1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Schumann, F.H.
Varadan, R.
Tayakuniyil, P.P.
Hall, J.B.
Camarero, J.A.
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
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 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
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
To be Published
0353
Changing protein backbone topology: Structural and dynamic consequences of the backbone cyclization in SH3 domain
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
308
1045
1062
10.1006/jmbi.2001.4631
Rescuing a destabilized protein fold through backbone cyclization
2001
10.2210/pdb1m3b/pdb
pdb_00001m3b
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
6831.592
Proto-oncogene C-crk
N-TERMINAL SH3 DOMAIN (residues 134-191)
R191G, E135G, A134C
1
man
polymer
P38, Adapter molecule crk
no
no
CGYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYG
CGYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYG
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
house mouse
Mus
Escherichia
sample
CRK
10090
Mus musculus
562
Escherichia coli
PLASMID
PGEX-6P-1
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-08-05
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
Solution structure of N-terminal SH3 domain from oncogene protein c-Crk
Solution structure of a circular form of the truncated N-terminal SH3 domain from oncogene protein c-Crk.
Solution structure of a circular form of the N-terminal SH3 domain from oncogene protein c-Crk
RCSB
Y
RCSB
2002-06-27
REL
REL
This structure was determined using standard 2D homonuclear techniques combined with 2D 1H-15N HSQC data.
structures with the lowest target function
200
20
2D TOCSY
2D NOESY
DQF-COSY
2D HSQC
2D TOCSY
100 mM NaCl
7.2
ambient
307
K
The structures are based on 1151 restraints, 1054 are NOE-derived distance contraints, 25 dihedral angle constraints, and 72 distance restraints from hydrogen bonds. Structures were calculated using program DYANA. No further refinement was performed.
Simulated annealing combined with torsion angle dynamics
1
lowest target function
1mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3
90% H2O/10% D2O
1mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN3
90% H2O/10% D2O
Bruker
collection
XwinNMR
2.6,3.0
Bartels, Xia, Wuethrich
data analysis
XEASY
1.3.1.3
Guentert
structure solution
DYANA
1.5
Guentert, Wuethrich
refinement
DYANA
500
Bruker
DMX
600
Bruker
DMX
600
Bruker
DRX
CYS
134
n
1
CYS
134
A
GLY
135
n
2
GLY
135
A
TYR
136
n
3
TYR
136
A
VAL
137
n
4
VAL
137
A
ARG
138
n
5
ARG
138
A
ALA
139
n
6
ALA
139
A
LEU
140
n
7
LEU
140
A
PHE
141
n
8
PHE
141
A
ASP
142
n
9
ASP
142
A
PHE
143
n
10
PHE
143
A
ASN
144
n
11
ASN
144
A
GLY
145
n
12
GLY
145
A
ASN
146
n
13
ASN
146
A
ASP
147
n
14
ASP
147
A
GLU
148
n
15
GLU
148
A
GLU
149
n
16
GLU
149
A
ASP
150
n
17
ASP
150
A
LEU
151
n
18
LEU
151
A
PRO
152
n
19
PRO
152
A
PHE
153
n
20
PHE
153
A
LYS
154
n
21
LYS
154
A
LYS
155
n
22
LYS
155
A
GLY
156
n
23
GLY
156
A
ASP
157
n
24
ASP
157
A
ILE
158
n
25
ILE
158
A
LEU
159
n
26
LEU
159
A
ARG
160
n
27
ARG
160
A
ILE
161
n
28
ILE
161
A
ARG
162
n
29
ARG
162
A
ASP
163
n
30
ASP
163
A
LYS
164
n
31
LYS
164
A
PRO
165
n
32
PRO
165
A
GLU
166
n
33
GLU
166
A
GLU
167
n
34
GLU
167
A
GLN
168
n
35
GLN
168
A
TRP
169
n
36
TRP
169
A
TRP
170
n
37
TRP
170
A
ASN
171
n
38
ASN
171
A
ALA
172
n
39
ALA
172
A
GLU
173
n
40
GLU
173
A
ASP
174
n
41
ASP
174
A
SER
175
n
42
SER
175
A
GLU
176
n
43
GLU
176
A
GLY
177
n
44
GLY
177
A
LYS
178
n
45
LYS
178
A
ARG
179
n
46
ARG
179
A
GLY
180
n
47
GLY
180
A
MET
181
n
48
MET
181
A
ILE
182
n
49
ILE
182
A
PRO
183
n
50
PRO
183
A
VAL
184
n
51
VAL
184
A
PRO
185
n
52
PRO
185
A
TYR
186
n
53
TYR
186
A
VAL
187
n
54
VAL
187
A
GLU
188
n
55
GLU
188
A
LYS
189
n
56
LYS
189
A
TYR
190
n
57
TYR
190
A
GLY
191
n
58
GLY
191
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
ILE
182
A
O
ILE
49
A
N
TRP
170
A
N
TRP
37
A
O
ASN
171
A
O
ASN
38
A
N
ASP
163
A
N
ASP
30
A
O
LEU
159
A
O
LEU
26
A
N
VAL
137
A
N
VAL
4
A
N
TYR
136
A
N
TYR
3
A
O
GLY
191
A
O
GLY
58
3
A
A
O
HE1
GLU
TRP
166
170
1.50
9
A
A
O
H
ALA
GLY
139
156
1.57
15
A
A
O
HE1
GLU
TRP
166
170
1.60
17
A
A
O
H
ASP
ASP
147
150
1.59
19
A
A
O
H
ASP
GLU
147
149
1.54
1
A
ASN
146
-159.47
60.66
1
A
GLU
148
-86.63
39.16
1
A
GLU
149
-144.49
-39.73
1
A
GLN
168
-155.40
-49.93
1
A
ASP
174
-57.41
176.69
2
A
ASN
146
176.38
48.20
2
A
GLU
148
-81.64
45.87
2
A
GLU
149
-160.41
-37.63
2
A
GLN
168
-171.67
-60.89
2
A
ASP
174
-55.02
171.07
2
A
SER
175
-77.94
29.93
3
A
PHE
141
-170.62
135.14
3
A
ASN
146
-173.70
-58.64
3
A
ASP
147
166.09
123.91
3
A
GLN
168
170.15
-66.52
3
A
SER
175
-80.59
31.61
4
A
PHE
141
-165.20
118.45
4
A
ASN
146
178.03
-36.36
4
A
GLU
148
-87.06
31.71
4
A
LYS
155
-47.16
106.77
4
A
GLN
168
79.43
-51.95
4
A
TYR
190
-111.18
75.34
5
A
TYR
136
-144.45
-144.83
5
A
LEU
140
-99.51
40.11
5
A
ASN
146
-179.05
74.55
5
A
GLU
148
-86.14
43.18
5
A
GLU
149
-154.83
-41.00
5
A
GLU
166
-51.61
176.67
5
A
GLN
168
-175.84
-56.71
5
A
ASP
174
-54.39
173.43
6
A
LEU
140
-106.12
42.17
6
A
ASN
146
-174.34
-45.24
6
A
GLU
148
-86.02
39.34
6
A
ARG
162
-101.24
-64.87
6
A
LYS
164
84.78
100.14
6
A
GLU
166
30.99
-145.73
6
A
GLU
167
-165.74
44.96
6
A
GLN
168
-175.23
-60.61
6
A
ASP
174
-57.33
172.55
6
A
TYR
186
-84.99
40.58
7
A
LEU
140
-107.77
47.45
7
A
PHE
141
178.12
134.40
7
A
ASN
146
178.57
43.55
7
A
ASP
147
54.72
174.22
7
A
GLU
149
178.60
-34.95
7
A
ASP
150
167.81
124.83
7
A
GLN
168
76.27
-52.45
7
A
ASP
174
-56.70
173.78
7
A
TYR
186
-91.55
33.74
8
A
LEU
140
-97.86
41.63
8
A
ASN
146
177.34
38.42
8
A
ASP
147
74.70
42.90
8
A
GLU
148
-98.36
46.91
8
A
LYS
155
-52.35
109.22
8
A
GLU
166
-78.74
-168.34
8
A
GLN
168
162.04
-60.26
8
A
ASP
174
-59.04
175.95
8
A
TYR
186
-88.90
44.38
9
A
LEU
140
-104.44
43.72
9
A
ASN
146
169.69
-54.84
9
A
GLU
148
-85.97
36.55
9
A
GLU
166
-61.80
-175.83
9
A
GLN
168
154.83
-74.49
9
A
SER
175
-81.74
31.41
10
A
ASN
146
-170.00
-42.82
10
A
GLU
166
-60.83
-178.10
10
A
GLN
168
-153.62
-45.01
10
A
ASP
174
-52.14
179.59
10
A
TYR
186
-90.95
30.65
11
A
PHE
141
-174.48
125.08
11
A
ASN
146
-177.94
-61.77
11
A
ASP
147
-176.97
124.04
11
A
LYS
155
-56.16
102.34
11
A
GLN
168
-148.97
-47.58
11
A
ASP
174
-55.37
178.22
12
A
LEU
140
-108.54
45.37
12
A
PHE
141
-171.73
125.72
12
A
ASN
146
-178.53
-42.18
12
A
GLU
148
-85.67
35.37
12
A
GLU
167
-113.80
57.55
12
A
GLN
168
-170.73
-67.84
13
A
LEU
140
-94.27
41.19
13
A
PHE
141
-178.90
130.42
13
A
ASN
144
176.01
141.77
13
A
ASN
146
-171.67
-46.08
13
A
GLU
148
-83.93
38.02
13
A
GLU
149
-160.52
39.85
13
A
PHE
153
-109.11
-163.53
13
A
LYS
154
-177.44
147.37
13
A
LYS
164
-150.44
58.44
13
A
GLN
168
85.49
-56.97
13
A
SER
175
-77.19
28.79
14
A
TYR
136
-109.25
-151.87
14
A
PHE
141
-173.96
131.43
14
A
ASN
146
177.72
47.99
14
A
GLU
148
-80.50
47.72
14
A
GLU
149
-165.96
-39.02
14
A
LYS
164
-156.58
63.78
14
A
GLN
168
171.73
-67.83
14
A
ASP
174
-55.75
174.88
15
A
LEU
140
-103.26
43.67
15
A
PHE
141
-174.52
121.36
15
A
ASN
144
-103.45
-79.94
15
A
ASN
146
164.47
88.68
15
A
ASP
147
-40.82
160.93
15
A
GLU
148
-76.88
44.58
15
A
GLU
149
-140.70
-36.82
15
A
PRO
165
-74.95
-76.35
15
A
GLU
166
-51.92
179.06
15
A
GLN
168
-155.03
-43.35
15
A
SER
175
-75.79
30.19
16
A
LEU
140
-109.37
48.08
16
A
ASN
146
-178.32
37.22
16
A
ASP
147
54.44
170.61
16
A
GLU
148
69.94
-60.94
16
A
ASP
150
179.80
149.35
16
A
LYS
164
-155.48
57.51
16
A
PRO
165
-75.01
40.16
16
A
GLN
168
176.14
-62.88
16
A
ASP
174
-57.29
172.72
16
A
SER
175
-79.54
27.60
17
A
LEU
140
-108.31
46.52
17
A
PHE
141
-171.87
119.88
17
A
ASN
144
-70.08
-71.12
17
A
ASN
146
172.57
39.16
17
A
GLU
148
-38.35
-39.15
17
A
ARG
162
-122.63
-52.68
17
A
GLN
168
78.65
-51.90
17
A
ASP
174
-53.35
171.27
17
A
SER
175
-77.55
29.89
18
A
ASN
144
-174.31
77.48
18
A
ASN
146
173.90
-53.97
18
A
ASP
147
-170.12
119.26
18
A
GLN
168
-172.81
-65.72
18
A
SER
175
-83.34
30.53
18
A
TYR
190
-123.13
-67.10
19
A
LEU
140
-119.77
50.30
19
A
PHE
141
-178.23
133.17
19
A
ASN
144
-103.43
-74.78
19
A
ASN
146
160.76
51.59
19
A
GLU
148
66.69
-58.23
19
A
LEU
151
-39.61
110.39
19
A
ARG
162
-120.54
-59.30
19
A
GLN
168
81.39
-54.54
19
A
ASP
174
-56.14
171.36
19
A
TYR
190
-157.90
82.54
20
A
ASN
146
174.20
68.11
20
A
GLU
148
-79.78
42.26
20
A
GLU
149
-142.99
-41.84
20
A
GLN
168
78.51
-51.91
20
A
ASP
174
-49.63
170.74
Solution structure of a circular form of the N-terminal SH3 domain (A134C, E135G, R191G mutant) from oncogene protein c-Crk.
1
N
N
covale
1.494
both
A
CYS
134
A
N
CYS
1
1_555
A
GLY
191
A
C
GLY
58
1_555
PROTEIN BINDING
SH3, SH3 DOMAIN, CIRCULAR PROTEIN, CYCLIZED PROTEIN, ADAPTOR PROTEIN, PROTEIN BINDING
CRK_MOUSE
UNP
1
134
Q64010
AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYR
134
191
1M3B
134
191
Q64010
A
1
1
58
1
ALA
engineered mutation
CYS
134
1M3B
A
Q64010
UNP
134
1
1
GLU
engineered mutation
GLY
135
1M3B
A
Q64010
UNP
135
2
1
ARG
engineered mutation
GLY
191
1M3B
A
Q64010
UNP
191
58
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ARG
179
A
ARG
46
A
PRO
183
A
PRO
50
A
TRP
169
A
TRP
36
A
ASP
174
A
ASP
41
A
LYS
155
A
LYS
22
A
ASP
163
A
ASP
30
A
TYR
136
A
TYR
3
A
LEU
140
A
LEU
7
A
VAL
187
A
VAL
54
A
GLY
191
A
GLY
58