1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hamilton, K.S.
Shaw, G.S.
Williams, R.S.
Huzil, J.T.
McKenna, S.
Ptak, C.
Glover, M.
Ellison, M.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 H8 N2 O3
132.118
y
ASPARAGINE
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
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
UK
Structure
STRUE6
2005
0969-2126
9
897
904
10.1016/S0969-2126(01)00657-8
11591345
Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.
2001
10.2210/pdb1fxt/pdb
pdb_00001fxt
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
16697.064
UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
6.3.2.19
1
man
polymer
8576.831
UBIQUITIN
1
man
polymer
no
no
SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNIS
SVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS
SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNIS
SVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS
A
polypeptide(L)
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
sample
4932
Saccharomyces cerevisiae
562
Escherichia coli
PET3A
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
PET3A-HUB
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-10-10
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2000-09-26
REL
Spectra of thiolester formation were
acquired every 10 minutes during
the first 60 minutes of reaction
time until a stable level of covalent
complex was formed
1
1
enhanced 1H-15N HSQC
450mM NaCl
7.5
ambient
30
K
Dynamic docking between Ubc1 and Ub
System covalently bound and minimized
1
lowest energy
Yeast Ubc1
0.8 mM Ubc1 10uM E1 0.8 mM Ub
10mM ATP, 5 mM MgCl, 40 mM Hepes,
450 mM NaCl,, 1 mM EDTA in water
Human Ub
0.8 mM Ubc1 10uM E1 0.8 mM Ub
10mM ATP, 5 mM MgCl, 40 mM Hepes,
450 mM NaCl,, 1 mM EDTA in water
Delagio and Garrett
data analysis
NMRDraw
1
Delagio and Garrett
collection
PIPP
1
Delagio and Garrett
collection
STAPP
1
500
Varian
UNITY
SER
2
n
1
SER
2
A
ARG
3
n
2
ARG
3
A
ALA
4
n
3
ALA
4
A
LYS
5
n
4
LYS
5
A
ARG
6
n
5
ARG
6
A
ILE
7
n
6
ILE
7
A
MET
8
n
7
MET
8
A
LYS
9
n
8
LYS
9
A
GLU
10
n
9
GLU
10
A
ILE
11
n
10
ILE
11
A
GLN
12
n
11
GLN
12
A
ALA
13
n
12
ALA
13
A
VAL
14
n
13
VAL
14
A
LYS
15
n
14
LYS
15
A
ASP
16
n
15
ASP
16
A
ASP
17
n
16
ASP
17
A
PRO
18
n
17
PRO
18
A
ALA
19
n
18
ALA
19
A
ALA
20
n
19
ALA
20
A
HIS
21
n
20
HIS
21
A
ILE
22
n
21
ILE
22
A
THR
23
n
22
THR
23
A
LEU
24
n
23
LEU
24
A
GLU
25
n
24
GLU
25
A
PHE
26
n
25
PHE
26
A
VAL
27
n
26
VAL
27
A
SER
28
n
27
SER
28
A
GLU
29
n
28
GLU
29
A
SER
30
n
29
SER
30
A
ASP
31
n
30
ASP
31
A
ILE
32
n
31
ILE
32
A
HIS
33
n
32
HIS
33
A
HIS
34
n
33
HIS
34
A
LEU
35
n
34
LEU
35
A
LYS
36
n
35
LYS
36
A
GLY
37
n
36
GLY
37
A
THR
38
n
37
THR
38
A
PHE
39
n
38
PHE
39
A
LEU
40
n
39
LEU
40
A
GLY
41
n
40
GLY
41
A
PRO
42
n
41
PRO
42
A
PRO
43
n
42
PRO
43
A
GLY
44
n
43
GLY
44
A
THR
45
n
44
THR
45
A
PRO
46
n
45
PRO
46
A
TYR
47
n
46
TYR
47
A
GLU
48
n
47
GLU
48
A
GLY
49
n
48
GLY
49
A
GLY
50
n
49
GLY
50
A
LYS
51
n
50
LYS
51
A
PHE
52
n
51
PHE
52
A
VAL
53
n
52
VAL
53
A
VAL
54
n
53
VAL
54
A
ASP
55
n
54
ASP
55
A
ILE
56
n
55
ILE
56
A
GLU
57
n
56
GLU
57
A
VAL
58
n
57
VAL
58
A
PRO
59
n
58
PRO
59
A
MET
60
n
59
MET
60
A
GLU
61
n
60
GLU
61
A
TYR
62
n
61
TYR
62
A
PRO
63
n
62
PRO
63
A
PHE
64
n
63
PHE
64
A
LYS
65
n
64
LYS
65
A
PRO
66
n
65
PRO
66
A
PRO
67
n
66
PRO
67
A
LYS
68
n
67
LYS
68
A
MET
69
n
68
MET
69
A
GLN
70
n
69
GLN
70
A
PHE
71
n
70
PHE
71
A
ASP
72
n
71
ASP
72
A
THR
73
n
72
THR
73
A
LYS
74
n
73
LYS
74
A
VAL
75
n
74
VAL
75
A
TYR
76
n
75
TYR
76
A
HIS
77
n
76
HIS
77
A
PRO
78
n
77
PRO
78
A
ASN
79
n
78
ASN
79
A
ILE
80
n
79
ILE
80
A
SER
81
n
80
SER
81
A
SER
82
n
81
SER
82
A
VAL
83
n
82
VAL
83
A
THR
84
n
83
THR
84
A
GLY
85
n
84
GLY
85
A
ALA
86
n
85
ALA
86
A
ILE
87
n
86
ILE
87
A
CYS
88
n
87
CYS
88
A
LEU
89
n
88
LEU
89
A
ASP
90
n
89
ASP
90
A
ILE
91
n
90
ILE
91
A
LEU
92
n
91
LEU
92
A
LYS
93
n
92
LYS
93
A
ASN
94
n
93
ASN
94
A
ALA
95
n
94
ALA
95
A
TRP
96
n
95
TRP
96
A
SER
97
n
96
SER
97
A
PRO
98
n
97
PRO
98
A
VAL
99
n
98
VAL
99
A
ILE
100
n
99
ILE
100
A
THR
101
n
100
THR
101
A
LEU
102
n
101
LEU
102
A
LYS
103
n
102
LYS
103
A
SER
104
n
103
SER
104
A
ALA
105
n
104
ALA
105
A
LEU
106
n
105
LEU
106
A
ILE
107
n
106
ILE
107
A
SER
108
n
107
SER
108
A
LEU
109
n
108
LEU
109
A
GLN
110
n
109
GLN
110
A
ALA
111
n
110
ALA
111
A
LEU
112
n
111
LEU
112
A
LEU
113
n
112
LEU
113
A
GLN
114
n
113
GLN
114
A
SER
115
n
114
SER
115
A
PRO
116
n
115
PRO
116
A
GLU
117
n
116
GLU
117
A
PRO
118
n
117
PRO
118
A
ASN
119
n
118
ASN
119
A
ASP
120
n
119
ASP
120
A
PRO
121
n
120
PRO
121
A
GLN
122
n
121
GLN
122
A
ASP
123
n
122
ASP
123
A
ALA
124
n
123
ALA
124
A
GLU
125
n
124
GLU
125
A
VAL
126
n
125
VAL
126
A
ALA
127
n
126
ALA
127
A
GLN
128
n
127
GLN
128
A
HIS
129
n
128
HIS
129
A
TYR
130
n
129
TYR
130
A
LEU
131
n
130
LEU
131
A
ARG
132
n
131
ARG
132
A
ASP
133
n
132
ASP
133
A
ARG
134
n
133
ARG
134
A
GLU
135
n
134
GLU
135
A
SER
136
n
135
SER
136
A
PHE
137
n
136
PHE
137
A
ASN
138
n
137
ASN
138
A
LYS
139
n
138
LYS
139
A
THR
140
n
139
THR
140
A
ALA
141
n
140
ALA
141
A
ALA
142
n
141
ALA
142
A
LEU
143
n
142
LEU
143
A
TRP
144
n
143
TRP
144
A
THR
145
n
144
THR
145
A
ARG
146
n
145
ARG
146
A
LEU
147
n
146
LEU
147
A
TYR
148
n
147
TYR
148
A
ALA
149
n
148
ALA
149
A
SER
150
n
149
SER
150
A
MET
1
n
1
MET
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
PHE
4
n
4
PHE
4
B
VAL
5
n
5
VAL
5
B
LYS
6
n
6
LYS
6
B
THR
7
n
7
THR
7
B
LEU
8
n
8
LEU
8
B
THR
9
n
9
THR
9
B
GLY
10
n
10
GLY
10
B
LYS
11
n
11
LYS
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
THR
14
n
14
THR
14
B
LEU
15
n
15
LEU
15
B
GLU
16
n
16
GLU
16
B
VAL
17
n
17
VAL
17
B
GLU
18
n
18
GLU
18
B
PRO
19
n
19
PRO
19
B
SER
20
n
20
SER
20
B
ASP
21
n
21
ASP
21
B
THR
22
n
22
THR
22
B
ILE
23
n
23
ILE
23
B
GLU
24
n
24
GLU
24
B
ASN
25
n
25
ASN
25
B
VAL
26
n
26
VAL
26
B
LYS
27
n
27
LYS
27
B
ALA
28
n
28
ALA
28
B
LYS
29
n
29
LYS
29
B
ILE
30
n
30
ILE
30
B
GLN
31
n
31
GLN
31
B
ASP
32
n
32
ASP
32
B
LYS
33
n
33
LYS
33
B
GLU
34
n
34
GLU
34
B
GLY
35
n
35
GLY
35
B
ILE
36
n
36
ILE
36
B
PRO
37
n
37
PRO
37
B
PRO
38
n
38
PRO
38
B
ASP
39
n
39
ASP
39
B
GLN
40
n
40
GLN
40
B
GLN
41
n
41
GLN
41
B
ARG
42
n
42
ARG
42
B
LEU
43
n
43
LEU
43
B
ILE
44
n
44
ILE
44
B
PHE
45
n
45
PHE
45
B
ALA
46
n
46
ALA
46
B
GLY
47
n
47
GLY
47
B
LYS
48
n
48
LYS
48
B
GLN
49
n
49
GLN
49
B
LEU
50
n
50
LEU
50
B
GLU
51
n
51
GLU
51
B
ASP
52
n
52
ASP
52
B
GLY
53
n
53
GLY
53
B
ARG
54
n
54
ARG
54
B
THR
55
n
55
THR
55
B
LEU
56
n
56
LEU
56
B
SER
57
n
57
SER
57
B
ASP
58
n
58
ASP
58
B
TYR
59
n
59
TYR
59
B
ASN
60
n
60
ASN
60
B
ILE
61
n
61
ILE
61
B
GLN
62
n
62
GLN
62
B
LYS
63
n
63
LYS
63
B
GLU
64
n
64
GLU
64
B
SER
65
n
65
SER
65
B
THR
66
n
66
THR
66
B
LEU
67
n
67
LEU
67
B
HIS
68
n
68
HIS
68
B
LEU
69
n
69
LEU
69
B
VAL
70
n
70
VAL
70
B
LEU
71
n
71
LEU
71
B
ARG
72
n
72
ARG
72
B
LEU
73
n
73
LEU
73
B
ARG
74
n
74
ARG
74
B
GLY
75
n
75
GLY
75
B
GLY
76
n
76
GLY
76
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
GLU
25
A
O
GLU
24
A
N
LYS
36
A
N
LYS
35
A
O
PHE
39
A
O
PHE
38
A
N
PHE
52
A
N
PHE
51
A
O
GLU
57
A
O
GLU
56
A
N
LYS
68
A
N
LYS
67
B
N
LEU
15
B
N
LEU
15
B
O
ILE
3
B
O
ILE
3
B
N
LYS
6
B
N
LYS
6
B
O
LEU
67
B
O
LEU
67
B
N
VAL
70
B
N
VAL
70
B
O
ARG
42
B
O
ARG
42
1
A
A
HG
OD1
SER
ASP
81
123
1.54
1
A
A
HG1
OE1
THR
GLU
23
25
1.56
1
A
A
HG
OD2
SER
ASP
28
31
1.58
1
A
B
SG
C
CYS
GLY
88
76
1.79
1
A
A
TYR
PRO
62
63
33.01
1
A
A
ASP
ARG
133
134
149.47
1
B
B
VAL
GLU
17
18
147.08
1
B
B
ILE
GLU
23
24
144.49
1
A
TYR
47
0.077
SIDE CHAIN
1
B
ARG
42
0.076
SIDE CHAIN
1
B
ARG
72
0.089
SIDE CHAIN
1
3.53
0.50
120.30
123.83
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
1
3.95
0.50
120.30
124.25
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
6
6
6
N
1
8.51
1.30
111.50
120.01
A
A
A
ND1
CE1
NE2
HIS
HIS
HIS
21
21
21
N
1
8.60
1.30
111.50
120.10
A
A
A
ND1
CE1
NE2
HIS
HIS
HIS
33
33
33
N
1
8.45
1.30
111.50
119.95
A
A
A
ND1
CE1
NE2
HIS
HIS
HIS
34
34
34
N
1
8.57
1.30
111.50
120.07
A
A
A
ND1
CE1
NE2
HIS
HIS
HIS
77
77
77
N
1
8.00
1.30
111.50
119.50
A
A
A
ND1
CE1
NE2
HIS
HIS
HIS
129
129
129
N
1
4.62
0.50
120.30
124.92
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
132
132
132
N
1
3.53
0.50
120.30
123.83
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
134
134
134
N
1
3.19
0.50
120.30
123.49
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
146
146
146
N
1
4.52
0.50
120.30
124.82
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
1
3.63
0.50
120.30
123.93
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
54
54
54
N
1
-3.13
0.50
120.30
117.17
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
54
54
54
N
1
8.60
1.30
111.50
120.10
B
B
B
ND1
CE1
NE2
HIS
HIS
HIS
68
68
68
N
1
3.75
0.50
120.30
124.05
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
72
72
72
N
1
4.70
0.50
120.30
125.00
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
74
74
74
N
1
A
A
CG
CD2
HIS
HIS
21
21
0.057
0.009
1.354
1.411
N
1
A
A
CG
CD2
HIS
HIS
34
34
0.055
0.009
1.354
1.409
N
1
A
A
C
OXT
SER
SER
150
150
0.136
0.019
1.229
1.365
N
1
A
LYS
5
-84.34
43.61
1
A
ARG
6
-142.92
-66.92
1
A
LEU
24
-100.34
79.90
1
A
SER
28
-81.13
-93.39
1
A
GLU
29
-136.82
-73.45
1
A
ASP
31
-83.89
-142.47
1
A
HIS
33
-159.20
-57.65
1
A
THR
45
-173.93
149.24
1
A
PRO
46
-47.08
-10.46
1
A
ASN
94
-120.30
-63.22
1
A
ASN
119
-126.73
-59.09
1
A
GLN
122
-105.77
-89.52
1
A
ARG
134
-141.90
42.86
1
A
GLU
135
-140.85
-60.57
1
A
LEU
147
-90.82
-65.02
1
B
LEU
8
-96.01
57.85
1
B
THR
9
-137.46
-33.65
1
B
PRO
19
-49.53
-18.35
1
B
ASP
32
-51.79
-85.48
1
B
ALA
46
51.41
86.72
1
B
LEU
73
-90.00
-136.12
1
B
ARG
74
-152.70
60.01
STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX
1
N
N
2
N
N
A
ARG
3
A
ARG
2
HELX_P
A
ASP
17
A
ASP
16
1
1
15
A
PRO
18
A
PRO
17
HELX_P
A
HIS
21
A
HIS
20
5
2
4
A
LEU
89
A
LEU
88
HELX_P
A
ASN
94
A
ASN
93
1
3
6
A
THR
101
A
THR
100
HELX_P
A
SER
115
A
SER
114
1
4
15
A
ASP
123
A
ASP
122
HELX_P
A
ASP
133
A
ASP
132
1
5
11
A
GLU
135
A
GLU
134
HELX_P
A
ALA
149
A
ALA
148
1
6
15
B
THR
22
B
THR
22
HELX_P
B
GLU
34
B
GLU
34
1
7
13
B
LEU
56
B
LEU
56
HELX_P
B
ASN
60
B
ASN
60
5
8
5
LIGASE
Model of the interaction between yeast Ubc1 and Ubiquitin after the formation of a covalent thiolester, LIGASE
UBC1_YEAST
UNP
1
2
P21734
SRAKRIMKEIQAVKDDPAAHITLEFVSESDIHHLKGTFLGPPGTPYEGGKFVVDIEVPMEYPFKPPKMQFDTKVYHPNIS
SVTGAICLDILKNAWSPVITLKSALISLQALLQSPEPNDPQDAEVAQHYLRDRESFNKTAALWTRLYAS
UBIQ_HUMAN
UNP
2
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
2
150
1FXT
2
150
P21734
A
1
1
149
1
76
1FXT
1
76
P62988
B
2
1
76
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
THR
23
A
THR
22
A
PHE
26
A
PHE
25
A
HIS
34
A
HIS
33
A
LEU
40
A
LEU
39
A
LYS
51
A
LYS
50
A
GLU
57
A
GLU
56
A
LYS
68
A
LYS
67
A
PHE
71
A
PHE
70
B
ILE
13
B
ILE
13
B
GLU
16
B
GLU
16
B
GLN
2
B
GLN
2
B
LYS
6
B
LYS
6
B
THR
66
B
THR
66
B
LEU
71
B
LEU
71
B
GLN
41
B
GLN
41
B
ILE
44
B
ILE
44