1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Fu, Q.S.
Zhou, C.J.
Gao, H.C.
Lin, D.H.
Hu, H.Y.
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
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
J.Biol.Chem.
JBCHA3
0071
0021-9258
284
19043
19052
10.1074/jbc.M109.009126
19423704
Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein.
2009
10.2210/pdb2k8c/pdb
pdb_00002k8c
8576.831
Ubiquitin
1
man
polymer
9032.011
Phospholipase A-2-activating protein
UNP residues 386-465
1
man
polymer
PLA2P, PLAP
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A
polypeptide(L)
no
no
ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP
ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP
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
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
RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
pET-22B
Human
sample
PLAA, PLAP
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
pET-32M
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Database references
Derived calculations
1
0
2009-05-05
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Solution structure of Ubiquitin-binding domain PLAA (PFUC, Gly76-Pro77 cis isomer)
Solution structure of Ubiquitin-binding domain PLAA (PFUC, Gly76-Pro77 trans isomer)
Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin
BMRB
Y
RCSB
2008-09-04
REL
REL
10 structures for lowest energy
200
10
2D 1H-15N HSQC
2D 1H-15N HSQC
0.2
mM
[U-100% 15N]
0.2
mM
[U-100% 15N]
50mM NaCl
6.5
ambient
298
K
The structures were calculated with HADDOCK by NMR restraint-guided docking
simulated annealing
1
lowest energy
0.2 mM [U-100% 15N] Ubiquitin, 90% H2O, 10% D2O
90% H2O/10% D2O
0.2 mM [U-100% 15N] PFUC_trans, 90% H2O, 10% D2O
90% H2O/10% D2O
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
600
Varian
UNITY
Varian Unity
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
GLU
16
n
16
GLU
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
PRO
19
n
19
PRO
19
A
SER
20
n
20
SER
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
ILE
23
n
23
ILE
23
A
GLU
24
n
24
GLU
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
GLN
31
n
31
GLN
31
A
ASP
32
n
32
ASP
32
A
LYS
33
n
33
LYS
33
A
GLU
34
n
34
GLU
34
A
GLY
35
n
35
GLY
35
A
ILE
36
n
36
ILE
36
A
PRO
37
n
37
PRO
37
A
PRO
38
n
38
PRO
38
A
ASP
39
n
39
ASP
39
A
GLN
40
n
40
GLN
40
A
GLN
41
n
41
GLN
41
A
ARG
42
n
42
ARG
42
A
LEU
43
n
43
LEU
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
LYS
48
n
48
LYS
48
A
GLN
49
n
49
GLN
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
GLY
53
n
53
GLY
53
A
ARG
54
n
54
ARG
54
A
THR
55
n
55
THR
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
ASP
58
n
58
ASP
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
ILE
61
n
61
ILE
61
A
GLN
62
n
62
GLN
62
A
LYS
63
n
63
LYS
63
A
GLU
64
n
64
GLU
64
A
SER
65
n
65
SER
65
A
THR
66
n
66
THR
66
A
LEU
67
n
67
LEU
67
A
HIS
68
n
68
HIS
68
A
LEU
69
n
69
LEU
69
A
VAL
70
n
70
VAL
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
LEU
73
n
73
LEU
73
A
ARG
74
n
74
ARG
74
A
GLY
75
n
75
GLY
75
A
GLY
76
n
76
GLY
76
A
ALA
49
n
1
ALA
49
B
ASN
50
n
2
ASN
50
B
GLN
51
n
3
GLN
51
B
GLN
52
n
4
GLN
52
B
THR
53
n
5
THR
53
B
SER
54
n
6
SER
54
B
GLY
55
n
7
GLY
55
B
LYS
56
n
8
LYS
56
B
VAL
57
n
9
VAL
57
B
LEU
58
n
10
LEU
58
B
TYR
59
n
11
TYR
59
B
GLU
60
n
12
GLU
60
B
GLY
61
n
13
GLY
61
B
LYS
62
n
14
LYS
62
B
GLU
63
n
15
GLU
63
B
PHE
64
n
16
PHE
64
B
ASP
65
n
17
ASP
65
B
TYR
66
n
18
TYR
66
B
VAL
67
n
19
VAL
67
B
PHE
68
n
20
PHE
68
B
SER
69
n
21
SER
69
B
ILE
70
n
22
ILE
70
B
ASP
71
n
23
ASP
71
B
VAL
72
n
24
VAL
72
B
ASN
73
n
25
ASN
73
B
GLU
74
n
26
GLU
74
B
GLY
75
n
27
GLY
75
B
GLY
76
n
28
GLY
76
B
PRO
77
n
29
PRO
77
B
SER
78
n
30
SER
78
B
TYR
79
n
31
TYR
79
B
LYS
80
n
32
LYS
80
B
LEU
81
n
33
LEU
81
B
PRO
82
n
34
PRO
82
B
TYR
83
n
35
TYR
83
B
ASN
84
n
36
ASN
84
B
THR
85
n
37
THR
85
B
SER
86
n
38
SER
86
B
ASP
87
n
39
ASP
87
B
ASP
88
n
40
ASP
88
B
PRO
89
n
41
PRO
89
B
TRP
90
n
42
TRP
90
B
LEU
91
n
43
LEU
91
B
THR
92
n
44
THR
92
B
ALA
93
n
45
ALA
93
B
TYR
94
n
46
TYR
94
B
ASN
95
n
47
ASN
95
B
PHE
96
n
48
PHE
96
B
LEU
97
n
49
LEU
97
B
GLN
98
n
50
GLN
98
B
LYS
99
n
51
LYS
99
B
ASN
100
n
52
ASN
100
B
ASP
101
n
53
ASP
101
B
LEU
102
n
54
LEU
102
B
ASN
103
n
55
ASN
103
B
PRO
104
n
56
PRO
104
B
MET
105
n
57
MET
105
B
PHE
106
n
58
PHE
106
B
LEU
107
n
59
LEU
107
B
ASP
108
n
60
ASP
108
B
GLN
109
n
61
GLN
109
B
VAL
110
n
62
VAL
110
B
ALA
111
n
63
ALA
111
B
LYS
112
n
64
LYS
112
B
PHE
113
n
65
PHE
113
B
ILE
114
n
66
ILE
114
B
ILE
115
n
67
ILE
115
B
ASP
116
n
68
ASP
116
B
ASN
117
n
69
ASN
117
B
THR
118
n
70
THR
118
B
LYS
119
n
71
LYS
119
B
GLY
120
n
72
GLY
120
B
GLN
121
n
73
GLN
121
B
MET
122
n
74
MET
122
B
LEU
123
n
75
LEU
123
B
GLY
124
n
76
GLY
124
B
LEU
125
n
77
LEU
125
B
GLY
126
n
78
GLY
126
B
ASN
127
n
79
ASN
127
B
PRO
128
n
80
PRO
128
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
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
ILE
13
A
O
ILE
13
A
N
VAL
5
A
N
VAL
5
A
N
LYS
6
A
N
LYS
6
A
O
LEU
67
A
O
LEU
67
A
O
VAL
70
A
O
VAL
70
A
N
ARG
42
A
N
ARG
42
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
B
N
TYR
59
B
N
TYR
11
B
O
LYS
62
B
O
LYS
14
B
N
TYR
66
B
N
TYR
18
B
O
TYR
83
B
O
TYR
35
1
B
B
HZ3
OD1
LYS
ASP
56
65
1.55
1
B
B
OD1
HZ1
ASP
LYS
108
112
1.56
1
A
B
HZ3
OD2
LYS
ASP
6
71
1.59
1
A
A
OE1
HZ3
GLU
LYS
16
33
1.59
2
B
B
OD1
HZ1
ASP
LYS
108
112
1.55
2
B
B
HZ1
OD1
LYS
ASP
56
65
1.58
3
B
B
HZ1
OD1
LYS
ASP
56
65
1.54
4
B
B
HZ1
OD1
LYS
ASP
56
65
1.54
4
B
B
OE2
HZ1
GLU
LYS
60
99
1.56
5
A
B
HZ3
OD2
LYS
ASP
6
71
1.59
5
A
B
HE2
OD1
HIS
ASP
68
71
1.60
6
B
B
HZ1
OD1
LYS
ASP
56
65
1.56
6
B
B
OE2
HZ1
GLU
LYS
60
99
1.59
6
A
B
HE2
OD1
HIS
ASP
68
71
1.59
6
A
B
HZ3
OD2
LYS
ASP
6
71
1.59
6
A
A
HZ3
OD1
LYS
ASP
27
52
1.60
8
A
B
HZ3
OD2
LYS
ASP
6
71
1.58
8
A
B
HE2
OD1
HIS
ASP
68
71
1.60
9
B
B
OD1
HZ1
ASP
LYS
108
112
1.56
9
A
A
OE2
HZ3
GLU
LYS
16
33
1.57
9
B
B
OE2
HZ1
GLU
LYS
60
99
1.59
9
B
B
HZ1
OD1
LYS
ASP
56
65
1.60
10
B
B
HZ1
OD1
LYS
ASP
56
65
1.55
10
B
B
OD2
HZ1
ASP
LYS
108
112
1.56
10
A
B
HE2
OD2
HIS
ASP
68
71
1.60
10
B
B
OE2
HZ2
GLU
LYS
60
99
1.60
1
A
LYS
33
-79.06
-71.26
1
A
LEU
71
-109.08
-159.65
1
B
GLN
51
-130.24
-50.56
1
B
THR
53
-79.48
38.22
1
B
ASP
65
-71.12
-70.30
1
B
THR
85
-74.08
24.47
1
B
SER
86
-151.30
30.10
1
B
ASP
101
63.40
91.57
1
B
LYS
119
-108.11
-89.17
1
B
LEU
123
-88.81
-84.59
2
A
PRO
38
-69.83
0.63
2
A
ALA
46
65.83
-73.52
2
A
LEU
71
-102.49
-101.93
2
A
ARG
74
-124.58
-83.69
2
B
ASN
50
63.37
70.88
2
B
SER
54
-96.78
-85.11
2
B
ASP
65
-69.17
-80.89
2
B
VAL
72
-166.29
-38.03
2
B
ASP
101
55.74
74.62
2
B
LYS
119
-127.14
-50.15
2
B
LEU
125
61.40
-90.54
3
A
LEU
71
-96.13
-97.10
3
B
ASN
50
64.61
68.49
3
B
ASP
65
-69.91
-79.01
3
B
VAL
72
177.10
-30.51
3
B
ASP
101
58.86
82.19
3
B
LEU
125
64.32
-95.40
4
A
LYS
33
-81.13
-76.51
4
A
ALA
46
68.10
-12.54
4
B
SER
54
-100.05
-77.84
4
B
GLU
60
59.08
19.50
4
B
ASP
65
-72.14
-84.09
4
B
VAL
72
-175.26
-38.87
4
B
SER
86
-105.75
50.86
4
B
ASP
101
60.92
67.79
4
B
LYS
119
-122.81
-51.93
4
B
LEU
125
67.91
-80.10
5
A
LEU
71
-92.17
-137.95
5
B
ASP
101
58.72
87.86
5
B
LYS
119
-95.74
-103.86
5
B
LEU
123
-100.00
-81.08
6
A
GLU
34
-99.15
-74.01
6
A
ALA
46
62.15
-83.66
6
B
ASN
50
58.80
81.61
6
B
SER
54
-101.88
-75.38
6
B
ASP
65
-65.49
-76.15
6
B
VAL
72
179.43
-25.41
6
B
LEU
125
66.06
-86.26
7
A
GLN
62
-120.63
-168.92
7
A
ARG
74
-112.00
-168.61
7
B
THR
53
-95.23
45.51
7
B
SER
54
-81.53
-72.23
7
B
ASP
65
-70.31
-84.23
7
B
VAL
72
178.33
-25.70
7
B
LYS
119
-138.82
-56.52
7
B
LEU
125
67.02
-80.39
8
B
LYS
119
-89.40
-74.23
8
B
LEU
123
-94.57
-79.71
9
A
LEU
71
-102.18
-153.38
9
B
ASN
50
60.20
61.89
9
B
THR
53
-96.08
46.56
9
B
PHE
64
-118.41
-169.31
9
B
ASP
65
-65.76
-85.72
9
B
VAL
72
-177.40
-41.88
9
B
SER
86
-106.28
41.81
9
B
ASP
101
60.27
76.61
9
B
LYS
119
-121.23
-52.72
9
B
GLN
121
-138.23
-41.72
9
B
LEU
125
65.41
-87.37
10
B
SER
54
-106.73
-87.22
10
B
ASP
65
-70.76
-86.23
10
B
VAL
72
-175.99
-28.94
10
B
ASP
101
60.29
81.70
10
B
GLN
121
-135.54
-55.27
10
B
LEU
125
62.14
-93.75
Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin
1
N
N
2
N
N
A
THR
22
A
THR
22
HELX_P
A
GLU
34
A
GLU
34
1
1
13
B
ASP
88
B
ASP
40
HELX_P
B
GLN
98
B
GLN
50
1
2
11
B
PRO
104
B
PRO
56
HELX_P
B
THR
118
B
THR
70
1
3
15
PROTEIN BINDING
Ubiquitin in complex with PFUC trans isomer, Cytoplasm, Nucleus, Phosphoprotein, Ubl conjugation, WD repeat, PROTEIN BINDING
UBIQ_HUMAN
UNP
1
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
PLAP_HUMAN
UNP
2
386
Q9Y263
ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP
1
76
2K8C
1
76
P62988
A
1
1
76
386
465
2K8C
49
128
Q9Y263
B
2
1
80
5
2
2
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
THR
7
A
THR
7
A
THR
66
A
THR
66
A
VAL
70
A
VAL
70
A
ARG
42
A
ARG
42
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49
B
VAL
57
B
VAL
9
B
TYR
59
B
TYR
11
B
LYS
62
B
LYS
14
B
PHE
64
B
PHE
16
B
TYR
66
B
TYR
18
B
ILE
70
B
ILE
22
B
TYR
79
B
TYR
31
B
TYR
83
B
TYR
35