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.
Yagi-Utsumi, M.
Kato, K.
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
52
1874
1885
10.1021/bi301420m
23421577
Solution Structure of the Q41N Variant of Ubiquitin as a Model for the Alternatively Folded N2 State of Ubiquitin
2013
10.2210/pdb2rsu/pdb
pdb_00002rsu
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
pGEX-6P1
vector
High-energy state model mutant (Q41N) for ubiquitin
database_2
pdbx_database_status
pdbx_nmr_software
struct_ref_seq_dif
repository
Initial release
Data collection
Database references
Other
1
0
2013-03-27
1
1
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
ubiquitin at 30 bar
ubiquitin at 3 kbar
BMRB
Y
PDBJ
2012-06-15
REL
REL
REL
REL
1455
structures with the lowest energy
200
20
0
0.418
1
2D 1H-15N HSQC
2D 1H-13C HSQC
3D CBCA(CO)NH
3D C(CO)NH
3D HNCO
3D HNCA
3D HBHA(CO)NH
3D HN(CO)CA
3D H(CCO)NH
3D HCCH-TOCSY
3D HNHA
3D 1H-15N NOESY
3D 1H-15N TOCSY
3D 1H-13C NOESY
3D 1H-13C NOESY aromatic
2D 1H-15N HSQC
0.5
mM
[U-15N]
20
mM
[U-99% 2H]
1
mM
250
mM
6
mg/mL
2.0
mM
[U-99% 13C; U-99% 15N]
20
mM
[U-99% 2H]
1
mM
20
7.2
ambient
298
K
torsion angle dynamics, Energy minimization
1
lowest energy
0.5 mM [U-15N] protein-1, 20 mM [U-99% 2H] TRIS-2, 1 mM DSS-3, 250 mM sodium chloride-4, 6 mg/mL Pf1 bacteriopharge-5, 93% H2O/7% D2O
93% H2O/7% D2O
2.0 mM [U-99% 13C; U-99% 15N] protein-6, 20 mM [U-99% 2H] TRIS-7, 1 mM DSS-8, 93% H2O/7% D2O
93% H2O/7% D2O
Guntert, Mumenthaler and Wuthrich
structure solution
CYANA
3.93
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
refinement
Amber
11
Johnson, One Moon Scientific
processing
NMRView
5.22
refinement
CYANA
600
Bruker
DRX
Bruker DRX
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
LEU
15
A
O
LEU
15
A
N
ILE
3
A
N
ILE
3
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
4
A
A
OE1
HG
GLU
SER
18
20
1.54
14
A
A
OE1
HG
GLU
SER
18
20
1.57
15
A
A
OE1
HG
GLU
SER
18
20
1.60
20
A
A
OE1
HG
GLU
SER
18
20
1.55
4
A
ARG
42
0.141
SIDE CHAIN
10
A
ARG
42
0.105
SIDE CHAIN
1
3.32
0.50
120.30
123.62
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
3
3.32
0.50
120.30
123.62
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
5
3.17
0.50
120.30
123.47
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
5
3.50
0.50
120.30
123.80
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
7
4.34
0.50
120.30
124.64
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
10
3.51
0.50
120.30
123.81
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
12
3.19
0.50
120.30
123.49
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
12
3.68
0.50
120.30
123.98
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
15
3.08
0.50
120.30
123.38
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
18
3.75
0.50
120.30
124.05
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
1
A
PRO
38
-68.97
2.79
1
A
LEU
73
56.27
92.87
3
A
PRO
38
-69.59
5.41
3
A
ARG
42
-116.31
-167.00
4
A
GLU
34
-125.62
-62.88
4
A
PRO
38
-67.50
2.90
4
A
LEU
73
-124.16
-60.04
4
A
ARG
74
-137.62
-76.28
5
A
GLU
34
-108.64
-70.75
6
A
GLU
34
-106.73
-61.28
7
A
GLU
34
-132.41
-56.00
7
A
ARG
74
-140.15
30.40
8
A
GLU
34
-106.81
-73.15
8
A
PRO
38
-66.35
2.52
8
A
LEU
73
56.55
17.29
8
A
ARG
74
62.98
174.55
9
A
GLU
34
-118.17
-70.27
9
A
PRO
38
-68.39
0.59
9
A
ARG
72
-101.56
71.28
10
A
GLU
34
-112.58
-73.18
11
A
GLU
34
-126.92
-61.21
11
A
PRO
38
-68.38
4.72
11
A
LEU
73
-130.58
-43.43
12
A
PRO
38
-67.70
3.62
13
A
ARG
74
-89.54
47.46
14
A
ARG
72
-85.63
47.05
14
A
LEU
73
-143.61
31.81
14
A
ARG
74
-137.90
-65.09
15
A
GLU
34
-99.60
-70.31
15
A
ARG
74
-152.94
38.33
16
A
GLU
34
-125.00
-55.68
16
A
PRO
38
-68.56
1.06
16
A
ASP
52
-87.13
42.28
17
A
GLU
34
-125.78
-64.21
17
A
LEU
73
-63.32
95.73
18
A
GLU
34
-132.47
-56.84
18
A
PRO
38
-69.83
0.90
18
A
ARG
74
-136.70
-45.05
19
A
GLU
34
-121.29
-63.03
19
A
ASP
52
-83.95
44.45
19
A
LEU
73
59.43
-162.43
20
A
PRO
38
-69.94
1.49
20
A
ARG
74
-135.11
-62.23
lowest energy, model1
Alternative structure of Ubiquitin
1
N
N
A
THR
22
A
THR
22
HELX_P
A
GLU
34
A
GLU
34
1
1
13
A
THR
55
A
THR
55
HELX_P
A
ASN
60
A
ASN
60
1
2
6
PROTEIN BINDING
ubiquitin, Q41N, high energy, N2, PROTEIN BINDING
UBC_HUMAN
UNP
1
1
P0CG48
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
1
76
2RSU
1
76
P0CG48
A
1
1
76
1
GLN
engineered mutation
ASN
41
2RSU
A
P0CG48
UNP
41
41
4
2
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
THR
7
A
THR
7
A
THR
66
A
THR
66
A
LEU
71
A
LEU
71
A
ASN
41
A
ASN
41
A
ARG
42
A
ARG
42
A
ILE
44
A
ILE
44
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49