1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kitazawa, S.
Kameda, T.
Kumo, A.
Utsumi, M.
Baxter, N.
Kato, K.
Williamson, M.P.
Kitahara, R.
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Biochemistry
BICHAW
0033
0006-2960
53
447
449
10.1021/bi401617n
24401037
Close Identity between Alternatively Folded State N2 of Ubiquitin and the Conformation of the Protein Bound to the Ubiquitin-Activating Enzyme
2014
10.2210/pdb2ru6/pdb
pdb_00002ru6
8562.805
Ubiquitin
Q41N
1
man
polymer
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQNRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQNRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
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
human
sample
UBC
9606
Homo sapiens
562
Escherichia coli
pCGN
vector
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_ref_seq_dif
repository
Initial release
Structure summary
Data collection
Database references
Other
1
0
2014-02-12
1
1
2014-03-05
1
2
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
alternatively folded state is 70% populated
BMRB
Y
PDBJ
2013-12-04
REL
REL
REL
REL
2450
0
454
231
1765
0
0
36
36
structures with the lowest energy
200
20
1
2D 1H-15N HSQC
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
2D HNCO
3D 1H-13C/15N simultaneous evolutio NOESY HSQC
20
mM
[U-100% 2H]
2
mM
[U-100% 13C; U-100% 15N]
0.2
mM
20
7.2
250
0
298
K
torsion angle dynamics, Energy minimization
1
lowest energy
20 mM [U-100% 2H] Tris(hydroxymethyl)aminomethane-1, 2 mM [U-100% 13C; U-100% 15N] ubiquitin-2, 0.2 mM DSS-3, 88% H2O/12% D2O
88% H2O/12% D2O
Guntert, Mumenthaler and Wuthrich
chemical shift assignment
CYANA
3.93
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
refinement
Amber
11
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Johnson, One Moon Scientific
peak picking
NMRView
refinement
CYANA_3.93
800
Bruker
AVANCE
Bruker Avance
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
ASN
41
n
41
ASN
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
author_defined_assembly
1
monomeric
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
PHE
4
A
N
PHE
4
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
8
A
A
HG1
OE2
THR
GLU
22
24
1.55
15
A
A
HG1
OE2
THR
GLU
22
24
1.55
2
A
A
LEU
VAL
69
70
136.04
2
A
A
VAL
LEU
70
71
143.70
3
A
A
LEU
VAL
69
70
140.11
3
A
A
VAL
LEU
70
71
142.94
4
A
A
LEU
VAL
69
70
147.17
4
A
A
VAL
LEU
70
71
147.36
4
A
A
LEU
ARG
71
72
145.21
5
A
A
LEU
VAL
69
70
141.79
5
A
A
VAL
LEU
70
71
146.22
5
A
A
LEU
ARG
71
72
142.12
5
A
A
ARG
LEU
72
73
-149.50
6
A
A
LEU
VAL
69
70
144.35
6
A
A
VAL
LEU
70
71
140.93
7
A
A
LEU
VAL
69
70
145.86
7
A
A
VAL
LEU
70
71
142.13
8
A
A
LEU
VAL
69
70
143.18
8
A
A
VAL
LEU
70
71
142.32
9
A
A
LEU
VAL
69
70
143.98
9
A
A
VAL
LEU
70
71
148.37
10
A
A
LEU
VAL
69
70
146.38
10
A
A
VAL
LEU
70
71
141.09
10
A
A
LEU
ARG
71
72
146.92
12
A
A
LEU
VAL
69
70
148.99
13
A
A
LEU
VAL
69
70
146.01
13
A
A
VAL
LEU
70
71
146.91
13
A
A
LEU
ARG
71
72
148.66
14
A
A
LEU
VAL
69
70
149.41
14
A
A
VAL
LEU
70
71
146.60
15
A
A
LEU
VAL
69
70
142.52
15
A
A
VAL
LEU
70
71
142.82
16
A
A
LEU
VAL
69
70
149.17
16
A
A
VAL
LEU
70
71
148.62
17
A
A
LEU
VAL
69
70
142.93
17
A
A
VAL
LEU
70
71
140.85
18
A
A
LEU
VAL
69
70
144.95
18
A
A
VAL
LEU
70
71
147.62
18
A
A
LEU
ARG
71
72
138.07
18
A
A
GLY
GLY
75
76
149.96
19
A
A
LEU
VAL
69
70
149.76
19
A
A
VAL
LEU
70
71
147.61
20
A
A
VAL
LEU
70
71
146.66
20
A
A
LEU
ARG
71
72
140.26
1
A
TYR
59
0.070
SIDE CHAIN
3
A
ARG
72
0.121
SIDE CHAIN
4
A
TYR
59
0.076
SIDE CHAIN
5
A
ARG
54
0.086
SIDE CHAIN
10
A
TYR
59
0.082
SIDE CHAIN
11
A
TYR
59
0.091
SIDE CHAIN
12
A
TYR
59
0.065
SIDE CHAIN
13
A
TYR
59
0.079
SIDE CHAIN
16
A
TYR
59
0.081
SIDE CHAIN
17
A
ARG
42
0.086
SIDE CHAIN
18
A
ARG
72
0.097
SIDE CHAIN
19
A
ARG
42
0.089
SIDE CHAIN
19
A
TYR
59
0.066
SIDE CHAIN
20
A
TYR
59
0.070
SIDE CHAIN
1
3.12
0.50
120.30
123.42
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
1
3.29
0.50
120.30
123.59
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
1
4.06
0.50
120.30
124.36
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
2
3.57
0.50
120.30
123.87
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
2
-3.03
0.50
120.30
117.27
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
42
42
42
N
2
3.94
0.50
120.30
124.24
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
3
4.76
0.50
120.30
125.06
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
3
3.28
0.50
120.30
123.58
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
4
3.82
0.50
120.30
124.12
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
4
3.57
0.50
120.30
123.87
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
5
3.34
0.50
120.30
123.64
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
5
3.04
0.50
120.30
123.34
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
6
4.07
0.50
120.30
124.37
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
7
4.72
0.50
120.30
125.02
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
8
3.54
0.50
120.30
123.84
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
9
3.65
0.50
120.30
123.95
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
9
3.69
0.50
120.30
123.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
9
3.14
0.50
120.30
123.44
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
10
3.61
0.50
120.30
123.91
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
10
4.11
0.50
120.30
124.41
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
10
3.14
0.50
120.30
123.44
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
11
4.04
0.50
120.30
124.34
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
11
3.17
0.50
120.30
123.47
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
11
4.26
0.50
120.30
124.56
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
11
3.84
0.50
120.30
124.14
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
12
3.55
0.50
120.30
123.85
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
12
3.26
0.50
120.30
123.56
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
12
3.55
0.50
120.30
123.85
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
12
3.74
0.50
120.30
124.04
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
13
3.91
0.50
120.30
124.21
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
14
3.51
0.50
120.30
123.81
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
14
5.24
0.50
120.30
125.54
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
15
3.44
0.50
120.30
123.74
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
17
3.09
0.50
120.30
123.39
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
17
3.56
0.50
120.30
123.86
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
72
72
72
N
18
3.43
0.50
120.30
123.73
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
19
3.53
0.50
120.30
123.83
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
20
3.63
0.50
120.30
123.93
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
20
4.20
0.50
120.30
124.50
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
20
3.21
0.50
120.30
123.51
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
1
A
GLU
34
-120.52
-55.64
1
A
ASP
39
-65.39
14.59
1
A
GLN
40
-140.77
-17.84
1
A
TYR
59
-65.36
3.15
1
A
GLU
64
59.05
9.79
2
A
THR
9
-65.95
12.61
2
A
GLU
34
-138.02
-56.15
2
A
ASP
39
-79.87
35.80
2
A
GLN
40
-156.64
-40.42
2
A
THR
66
-105.76
62.14
2
A
LEU
71
-39.45
161.73
3
A
LEU
71
-45.26
161.69
3
A
LEU
73
-136.06
-55.31
4
A
GLU
34
-145.44
14.50
4
A
ASP
39
-66.28
4.37
4
A
LEU
71
-54.54
172.05
4
A
ARG
72
-69.76
-82.60
4
A
LEU
73
-156.64
-46.43
5
A
GLU
34
-136.65
-30.56
5
A
GLU
64
57.18
15.74
5
A
LEU
71
-52.19
178.02
5
A
ARG
72
-71.62
-89.85
5
A
LEU
73
60.93
158.88
6
A
THR
9
-69.63
10.89
6
A
GLN
40
-133.66
-37.81
6
A
ALA
46
52.13
19.45
6
A
GLU
64
58.87
10.21
6
A
LEU
71
-49.60
165.71
6
A
ARG
72
-77.54
-75.08
6
A
ARG
74
-71.76
41.96
7
A
GLU
34
-131.52
-36.10
7
A
GLN
40
-130.64
-30.52
7
A
ALA
46
52.48
19.63
7
A
ASP
52
-63.37
-179.73
7
A
TYR
59
-69.46
7.33
7
A
LEU
71
-46.66
174.91
8
A
LEU
71
-47.39
161.51
9
A
GLU
34
-145.13
-12.63
9
A
LEU
71
-55.10
172.22
9
A
LEU
73
64.34
170.67
10
A
THR
9
-66.86
4.02
10
A
GLU
34
-136.95
-31.61
10
A
ALA
46
49.60
28.50
10
A
TYR
59
-68.80
9.61
10
A
GLU
64
59.97
13.77
10
A
LEU
71
-48.07
164.00
11
A
THR
9
-82.95
35.73
11
A
GLU
34
-141.56
-30.04
11
A
ALA
46
54.60
-1.36
11
A
GLU
51
-62.93
-175.65
11
A
ASP
52
-91.50
-159.21
11
A
LEU
73
54.79
-170.86
12
A
GLU
34
-137.76
-39.55
12
A
ASP
39
-64.40
9.57
12
A
GLU
64
58.37
15.48
13
A
ALA
46
54.29
-3.31
13
A
GLU
64
70.77
-12.11
13
A
LEU
71
-52.82
170.35
13
A
ARG
74
62.65
-177.07
14
A
GLU
16
-115.98
59.11
14
A
GLU
34
-144.96
-16.71
15
A
GLU
34
-140.47
-26.35
15
A
GLN
40
-132.89
-45.17
15
A
TYR
59
-67.84
2.62
15
A
GLU
64
58.71
19.44
15
A
LEU
71
-48.18
167.49
16
A
ALA
46
51.95
17.86
16
A
ARG
74
52.58
75.99
17
A
GLU
34
-132.96
-43.21
17
A
GLN
40
-145.14
-44.13
17
A
LEU
71
-47.90
164.65
17
A
ARG
74
58.90
6.64
18
A
ALA
46
51.50
19.04
18
A
ARG
72
-35.70
156.96
18
A
LEU
73
-138.51
-90.91
19
A
GLU
34
-141.36
-52.67
19
A
ALA
46
55.43
-6.38
19
A
LEU
71
-53.00
174.94
20
A
LEU
8
-68.69
5.56
20
A
GLU
34
-141.77
10.65
20
A
ARG
72
-76.34
-80.52
20
A
LEU
73
-155.18
-63.13
lowest energy, model1
The pure alternative state of ubiquitin
1
N
N
A
THR
22
A
THR
22
HELX_P
A
GLU
34
A
GLU
34
1
1
13
A
PRO
37
A
PRO
37
HELX_P
A
ASP
39
A
ASP
39
5
2
3
PROTEIN BINDING
ubiquitin, alternatively folded state, high-pressure NMR, Q41N variant, PROTEIN BINDING
UBC_HUMAN
UNP
1
1
P0CG48
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
1
76
2RU6
1
76
P0CG48
A
1
1
76
1
GLN
engineered mutation
ASN
41
2RU6
A
P0CG48
UNP
41
41
5
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
LYS
6
A
LYS
6
A
THR
66
A
THR
66
A
LEU
71
A
LEU
71
A
ASN
41
A
ASN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49