.99
4
A
PRO
12
-71.62
-87.89
4
A
ALA
20
-170.21
145.63
4
A
SER
23
-176.43
-151.70
4
A
SER
24
-66.55
74.77
4
A
ARG
27
-63.98
74.10
4
A
TRP
39
-100.38
-64.95
4
A
ARG
43
-101.52
78.78
5
A
ASP
9
-91.06
41.64
5
A
ASP
10
-173.40
83.65
5
A
LEU
13
53.56
-179.30
5
A
ALA
20
-171.19
145.66
5
A
SER
23
-178.08
-153.65
5
A
ARG
27
-65.67
75.41
5
A
GLN
35
54.06
71.07
5
A
TRP
39
-106.62
-61.33
6
A
GLU
6
-53.67
172.16
6
A
ASP
10
-67.39
74.62
6
A
VAL
11
54.16
99.06
6
A
PRO
12
-71.69
-158.38
6
A
LEU
13
-51.44
177.02
6
A
SER
23
-177.89
-153.07
6
A
SER
24
-53.73
-70.17
6
A
ARG
27
-65.72
69.08
6
A
GLN
35
51.98
78.66
6
A
TRP
39
-102.34
-67.14
6
A
GLN
40
-58.07
103.07
6
A
ARG
43
-81.73
-74.79
7
A
GLU
6
-73.33
-159.73
7
A
PRO
8
-72.99
-163.51
7
A
VAL
11
-175.06
106.89
7
A
PRO
12
-71.10
-159.07
7
A
ALA
20
-170.82
142.31
7
A
SER
23
-178.58
-155.37
7
A
GLN
35
35.75
65.84
7
A
ASP
41
-51.87
107.98
7
A
ARG
43
-167.94
29.52
8
A
GLU
6
-68.24
-161.28
8
A
ILE
7
-117.02
68.48
8
A
ASP
10
-127.92
-80.49
8
A
PRO
12
-72.00
-159.27
8
A
SER
23
-179.89
95.69
8
A
SER
24
61.37
-78.28
8
A
GLN
26
-58.92
89.86
8
A
GLN
35
55.36
74.75
8
A
GLN
40
50.17
-176.28
8
A
ARG
43
-119.15
-78.93
9
A
ILE
7
-115.37
72.03
9
A
PRO
12
-72.00
-159.46
9
A
SER
23
178.71
-152.66
9
A
SER
24
-52.59
-80.69
9
A
GLN
26
-69.02
71.23
9
A
ASP
41
-176.80
-60.03
10
A
ASP
9
-103.23
70.47
10
A
PRO
12
-72.99
-85.91
10
A
ALA
20
-172.11
146.34
10
A
SER
23
-175.58
-154.32
10
A
SER
24
-66.65
74.37
10
A
ARG
27
-63.91
75.92
10
A
GLN
35
50.36
77.43
10
A
ARG
43
-175.02
33.16
11
A
GLU
6
-98.08
-68.13
11
A
PRO
8
-75.89
-163.23
11
A
ASP
10
-73.52
-80.29
11
A
ALA
20
-171.28
148.03
11
A
SER
23
-157.87
-154.39
11
A
GLN
35
55.49
72.71
11
A
TRP
39
-106.84
-64.20
12
A
ASP
9
-118.59
52.94
12
A
ASP
10
-158.40
-71.73
12
A
ALA
20
-171.02
144.82
12
A
SER
23
-175.76
58.00
12
A
SER
24
50.13
96.24
12
A
ARG
27
-63.45
74.46
12
A
ASP
41
56.22
94.30
12
A
ARG
43
53.24
96.63
13
A
PRO
8
-72.46
-166.35
13
A
PRO
12
-71.44
-159.48
13
A
LEU
13
-51.42
177.51
13
A
SER
23
52.15
95.41
13
A
SER
24
63.35
-77.28
13
A
GLN
26
51.08
74.51
13
A
GLN
35
55.30
70.72
13
A
GLN
40
52.35
-160.48
14
A
GLU
6
-174.88
124.84
14
A
PRO
12
-71.23
-159.05
14
A
SER
23
-177.12
-152.52
14
A
ARG
27
-65.86
70.04
14
A
TRP
39
-77.99
-149.05
14
A
ASP
41
-176.51
-60.06
14
A
ARG
43
-151.57
-78.82
15
A
GLU
6
-173.79
-156.01
15
A
ASP
10
-175.30
-64.72
15
A
PRO
12
-71.37
-87.93
15
A
SER
23
-163.56
-147.81
15
A
GLN
26
-60.69
89.05
15
A
GLN
35
55.11
75.53
15
A
ASP
41
62.63
132.63
16
A
GLU
6
-87.41
49.62
16
A
ASP
10
-151.07
53.17
16
A
LEU
13
54.05
-177.08
16
A
SER
23
53.82
-139.82
16
A
SER
24
-68.29
70.59
16
A
GLN
26
-55.92
92.94
16
A
ARG
27
-66.72
89.92
16
A
GLN
40
-52.35
101.55
16
A
ARG
43
-176.87
-75.62
17
A
GLU
6
53.89
-159.14
17
A
PRO
12
-73.52
-89.94
17
A
LEU
13
-171.42
-165.19
17
A
ALA
20
-171.30
144.66
17
A
SER
23
-176.27
-157.72
17
A
SER
24
-66.87
73.92
17
A
ARG
27
-67.20
80.54
17
A
ASP
34
-141.48
17.65
17
A
GLN
35
49.43
81.86
17
A
GLN
40
-57.97
-165.65
18
A
PRO
8
-72.55
-163.39
18
A
ASP
9
-105.97
61.12
18
A
ASP
10
-153.11
21.75
18
A
PRO
12
-72.19
-159.65
18
A
SER
23
55.10
-142.74
18
A
SER
24
-50.22
-81.04
18
A
GLN
26
-52.68
94.64
18
A
GLN
35
57.38
81.14
18
A
ASP
41
-179.77
-59.35
18
A
ARG
43
-175.26
67.76
19
A
ASP
9
-61.95
84.57
19
A
ASP
10
-177.09
-34.13
19
A
LEU
13
57.28
173.20
19
A
SER
23
-178.49
-91.61
19
A
GLN
35
54.96
76.68
19
A
TRP
39
-103.70
-60.23
19
A
ARG
43
-174.83
-56.45
20
A
PRO
8
-72.83
-163.14
20
A
ASP
9
-156.65
23.38
20
A
LEU
13
58.61
-175.32
20
A
SER
23
-177.70
103.34
20
A
GLN
26
-59.00
90.12
20
A
ARG
27
-63.48
85.23
20
A
GLN
35
55.01
72.75
20
A
GLN
40
-51.24
94.50
20
A
ARG
43
-151.49
19.82
YAP65 WW domain complexed to N-(n-octyl)-GPPPY-NH2
1
N
N
2
N
N
3
N
N
covale
1.490
one
B
OCT
2
C
C1
OCT
1_555
B
GLY
3
B
N
GLY
1
1_555
covale
1.304
both
B
TYR
7
B
C
TYR
5
1_555
B
NH2
8
B
N
NH2
6
1_555
STRUCTURAL PROTEIN
WW domain, YAP65, beta-sheet proteins, ligands, proline-rich peptides, STRUCTURAL PROTEIN
YAP1_HUMAN
UNP
1
165
P46937
FEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRK
AAD10950
GB
2
149
4205084
PPPPY
165
204
1K9Q
5
44
P46937
A
1
1
40
149
153
1K9Q
3
7
4205084
B
2
1
5
2
PRO
engineered mutation
GLY
3
1K9Q
B
4205084
GB
149
1
2
amidation
NH2
8
1K9Q
B
4205084
GB
6
3
anti-parallel
anti-parallel
A
TRP
17
A
TRP
13
A
LYS
21
A
LYS
17
A
ARG
27
A
ARG
23
A
ASN
31
A
ASN
27
A
THR
36
A
THR
32
A
THR
38
A
THR
34
BINDING SITE FOR RESIDUE OCT B 2
B
OCT
2
Software
1
B
GLY
3
B
GLY
1
1
1_555