1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Zhang, D.
Fushman, D.
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
UK
Structure
STRUE6
2005
0969-2126
23
542
557
10.1016/j.str.2015.01.010
25703377
DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.
2015
10.2210/pdb2mro/pdb
pdb_00002mro
8576.831
Polyubiquitin-B
Human Ubiquitin
1
man
polymer
4745.367
DNA damage-inducible protein 1
Ubiquitin associated domain, UNP residues 389-428
1
man
polymer
Ubiquitin
v-SNARE-master 1
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A
polypeptide(L)
no
no
GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS
GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS
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
human
sample
UBB
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)pLysS
pET3a
Baker's yeast
ATCC 204508 / S288c
sample
DDI1, VSM1, YER143W
559292
Saccharomyces cerevisiae
562
Escherichia coli
BL21(DE3)pLysS
pGEX 4T2
Complex structure based on chemical shift perturbation data and spin-labeling data, calculated using Haddock program
database_2
pdbx_database_related
pdbx_nmr_sample_details
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_ref_seq_dif
database_2
pdbx_database_status
repository
Initial release
Database references
Data collection
Database references
Experimental preparation
Database references
Other
1
0
2015-02-04
1
1
2015-03-18
1
2
2019-11-06
1
3
2023-06-14
_pdbx_database_related.db_name
_pdbx_nmr_sample_details.contents
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
UBIQUITIN NMR STRUCTURE
UBA domain of DNA-damage-inducible 1 protein (Ddi1)
BMRB
Y
RCSB
2014-07-14
REL
REL
REL
REL
Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution.
structures with the least restraint violations
10
10
2D 1H-15N HSQC
2D 1H-15N HSQC
1
mM
[U-100% 15N]
20
mM
7
%
[U-99% 2H]
93
%
1
mM
[U-100% 15N]
20
mM
7
%
[U-99% 2H]
93
%
20
6.8
ambient
298.2
K
simulated annealing
1
lowest energy
1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O
93% H2O/7% D2O
1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O
93% H2O/7% D2O
Bruker Biospin
collection
TopSpin
2.1
Bruker Biospin
processing
TopSpin
2.1
Keller and Wuthrich
chemical shift assignment
CARA
1.8.1
Alexandre Bonvin
geometry optimization
HADDOCK
2.1
Alexandre Bonvin
refinement
HADDOCK
2.1
Alexandre Bonvin
structure solution
HADDOCK
2.1
600
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
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
GLY
386
n
1
GLY
386
B
SER
387
n
2
SER
387
B
ALA
388
n
3
ALA
388
B
THR
389
n
4
THR
389
B
PHE
390
n
5
PHE
390
B
PRO
391
n
6
PRO
391
B
GLU
392
n
7
GLU
392
B
GLN
393
n
8
GLN
393
B
THR
394
n
9
THR
394
B
ILE
395
n
10
ILE
395
B
LYS
396
n
11
LYS
396
B
GLN
397
n
12
GLN
397
B
LEU
398
n
13
LEU
398
B
MET
399
n
14
MET
399
B
ASP
400
n
15
ASP
400
B
LEU
401
n
16
LEU
401
B
GLY
402
n
17
GLY
402
B
PHE
403
n
18
PHE
403
B
PRO
404
n
19
PRO
404
B
ARG
405
n
20
ARG
405
B
ASP
406
n
21
ASP
406
B
ALA
407
n
22
ALA
407
B
VAL
408
n
23
VAL
408
B
VAL
409
n
24
VAL
409
B
LYS
410
n
25
LYS
410
B
ALA
411
n
26
ALA
411
B
LEU
412
n
27
LEU
412
B
LYS
413
n
28
LYS
413
B
GLN
414
n
29
GLN
414
B
THR
415
n
30
THR
415
B
ASN
416
n
31
ASN
416
B
GLY
417
n
32
GLY
417
B
ASN
418
n
33
ASN
418
B
ALA
419
n
34
ALA
419
B
GLU
420
n
35
GLU
420
B
PHE
421
n
36
PHE
421
B
ALA
422
n
37
ALA
422
B
ALA
423
n
38
ALA
423
B
SER
424
n
39
SER
424
B
LEU
425
n
40
LEU
425
B
LEU
426
n
41
LEU
426
B
PHE
427
n
42
PHE
427
B
GLN
428
n
43
GLN
428
B
SER
429
n
44
SER
429
B
author_defined_assembly
2
dimeric
1540
-6
7120
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
1
A
B
HZ2
OD2
LYS
ASP
6
400
1.57
1
A
A
OD2
HZ2
ASP
LYS
21
29
1.57
2
B
B
OD1
HZ3
ASP
LYS
406
410
1.56
2
A
A
HZ2
OE2
LYS
GLU
11
34
1.58
2
A
A
HZ3
OD1
LYS
ASP
27
52
1.59
2
A
B
HZ2
OD2
LYS
ASP
6
400
1.59
5
A
A
OD2
HZ1
ASP
LYS
21
29
1.54
6
A
A
H1
OE2
MET
GLU
1
16
1.56
6
A
B
HZ2
OD2
LYS
ASP
6
400
1.60
7
A
B
HZ2
OD2
LYS
ASP
6
400
1.59
8
A
A
OD2
HZ3
ASP
LYS
21
29
1.57
8
B
B
OD2
HZ2
ASP
LYS
406
410
1.58
9
A
A
HZ1
OD2
LYS
ASP
27
52
1.56
9
A
A
OD2
HZ1
ASP
LYS
21
29
1.59
10
A
A
HZ2
OD2
LYS
ASP
27
52
1.57
10
A
B
HZ3
OD2
LYS
ASP
6
400
1.59
1
B
ASN
416
70.09
63.56
2
A
GLU
34
-92.00
-65.27
2
A
GLN
62
-106.33
-167.69
3
A
THR
9
-79.26
29.84
3
A
GLN
62
-114.94
-166.23
4
B
SER
387
-143.00
39.88
4
B
ASN
416
68.30
62.10
5
A
GLN
62
-106.14
-166.60
6
A
GLN
62
-101.46
-167.06
6
B
ASN
416
61.82
60.85
7
A
ARG
42
-160.37
94.51
7
A
GLN
62
-109.50
-163.24
7
A
ARG
74
-103.36
-63.25
7
B
ASN
418
-67.80
93.99
8
A
GLN
62
-107.92
-165.99
9
A
GLN
62
-113.24
-164.35
9
B
ASN
416
61.96
61.10
10
A
GLN
62
-110.96
-167.99
10
A
GLU
64
70.40
-1.53
lowest energy, model1
Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)
1
N
N
2
N
N
A
THR
22
A
THR
22
HELX_P
A
GLY
35
A
GLY
35
1
1
14
A
THR
55
A
THR
55
HELX_P
A
ASN
60
A
ASN
60
5
2
6
B
PRO
391
B
PRO
6
HELX_P
B
LEU
401
B
LEU
16
1
3
11
B
PRO
404
B
PRO
19
HELX_P
B
GLN
414
B
GLN
29
1
4
11
B
ASN
418
B
ASN
33
HELX_P
B
PHE
427
B
PHE
42
1
5
10
TRANSPORT PROTEIN/SIGNALING PROTEIN
DNA-damage-inducible 1 protein, Ubiquitin associated domain, Ddi1, UBA, HYDROLASE-SIGNALING PROTEIN complex, TRANSPORT PROTEIN-SIGNALING PROTEIN complex
UBB_HUMAN
UNP
1
1
P0CG47
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
DDI1_YEAST
UNP
2
389
P40087
TFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQ
1
76
2MRO
1
76
P0CG47
A
1
1
76
389
428
2MRO
389
428
P40087
B
2
4
43
2
expression tag
GLY
386
2MRO
B
P40087
UNP
1
2
expression tag
SER
387
2MRO
B
P40087
UNP
2
2
expression tag
ALA
388
2MRO
B
P40087
UNP
3
2
expression tag
SER
429
2MRO
B
P40087
UNP
44
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
THR
7
A
THR
7
A
THR
66
A
THR
66
A
LEU
71
A
LEU
71
A
GLN
41
A
GLN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49