1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Donaldson, L.W.
Pawson, T.
Kay, L.E.
Forman-Kay, J.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C9 H12 N O6 P
261.168
n
O-PHOSPHOTYROSINE
PHOSPHONOTYROSINE
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
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
99
14053
14058
10.1073/pnas.212518799
12384576
Structure of a regulatory complex involving the Abl SH3 domain, the Crk
SH2 domain, and a Crk-derived phosphopeptide
2002
10.2210/pdb1ju5/pdb
pdb_00001ju5
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
12142.571
Crk
Crk SH2 domain
1
man
polymer
1468.480
Crk
Crk phosphopeptide
1
man
polymer
6764.461
Abl
2.7.1.112
Abl SH3 domain
L122K
1
man
polymer
PROTO-ONCOGENE C-CRK, ADAPTER MOLECULE CRK, P38
PROTO-ONCOGENE C-CRK, ADAPTER MOLECULE CRK, P38
proto-oncogene tyrosine-protein kinase
no
no
SWYWGRLSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSGPRPPVPPSPAQPPPGVSPSRLRIGD
QEFDSLPALLEFYKIHYLDTTTLIEPVSR
SWYWGRLSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSSGPRPPVPPSPAQPPPGVSPSRLRIGD
QEFDSLPALLEFYKIHYLDTTTLIEPVSR
A
polypeptide(L)
no
yes
EPGP(PTR)AQPSVNTK
EPGPYAQPSVNTK
B
polypeptide(L)
no
no
DPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSK
DPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSK
C
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
human
Homo
Escherichia
Escherichia coli
sample
9606
Homo sapiens
511693
Escherichia coli BL21
BL21
plasmid
pGEX-2T
house mouse
Mus
Escherichia
Escherichia coli
sample
10090
Mus musculus
511693
Escherichia coli BL21
BL21
PLASMID
pAED4-MMHB
human
Homo
Escherichia
Escherichia coli
sample
9606
Homo sapiens
511693
Escherichia coli BL21
BL21
PLASMID
pET15
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-11-06
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
1AWO contains NMR structure of Abl SH3 domain in an SH(32) fragment
1BBZ contains Crystal structure of Abl SH3 domain with high-affinity ligand
2ABL contains Sh3-Sh2 Domain Fragment Of Human Bcr-Abl Tyrosine Kinase
1AYA contains Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase.
2PLD contains Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-1 complexed with a high affinity binding peptide.
1SPS contains Crystal structure of the Src SH2 in complex with YEEI
RCSB
Y
PDBJ
2001-08-23
REL
REL
Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% 13C-labeled sample according to Neri et al (Biochemistry 28:7510; 1989). HACAN and CBCA(CO)N(CA)HA experiments were used to assign the proline residues in the Crk SH2 domain according to Kanelis et al (JBNMR 16:253; 2000)
structures with the lowest energy
40
1
3D_13C-separated_NOESY
3D_15N-separated_NOESY
3D_13C_F1-FILTERED_F3-EDITED_NOESY
J-HNHA
IPAP-15N_HSQC
50mM sodium phosphate
6.8
ambient
303
K
This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2-phosphopeptide intermolecular restraints, 50 hydrogen bonds, 54 direct 3J-HNHA couplings and 166 dihedral angle restraints from TALOS
Residues 217-220 and 225-229 of the Crk phosphopeptide (Chain B) are disordered. As intermolecular contacts between the SH2 domain (Chain A) and the SH3 domain (Chain C) limited to amino acids 67-75 in DE-loop of the SH2 domain, there is no unique orientation between the SH2 domain and SH3 domain.
ARIA 1.0, CNS 1.0
1
lowest energy
0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide
90% H2O/10% D2O
Delaglio
processing
NMRPipe
1.8
Garrett
data analysis
PIPP
4.3.2
Brunger
structure solution
CNS
1.0
Brunger
structure solution
ARIA
1.0
Brunger
refinement
ARIA
1.0
500
Varian
UNITYPLUS
600
Varian
UNITYPLUS
800
Varian
UNITYPLUS
SER
12
n
1
SER
12
A
TRP
13
n
2
TRP
13
A
TYR
14
n
3
TYR
14
A
TRP
15
n
4
TRP
15
A
GLY
16
n
5
GLY
16
A
ARG
17
n
6
ARG
17
A
LEU
18
n
7
LEU
18
A
SER
19
n
8
SER
19
A
ARG
20
n
9
ARG
20
A
GLN
21
n
10
GLN
21
A
GLU
22
n
11
GLU
22
A
ALA
23
n
12
ALA
23
A
VAL
24
n
13
VAL
24
A
ALA
25
n
14
ALA
25
A
LEU
26
n
15
LEU
26
A
LEU
27
n
16
LEU
27
A
GLN
28
n
17
GLN
28
A
GLY
29
n
18
GLY
29
A
GLN
30
n
19
GLN
30
A
ARG
31
n
20
ARG
31
A
HIS
32
n
21
HIS
32
A
GLY
33
n
22
GLY
33
A
VAL
34
n
23
VAL
34
A
PHE
35
n
24
PHE
35
A
LEU
36
n
25
LEU
36
A
VAL
37
n
26
VAL
37
A
ARG
38
n
27
ARG
38
A
ASP
39
n
28
ASP
39
A
SER
40
n
29
SER
40
A
SER
41
n
30
SER
41
A
THR
42
n
31
THR
42
A
SER
43
n
32
SER
43
A
PRO
44
n
33
PRO
44
A
GLY
45
n
34
GLY
45
A
ASP
46
n
35
ASP
46
A
TYR
47
n
36
TYR
47
A
VAL
48
n
37
VAL
48
A
LEU
49
n
38
LEU
49
A
SER
50
n
39
SER
50
A
VAL
51
n
40
VAL
51
A
SER
52
n
41
SER
52
A
GLU
53
n
42
GLU
53
A
ASN
54
n
43
ASN
54
A
SER
55
n
44
SER
55
A
ARG
56
n
45
ARG
56
A
VAL
57
n
46
VAL
57
A
SER
58
n
47
SER
58
A
HIS
59
n
48
HIS
59
A
TYR
60
n
49
TYR
60
A
ILE
61
n
50
ILE
61
A
ILE
62
n
51
ILE
62
A
ASN
63
n
52
ASN
63
A
SER
64
n
53
SER
64
A
SER
65
n
54
SER
65
A
GLY
66
n
55
GLY
66
A
PRO
67
n
56
PRO
67
A
ARG
68
n
57
ARG
68
A
PRO
69
n
58
PRO
69
A
PRO
70
n
59
PRO
70
A
VAL
71
n
60
VAL
71
A
PRO
72
n
61
PRO
72
A
PRO
73
n
62
PRO
73
A
SER
74
n
63
SER
74
A
PRO
75
n
64
PRO
75
A
ALA
76
n
65
ALA
76
A
GLN
77
n
66
GLN
77
A
PRO
78
n
67
PRO
78
A
PRO
79
n
68
PRO
79
A
PRO
80
n
69
PRO
80
A
GLY
81
n
70
GLY
81
A
VAL
82
n
71
VAL
82
A
SER
83
n
72
SER
83
A
PRO
84
n
73
PRO
84
A
SER
85
n
74
SER
85
A
ARG
86
n
75
ARG
86
A
LEU
87
n
76
LEU
87
A
ARG
88
n
77
ARG
88
A
ILE
89
n
78
ILE
89
A
GLY
90
n
79
GLY
90
A
ASP
91
n
80
ASP
91
A
GLN
92
n
81
GLN
92
A
GLU
93
n
82
GLU
93
A
PHE
94
n
83
PHE
94
A
ASP
95
n
84
ASP
95
A
SER
96
n
85
SER
96
A
LEU
97
n
86
LEU
97
A
PRO
98
n
87
PRO
98
A
ALA
99
n
88
ALA
99
A
LEU
100
n
89
LEU
100
A
LEU
101
n
90
LEU
101
A
GLU
102
n
91
GLU
102
A
PHE
103
n
92
PHE
103
A
TYR
104
n
93
TYR
104
A
LYS
105
n
94
LYS
105
A
ILE
106
n
95
ILE
106
A
HIS
107
n
96
HIS
107
A
TYR
108
n
97
TYR
108
A
LEU
109
n
98
LEU
109
A
ASP
110
n
99
ASP
110
A
THR
111
n
100
THR
111
A
THR
112
n
101
THR
112
A
THR
113
n
102
THR
113
A
LEU
114
n
103
LEU
114
A
ILE
115
n
104
ILE
115
A
GLU
116
n
105
GLU
116
A
PRO
117
n
106
PRO
117
A
VAL
118
n
107
VAL
118
A
SER
119
n
108
SER
119
A
ARG
120
n
109
ARG
120
A
GLU
217
n
1
GLU
217
B
PRO
218
n
2
PRO
218
B
GLY
219
n
3
GLY
219
B
PRO
220
n
4
PRO
220
B
TYR
221
n
5
PTR
221
B
ALA
222
n
6
ALA
222
B
GLN
223
n
7
GLN
223
B
PRO
224
n
8
PRO
224
B
SER
225
n
9
SER
225
B
VAL
226
n
10
VAL
226
B
ASN
227
n
11
ASN
227
B
THR
228
n
12
THR
228
B
LYS
229
n
13
LYS
229
B
ASP
62
n
1
ASP
62
C
PRO
63
n
2
PRO
63
C
ASN
64
n
3
ASN
64
C
LEU
65
n
4
LEU
65
C
PHE
66
n
5
PHE
66
C
VAL
67
n
6
VAL
67
C
ALA
68
n
7
ALA
68
C
LEU
69
n
8
LEU
69
C
TYR
70
n
9
TYR
70
C
ASP
71
n
10
ASP
71
C
PHE
72
n
11
PHE
72
C
VAL
73
n
12
VAL
73
C
ALA
74
n
13
ALA
74
C
SER
75
n
14
SER
75
C
GLY
76
n
15
GLY
76
C
ASP
77
n
16
ASP
77
C
ASN
78
n
17
ASN
78
C
THR
79
n
18
THR
79
C
LEU
80
n
19
LEU
80
C
SER
81
n
20
SER
81
C
ILE
82
n
21
ILE
82
C
THR
83
n
22
THR
83
C
LYS
84
n
23
LYS
84
C
GLY
85
n
24
GLY
85
C
GLU
86
n
25
GLU
86
C
LYS
87
n
26
LYS
87
C
LEU
88
n
27
LEU
88
C
ARG
89
n
28
ARG
89
C
VAL
90
n
29
VAL
90
C
LEU
91
n
30
LEU
91
C
GLY
92
n
31
GLY
92
C
TYR
93
n
32
TYR
93
C
ASN
94
n
33
ASN
94
C
HIS
95
n
34
HIS
95
C
ASN
96
n
35
ASN
96
C
GLY
97
n
36
GLY
97
C
GLU
98
n
37
GLU
98
C
TRP
99
n
38
TRP
99
C
CYS
100
n
39
CYS
100
C
GLU
101
n
40
GLU
101
C
ALA
102
n
41
ALA
102
C
GLN
103
n
42
GLN
103
C
THR
104
n
43
THR
104
C
LYS
105
n
44
LYS
105
C
ASN
106
n
45
ASN
106
C
GLY
107
n
46
GLY
107
C
GLN
108
n
47
GLN
108
C
GLY
109
n
48
GLY
109
C
TRP
110
n
49
TRP
110
C
VAL
111
n
50
VAL
111
C
PRO
112
n
51
PRO
112
C
SER
113
n
52
SER
113
C
ASN
114
n
53
ASN
114
C
TYR
115
n
54
TYR
115
C
ILE
116
n
55
ILE
116
C
THR
117
n
56
THR
117
C
PRO
118
n
57
PRO
118
C
VAL
119
n
58
VAL
119
C
ASN
120
n
59
ASN
120
C
SER
121
n
60
SER
121
C
n
61
122
C
author_defined_assembly
3
trimeric
B
PTR
221
O-PHOSPHOTYROSINE
B
PTR
5
TYR
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
ILE
62
A
O
ILE
51
A
N
TYR
47
A
N
TYR
36
A
O
SER
50
A
O
SER
39
A
N
LEU
36
A
N
LEU
25
A
O
VAL
37
A
O
VAL
26
A
N
TRP
15
A
N
TRP
4
A
O
ILE
62
A
O
ILE
51
A
N
TYR
47
A
N
TYR
36
A
O
SER
50
A
O
SER
39
A
N
LEU
36
A
N
LEU
25
A
N
PHE
35
A
N
PHE
24
A
O
GLU
116
A
O
GLU
105
A
N
ILE
89
A
N
ILE
78
A
O
GLN
92
A
O
GLN
81
C
O
VAL
111
C
O
VAL
50
C
N
CYS
100
C
N
CYS
39
C
O
GLN
103
C
O
GLN
42
C
N
ARG
89
C
N
ARG
28
C
O
LEU
88
C
O
LEU
27
C
N
PHE
66
C
N
PHE
5
C
N
VAL
67
C
N
VAL
6
C
O
THR
117
C
O
THR
56
1
C
LYS
122
C
LYS
61
1
Y
1
A
ARG
31
-49.28
164.49
1
A
GLU
53
-75.02
-160.31
1
A
SER
55
80.47
14.86
1
A
PRO
75
-49.77
164.09
1
A
SER
83
-151.10
89.59
1
A
TYR
108
-108.61
45.86
1
A
THR
112
47.45
-176.15
1
B
GLN
223
69.82
95.24
1
B
SER
225
-133.71
-46.51
1
B
VAL
226
53.63
71.30
1
B
ASN
227
-138.22
-74.76
1
B
THR
228
53.34
-170.68
1
C
ASN
64
-176.91
40.61
1
C
ASP
77
-57.31
-161.80
1
C
PRO
112
-49.94
163.62
Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy
1
N
N
2
N
N
3
N
N
A
SER
19
A
SER
8
HELX_P
A
GLN
28
A
GLN
17
1
1
10
A
SER
96
A
SER
85
HELX_P
A
HIS
107
A
HIS
96
1
2
12
covale
1.329
both
B
PRO
220
B
C
PRO
4
1_555
B
PTR
221
B
N
PTR
5
1_555
covale
1.330
both
B
PTR
221
B
C
PTR
5
1_555
B
ALA
222
B
N
ALA
6
1_555
PROTEIN BINDING/TRANSFERASE
Crk, SH2, Abl, SH3, adaptor protein, phosphopeptide, PROTEIN BINDING-TRANSFERASE COMPLEX
CRK_HUMAN
UNP
1
P46108
CRK_MOUSE
UNP
2
Q64010
ABL1_HUMAN
UNP
3
P00519
12
120
1JU5
12
120
P46108
A
1
1
109
217
228
1JU5
217
228
Q64010
B
2
1
12
62
122
1JU5
62
122
P00519
C
3
1
61
3
LEU
engineered mutation
LYS
122
1JU5
C
P00519
UNP
122
61
4
4
2
5
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
57
A
VAL
46
A
ASN
63
A
ASN
52
A
ASP
46
A
ASP
35
A
SER
52
A
SER
41
A
VAL
34
A
VAL
23
A
ASP
39
A
ASP
28
A
TYR
14
A
TYR
3
A
TRP
15
A
TRP
4
A
VAL
57
A
VAL
46
A
ASN
63
A
ASN
52
A
ASP
46
A
ASP
35
A
SER
52
A
SER
41
A
VAL
34
A
VAL
23
A
ASP
39
A
ASP
28
A
GLU
116
A
GLU
105
A
PRO
117
A
PRO
106
A
LEU
87
A
LEU
76
A
ILE
89
A
ILE
78
A
GLN
92
A
GLN
81
A
PHE
94
A
PHE
83
C
GLY
107
C
GLY
46
C
PRO
112
C
PRO
51
C
TRP
99
C
TRP
38
C
THR
104
C
THR
43
C
LYS
87
C
LYS
26
C
TYR
93
C
TYR
32
C
PHE
66
C
PHE
5
C
ALA
68
C
ALA
7
C
ILE
116
C
ILE
55
C
PRO
118
C
PRO
57