1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Huang, A.
De Jong, R.N.
Wienk, H.
Winkler, S.G.
Timmers, H.T.M.
Boelens, 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
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
Zn 2
65.409
ZINC ION
non-polymer
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
385
507
519
10.1016/j.jmb.2008.10.044
18996392
E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity
2009
10.2210/pdb2k4d/pdb
pdb_00002k4d
9387.662
E3 ubiquitin-protein ligase CBL
6.3.2.-
RING domain, residues 358-437
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
Signal transduction protein CBL, Proto-oncogene c-CBL, Casitas B-lineage lymphoma proto-oncogene, RING finger protein 55
no
no
GSLQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF
DPR
GSLQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF
DPR
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
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
CBL, CBL2, RNF55
9606
Homo sapiens
562
Escherichia coli
BL21(DE3) Rosetta 2
pLICHISGST
vector
pdbx_database_status
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
database_2
pdbx_database_status
struct_ref
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
Other
Database references
Derived calculations
Other
1
0
2009-01-20
1
1
2011-07-13
1
2
2020-02-26
1
3
2023-06-14
_pdbx_database_status.status_code_cs
_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
_struct_ref.pdbx_seq_one_letter_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
c-Cbl UbcH7 crystal structure
BMRB
Y
PDBJ
2008-06-06
REL
REL
REL
REL
ZN
ZINC ION
target function
100
20
1
2D 1H-15N HSQC
2D 1H-13C HSQC
2D 1H-1H NOESY
3D CBCA(CO)NH
3D C(CO)NH
3D HNCO
3D HNCA
3D HNCACB
3D HBHA(CO)NH
3D HN(CO)CA
3D HCCH-TOCSY
3D 1H-15N NOESY
3D 1H-15N TOCSY
3D 1H-13C NOESY
3D HNCACO
3D CNH-NOESY
1
mM
[U-99% 15N]
50
mM
100
mM
100
uM
0.2
mM
5
mM
1
mM
[U-99% 13C; U-99% 15N]
50
mM
100
mM
100
uM
0.2
mM
5
mM
150
7.3
ambient
298
K
RECOORD approach
simulated annealing
1
lowest energy
1mM [U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O
95% H2O/5% D2O
1mM [U-99% 13C; U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O
95% H2O/5% D2O
Guntert, Mumenthaler and Wuthrich
structure solution
CYANA
2.1.1
Guntert, Mumenthaler and Wuthrich
refinement
CYANA
2.1.1
600
Bruker
AVANCE
Bruker Avance
700
Bruker
AVANCE
Bruker Avance
ZN
500
2
ZN
ZN
500
A
ZN
600
2
ZN
ZN
600
A
GLY
355
n
1
GLY
355
A
SER
356
n
2
SER
356
A
LEU
357
n
3
LEU
357
A
GLN
358
n
4
GLN
358
A
ASP
359
n
5
ASP
359
A
HIS
360
n
6
HIS
360
A
ILE
361
n
7
ILE
361
A
LYS
362
n
8
LYS
362
A
VAL
363
n
9
VAL
363
A
THR
364
n
10
THR
364
A
GLN
365
n
11
GLN
365
A
GLU
366
n
12
GLU
366
A
GLN
367
n
13
GLN
367
A
TYR
368
n
14
TYR
368
A
GLU
369
n
15
GLU
369
A
LEU
370
n
16
LEU
370
A
TYR
371
n
17
TYR
371
A
CYS
372
n
18
CYS
372
A
GLU
373
n
19
GLU
373
A
MET
374
n
20
MET
374
A
GLY
375
n
21
GLY
375
A
SER
376
n
22
SER
376
A
THR
377
n
23
THR
377
A
PHE
378
n
24
PHE
378
A
GLN
379
n
25
GLN
379
A
LEU
380
n
26
LEU
380
A
CYS
381
n
27
CYS
381
A
LYS
382
n
28
LYS
382
A
ILE
383
n
29
ILE
383
A
CYS
384
n
30
CYS
384
A
ALA
385
n
31
ALA
385
A
GLU
386
n
32
GLU
386
A
ASN
387
n
33
ASN
387
A
ASP
388
n
34
ASP
388
A
LYS
389
n
35
LYS
389
A
ASP
390
n
36
ASP
390
A
VAL
391
n
37
VAL
391
A
LYS
392
n
38
LYS
392
A
ILE
393
n
39
ILE
393
A
GLU
394
n
40
GLU
394
A
PRO
395
n
41
PRO
395
A
CYS
396
n
42
CYS
396
A
GLY
397
n
43
GLY
397
A
HIS
398
n
44
HIS
398
A
LEU
399
n
45
LEU
399
A
MET
400
n
46
MET
400
A
CYS
401
n
47
CYS
401
A
THR
402
n
48
THR
402
A
SER
403
n
49
SER
403
A
CYS
404
n
50
CYS
404
A
LEU
405
n
51
LEU
405
A
THR
406
n
52
THR
406
A
SER
407
n
53
SER
407
A
TRP
408
n
54
TRP
408
A
GLN
409
n
55
GLN
409
A
GLU
410
n
56
GLU
410
A
SER
411
n
57
SER
411
A
GLU
412
n
58
GLU
412
A
GLY
413
n
59
GLY
413
A
GLN
414
n
60
GLN
414
A
GLY
415
n
61
GLY
415
A
CYS
416
n
62
CYS
416
A
PRO
417
n
63
PRO
417
A
PHE
418
n
64
PHE
418
A
CYS
419
n
65
CYS
419
A
ARG
420
n
66
ARG
420
A
CYS
421
n
67
CYS
421
A
GLU
422
n
68
GLU
422
A
ILE
423
n
69
ILE
423
A
LYS
424
n
70
LYS
424
A
GLY
425
n
71
GLY
425
A
THR
426
n
72
THR
426
A
GLU
427
n
73
GLU
427
A
PRO
428
n
74
PRO
428
A
ILE
429
n
75
ILE
429
A
VAL
430
n
76
VAL
430
A
VAL
431
n
77
VAL
431
A
ASP
432
n
78
ASP
432
A
PRO
433
n
79
PRO
433
A
PHE
434
n
80
PHE
434
A
ASP
435
n
81
ASP
435
A
PRO
436
n
82
PRO
436
A
ARG
437
n
83
ARG
437
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
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
MET
400
A
O
MET
46
A
N
VAL
391
A
N
VAL
37
A
N
LYS
392
A
N
LYS
38
A
O
GLU
427
A
O
GLU
73
1
A
A
HZ3
OE2
LYS
GLU
392
394
1.59
2
A
A
HZ1
OE2
LYS
GLU
392
394
1.57
3
A
A
HZ2
OE2
LYS
GLU
392
394
1.57
12
A
A
OD1
HZ3
ASP
LYS
388
389
1.56
17
A
A
HZ2
OE1
LYS
GLU
392
394
1.57
20
A
A
HZ2
OE2
LYS
GLU
392
394
1.60
13
A
ARG
420
0.080
SIDE CHAIN
1
A
GLU
366
175.34
134.34
1
A
LEU
370
-76.19
30.66
1
A
MET
374
62.08
84.06
1
A
LEU
380
89.79
142.71
1
A
ALA
385
71.66
-7.94
1
A
MET
400
-173.04
-176.86
1
A
GLU
412
74.84
107.03
1
A
GLN
414
-78.11
49.18
1
A
PHE
418
-80.29
-73.35
1
A
GLU
422
-36.99
116.43
1
A
ILE
429
-108.54
-86.99
1
A
VAL
430
72.46
87.73
1
A
PHE
434
64.69
-78.83
1
A
ASP
435
-154.36
89.19
2
A
GLN
358
66.42
178.88
2
A
ASP
359
-123.31
-78.40
2
A
HIS
360
66.57
-53.37
2
A
THR
364
-103.50
-100.37
2
A
CYS
372
81.12
107.52
2
A
GLU
386
-126.20
-54.00
2
A
GLU
412
63.04
78.28
2
A
PHE
418
-90.67
-67.67
2
A
GLU
422
-44.55
109.68
3
A
LYS
362
66.27
-177.96
3
A
VAL
363
-100.73
74.94
3
A
MET
374
72.31
-52.24
3
A
GLU
412
66.31
89.44
3
A
ARG
420
57.95
72.37
3
A
CYS
421
-126.56
-158.91
3
A
LYS
424
-123.65
-57.40
3
A
ILE
429
61.07
149.68
3
A
ASP
435
52.10
71.46
4
A
SER
356
-102.51
-74.96
4
A
GLN
358
60.97
-175.12
4
A
ASP
359
-94.66
-70.51
4
A
GLU
412
74.50
89.21
4
A
PHE
418
-93.38
-72.44
4
A
GLU
422
-38.34
115.53
4
A
LYS
424
-134.99
-39.80
4
A
PRO
433
-61.62
92.04
5
A
ASP
359
59.60
80.04
5
A
GLN
367
-72.57
31.24
5
A
MET
374
-177.31
91.72
5
A
ALA
385
70.87
-37.00
5
A
GLU
412
72.72
92.93
5
A
PHE
418
-91.91
-72.45
5
A
GLU
422
-35.73
124.30
5
A
PHE
434
-92.14
-63.21
6
A
SER
356
63.66
95.76
6
A
ILE
361
75.34
126.98
6
A
GLU
366
-153.21
-48.96
6
A
CYS
372
-56.07
108.72
6
A
GLU
386
-122.91
-55.93
6
A
MET
400
176.94
-168.93
6
A
GLU
412
63.79
79.76
6
A
GLU
422
-39.01
129.05
6
A
PRO
433
-66.72
88.40
7
A
ILE
361
-154.96
-48.48
7
A
CYS
372
68.62
115.58
7
A
MET
400
-177.93
-173.23
7
A
GLU
412
65.29
94.22
7
A
VAL
430
-106.46
41.90
8
A
ASP
359
59.54
-158.94
8
A
HIS
360
59.53
-164.23
8
A
GLU
366
58.44
71.89
8
A
LEU
370
-68.26
2.13
8
A
MET
374
61.34
-175.40
8
A
MET
400
-170.46
-174.96
8
A
GLU
412
68.25
104.05
8
A
PHE
418
-77.47
-70.74
8
A
ILE
429
-102.10
-66.98
8
A
VAL
430
71.04
86.03
8
A
PRO
436
-90.20
34.59
9
A
THR
364
-64.40
-98.26
9
A
GLU
412
70.99
94.79
9
A
PHE
418
-81.99
-79.02
9
A
PRO
433
-74.16
35.30
10
A
GLN
358
-174.13
86.84
10
A
LYS
362
-137.36
-68.81
10
A
GLU
366
71.59
122.13
10
A
LEU
370
-64.38
6.61
10
A
CYS
372
-70.77
-75.87
10
A
GLU
373
-155.96
13.77
10
A
MET
374
55.74
-148.96
10
A
THR
377
-66.67
97.27
10
A
PHE
378
-132.93
-38.85
10
A
GLU
386
-126.24
-55.82
10
A
MET
400
-170.71
-175.01
10
A
GLU
412
83.51
87.44
10
A
PHE
418
-92.24
-71.28
10
A
GLU
422
-33.91
118.32
11
A
SER
356
62.53
173.59
11
A
HIS
360
-128.96
-78.11
11
A
THR
364
-125.28
-55.36
11
A
GLU
369
-47.96
-15.97
11
A
GLU
386
-122.24
-50.57
11
A
GLU
412
164.57
-72.77
11
A
PHE
418
-83.80
-76.65
11
A
GLU
422
-27.65
120.16
11
A
PHE
434
66.48
-68.60
11
A
ASP
435
-155.15
89.96
12
A
HIS
360
-122.70
-79.35
12
A
ILE
361
60.31
95.27
12
A
LYS
362
68.23
-177.68
12
A
GLN
367
-66.51
32.05
12
A
MET
374
-134.43
-65.57
12
A
GLU
386
-138.28
-50.99
12
A
GLU
412
179.31
-75.14
12
A
GLU
422
-34.14
113.77
13
A
GLN
358
73.66
-77.31
13
A
ASP
359
61.01
-69.98
13
A
GLU
366
58.65
89.18
13
A
MET
374
67.35
165.67
13
A
GLU
412
81.54
87.33
13
A
GLU
422
1.26
105.58
13
A
PRO
433
-69.68
59.03
14
A
THR
364
-144.01
-59.94
14
A
CYS
372
59.23
-86.96
14
A
MET
374
73.04
-56.29
14
A
GLN
379
69.22
-71.97
14
A
GLU
412
69.44
100.56
14
A
ARG
420
53.56
70.10
14
A
GLU
422
-28.27
115.35
14
A
PHE
434
62.07
-77.03
15
A
PHE
378
-154.57
-32.02
15
A
GLN
379
-87.10
36.35
15
A
GLU
412
71.58
98.83
15
A
PHE
418
-80.13
-71.95
15
A
GLU
422
-26.68
131.41
15
A
ILE
429
-80.09
-75.32
15
A
VAL
430
70.73
94.66
15
A
ASP
435
-154.59
85.19
16
A
ASP
359
82.22
-4.42
16
A
LYS
362
178.21
151.14
16
A
CYS
372
52.26
78.27
16
A
GLU
412
76.65
97.96
16
A
GLU
422
-32.58
119.99
16
A
LYS
424
-134.92
-41.89
16
A
PRO
433
-83.37
39.58
16
A
PRO
436
-94.92
32.15
17
A
ASP
359
-155.45
-71.16
17
A
LYS
362
71.34
167.06
17
A
THR
364
40.15
-97.36
17
A
GLU
373
76.33
103.53
17
A
GLU
412
75.93
94.36
17
A
ARG
420
67.20
69.96
17
A
GLU
422
-19.16
110.07
17
A
PRO
433
-65.61
80.77
17
A
PRO
436
-89.24
43.27
18
A
THR
364
-120.42
-58.90
18
A
CYS
372
-168.05
-45.74
18
A
GLN
379
137.98
-38.27
18
A
MET
400
-172.62
-174.84
18
A
GLU
412
79.50
98.19
18
A
ARG
420
62.11
76.66
18
A
GLU
422
-22.72
109.15
18
A
PHE
434
64.50
-69.75
18
A
PRO
436
-101.88
-165.92
19
A
GLN
358
-168.48
-46.52
19
A
HIS
360
68.13
83.30
19
A
GLU
366
-144.64
-6.67
19
A
CYS
372
-127.92
-69.41
19
A
GLN
379
-79.65
-164.92
19
A
LEU
380
59.38
109.93
19
A
ALA
385
70.70
-28.91
19
A
GLU
412
66.55
98.16
19
A
ASP
435
-153.32
89.11
20
A
ASP
359
-138.95
-42.46
20
A
ILE
361
62.42
158.50
20
A
THR
364
-134.25
-40.53
20
A
ALA
385
71.50
-3.64
20
A
GLU
412
68.67
95.42
20
A
ASP
435
58.81
80.96
E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity
1
N
N
2
N
N
2
N
N
A
CYS
401
A
CYS
47
HELX_P
A
GLU
410
A
GLU
56
1
1
10
disulf
2.950
A
CYS
401
A
SG
CYS
47
1_555
A
CYS
404
A
SG
CYS
50
1_555
metalc
1.913
A
CYS
381
A
SG
CYS
27
1_555
A
ZN
500
B
ZN
ZN
1_555
LIGASE
protein, ubiquitin, c-Cbl, UbcH5B, UbcH7, Calcium, Cytoplasm, Ligase, Metal-binding, Phosphoprotein, Proto-oncogene, SH2 domain, Ubl conjugation pathway, Zinc, Zinc-finger
A
GLU
394
A
GLU
40
1
A
PRO
395
A
PRO
41
0.44
A
GLU
394
A
GLU
40
2
A
PRO
395
A
PRO
41
-1.57
A
GLU
394
A
GLU
40
3
A
PRO
395
A
PRO
41
0.29
A
GLU
394
A
GLU
40
4
A
PRO
395
A
PRO
41
-0.05
A
GLU
394
A
GLU
40
5
A
PRO
395
A
PRO
41
1.72
A
GLU
394
A
GLU
40
6
A
PRO
395
A
PRO
41
-0.20
A
GLU
394
A
GLU
40
7
A
PRO
395
A
PRO
41
2.15
A
GLU
394
A
GLU
40
8
A
PRO
395
A
PRO
41
0.96
A
GLU
394
A
GLU
40
9
A
PRO
395
A
PRO
41
-2.28
A
GLU
394
A
GLU
40
10
A
PRO
395
A
PRO
41
-0.66
A
GLU
394
A
GLU
40
11
A
PRO
395
A
PRO
41
-2.47
A
GLU
394
A
GLU
40
12
A
PRO
395
A
PRO
41
-1.33
A
GLU
394
A
GLU
40
13
A
PRO
395
A
PRO
41
1.99
A
GLU
394
A
GLU
40
14
A
PRO
395
A
PRO
41
-1.60
A
GLU
394
A
GLU
40
15
A
PRO
395
A
PRO
41
1.26
A
GLU
394
A
GLU
40
16
A
PRO
395
A
PRO
41
0.64
A
GLU
394
A
GLU
40
17
A
PRO
395
A
PRO
41
-1.40
A
GLU
394
A
GLU
40
18
A
PRO
395
A
PRO
41
1.95
A
GLU
394
A
GLU
40
19
A
PRO
395
A
PRO
41
-0.96
A
GLU
394
A
GLU
40
20
A
PRO
395
A
PRO
41
0.98
CBL_HUMAN
UNP
1
358
P22681
QDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFDPR
358
437
2K4D
358
437
P22681
A
1
4
83
1
expression tag
GLY
355
2K4D
A
P22681
UNP
1
1
expression tag
SER
356
2K4D
A
P22681
UNP
2
1
expression tag
LEU
357
2K4D
A
P22681
UNP
3
3
anti-parallel
anti-parallel
A
HIS
398
A
HIS
44
A
MET
400
A
MET
46
A
VAL
391
A
VAL
37
A
PRO
395
A
PRO
41
A
ILE
423
A
ILE
69
A
PRO
428
A
PRO
74
BINDING SITE FOR RESIDUE ZN A 500
A
ZN
500
Software
5
BINDING SITE FOR RESIDUE ZN A 600
A
ZN
600
Software
4
A
CYS
381
A
CYS
27
5
1_555
A
ILE
383
A
ILE
29
5
1_555
A
CYS
384
A
CYS
30
5
1_555
A
ASN
387
A
ASN
33
5
1_555
A
ASP
388
A
ASP
34
5
1_555
A
ILE
393
A
ILE
39
4
1_555
A
CYS
396
A
CYS
42
4
1_555
A
HIS
398
A
HIS
44
4
1_555
A
CYS
421
A
CYS
67
4
1_555