1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
He, Y.
Radhakrishnan, I.
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
373
190
196
10.1016/j.jmb.2007.07.074
17765920
Structural Basis for Ubiquitin Recognition by SH3 Domains
2007
10.2210/pdb2jt4/pdb
pdb_00002jt4
8179.383
Cytoskeleton assembly control protein SLA1
1
man
polymer
8568.769
Ubiquitin
SH3 domain sequence database residues 350-420
1
man
polymer
no
no
MASKSKKRGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPVRDKKHTE
MASKSKKRGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPVRDKKHTE
A
polypeptide(L)
no
no
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
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
baker's yeast
Saccharomyces
Escherichia
sample
SLA1
4932
Saccharomyces cerevisiae
562
Escherichia coli
pET30
vector
baker's yeast
Saccharomyces
Escherichia
sample
UBI1, RPL40A
4932
Saccharomyces cerevisiae
562
Escherichia coli
pET3a
vector
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Database references
Derived calculations
1
0
2007-09-25
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
HELIX
DETERMINATION METHOD: AUTHOR
The authors state that these records reflect consensus
start and end residues in the 20 NMR models.
SHEET
DETERMINATION METHOD: AUTHOR
The authors state that these records reflect consensus
start and end residues in the 20 NMR models.
BMRB
Y
RCSB
2007-07-18
REL
REL
structures with the least restraint energies, restraint violations and rms deviations from ideal covalent geometry
80
20
3D HNCACB
3D HNCACB
3D C(CO)NH-TOCSY
3D C(CO)NH-TOCSY
3D HNCO
3D HNCO
3D H(CCO)NH-TOCSY
3D H(CCO)NH-TOCSY
3D 15N-edited NOESY
3D 15N-edited NOESY
3D HCCH-COSY
3D HCCH-COSY
3D HCCH-TOCSY
3D HCCH-TOCSY
3D 13C-edited NOESY
3D 13C-edited NOESY
3D 13C-filtered, 13C-edited NOESY
3D 13C-filtered, 13C-edited NOESY
2D 15N,13C-double-half-filtered NOESY
2D 15N,13C-double-half-filtered NOESY
0.9
mM
[U-98% 13C; U-98% 15N]
0.9
mM
0.9
mM
[U-98% 13C; U-98% 15N]
0.9
mM
0.9
mM
[U-98% 13C; U-98% 15N]
0.9
mM
0.9
mM
[U-98% 13C; U-98% 15N]
0.9
mM
20
6
ambient
318
K
torsion angle dynamics, simulated annealing
1
closest to the average
0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O
90% H2O/10% D2O
0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O
90% H2O/10% D2O
0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O
100% D2O
0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O
100% D2O
Varian
collection
VNMR
Accelrys Software Inc.
processing
Felix
Accelrys Software Inc.
data analysis
Felix
Johnson, One Moon Scientific
data analysis
NMRView
Johnson, One Moon Scientific
chemical shift assignment
NMRView
Linge, O'Donoghue and Nilges
refinement
ARIA
Linge, O'Donoghue and Nilges
structure solution
ARIA
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
600
Varian
INOVA
Varian INOVA
MET
1
n
1
MET
1
A
ALA
2
n
2
ALA
2
A
SER
3
n
3
SER
3
A
LYS
4
n
4
LYS
4
A
SER
5
n
5
SER
5
A
LYS
6
n
6
LYS
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
GLY
9
n
9
GLY
9
A
ILE
10
n
10
ILE
10
A
VAL
11
n
11
VAL
11
A
GLN
12
n
12
GLN
12
A
TYR
13
n
13
TYR
13
A
ASP
14
n
14
ASP
14
A
PHE
15
n
15
PHE
15
A
MET
16
n
16
MET
16
A
ALA
17
n
17
ALA
17
A
GLU
18
n
18
GLU
18
A
SER
19
n
19
SER
19
A
GLN
20
n
20
GLN
20
A
ASP
21
n
21
ASP
21
A
GLU
22
n
22
GLU
22
A
LEU
23
n
23
LEU
23
A
THR
24
n
24
THR
24
A
ILE
25
n
25
ILE
25
A
LYS
26
n
26
LYS
26
A
SER
27
n
27
SER
27
A
GLY
28
n
28
GLY
28
A
ASP
29
n
29
ASP
29
A
LYS
30
n
30
LYS
30
A
VAL
31
n
31
VAL
31
A
TYR
32
n
32
TYR
32
A
ILE
33
n
33
ILE
33
A
LEU
34
n
34
LEU
34
A
ASP
35
n
35
ASP
35
A
ASP
36
n
36
ASP
36
A
LYS
37
n
37
LYS
37
A
LYS
38
n
38
LYS
38
A
SER
39
n
39
SER
39
A
LYS
40
n
40
LYS
40
A
ASP
41
n
41
ASP
41
A
TRP
42
n
42
TRP
42
A
TRP
43
n
43
TRP
43
A
MET
44
n
44
MET
44
A
CYS
45
n
45
CYS
45
A
GLN
46
n
46
GLN
46
A
LEU
47
n
47
LEU
47
A
VAL
48
n
48
VAL
48
A
ASP
49
n
49
ASP
49
A
SER
50
n
50
SER
50
A
GLY
51
n
51
GLY
51
A
LYS
52
n
52
LYS
52
A
SER
53
n
53
SER
53
A
GLY
54
n
54
GLY
54
A
LEU
55
n
55
LEU
55
A
VAL
56
n
56
VAL
56
A
PRO
57
n
57
PRO
57
A
ALA
58
n
58
ALA
58
A
GLN
59
n
59
GLN
59
A
PHE
60
n
60
PHE
60
A
ILE
61
n
61
ILE
61
A
GLU
62
n
62
GLU
62
A
PRO
63
n
63
PRO
63
A
VAL
64
n
64
VAL
64
A
ARG
65
n
65
ARG
65
A
ASP
66
n
66
ASP
66
A
LYS
67
n
67
LYS
67
A
LYS
68
n
68
LYS
68
A
HIS
69
n
69
HIS
69
A
THR
70
n
70
THR
70
A
GLU
71
n
71
GLU
71
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
SER
19
n
19
SER
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
ASP
24
n
24
ASP
24
B
ASN
25
n
25
ASN
25
B
VAL
26
n
26
VAL
26
B
LYS
27
n
27
LYS
27
B
SER
28
n
28
SER
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
VAL
56
A
O
VAL
56
A
N
TRP
43
A
N
TRP
43
A
O
GLN
46
A
O
GLN
46
A
N
TYR
32
A
N
TYR
32
A
O
ILE
33
A
O
ILE
33
A
N
LYS
7
A
N
LYS
7
A
N
ILE
10
A
N
ILE
10
A
O
GLU
62
A
O
GLU
62
B
O
LEU
15
B
O
LEU
15
B
N
ILE
3
B
N
ILE
3
B
N
LYS
6
B
N
LYS
6
B
O
LEU
67
B
O
LEU
67
B
O
HIS
68
B
O
HIS
68
B
N
ILE
44
B
N
ILE
44
B
N
PHE
45
B
N
PHE
45
B
O
LYS
48
B
O
LYS
48
1
A
A
HZ1
OD1
LYS
ASP
7
36
1.56
1
B
B
HZ3
OE2
LYS
GLU
11
34
1.58
2
B
B
HH12
OE1
ARG
GLU
42
51
1.58
3
A
A
HZ1
OD2
LYS
ASP
7
36
1.55
3
A
A
OE1
HZ2
GLU
LYS
62
67
1.58
3
B
B
HZ2
OE1
LYS
GLU
33
34
1.59
5
B
B
HZ3
OE1
LYS
GLU
11
34
1.57
6
A
A
HZ1
OD1
LYS
ASP
7
36
1.59
7
A
A
HG3
H
ARG
ASP
65
66
1.31
9
A
A
HG3
HD2
PRO
LYS
63
68
1.25
10
A
A
HZ2
O
LYS
GLU
40
71
1.56
10
A
A
HZ1
OD2
LYS
ASP
7
66
1.58
10
A
B
OE2
HH12
GLU
ARG
22
72
1.60
10
B
B
H1
OE2
MET
GLU
1
16
1.60
11
B
B
OD2
HH12
ASP
ARG
39
74
1.56
12
B
B
HZ3
OE2
LYS
GLU
11
34
1.54
13
A
A
OD2
HZ3
ASP
LYS
35
38
1.56
13
A
B
OE2
HH12
GLU
ARG
22
42
1.57
13
A
A
HG
OD1
SER
ASP
19
21
1.59
14
A
A
OD2
HZ3
ASP
LYS
66
68
1.57
15
B
B
HD13
H
LEU
LEU
8
71
1.26
15
A
B
OE2
HH12
GLU
ARG
22
42
1.57
15
B
B
H2
OE2
MET
GLU
1
16
1.58
17
A
A
HZ3
OD1
LYS
ASP
7
36
1.57
18
B
B
OD2
HZ2
ASP
LYS
21
29
1.58
19
A
A
OE1
HZ3
GLU
LYS
62
68
1.60
1
A
ARG
65
70.14
-42.86
1
A
ASP
66
-49.33
-71.73
2
A
SER
5
-100.10
-64.10
2
A
SER
50
-149.93
-62.47
2
A
ARG
65
73.75
-23.53
2
A
ASP
66
71.92
138.06
2
A
LYS
67
-159.37
29.24
2
B
VAL
17
-127.17
-157.98
2
B
LEU
73
-78.01
23.32
3
A
SER
3
63.16
86.46
3
A
SER
39
-106.30
-89.88
3
A
LYS
40
165.17
-55.04
3
A
ARG
65
-56.48
-71.33
3
A
ASP
66
-151.48
4.85
3
A
HIS
69
63.71
-174.62
3
B
LYS
33
-77.98
-72.73
4
A
SER
3
65.41
-166.72
4
A
GLU
18
-130.87
-33.97
4
A
ASP
41
-120.71
-63.44
4
A
ARG
65
-103.99
-64.24
4
B
LYS
33
-107.82
-60.92
4
B
ALA
46
58.53
17.22
4
B
ARG
74
43.93
80.71
5
A
LYS
4
64.69
83.13
5
A
LYS
6
62.74
-167.30
5
A
ASP
49
-62.84
-70.73
5
A
ARG
65
-163.91
-54.58
5
A
ASP
66
-170.47
-173.16
5
A
THR
70
49.16
93.90
5
B
LYS
33
-92.68
-63.05
5
B
ASN
60
58.86
71.69
5
B
LEU
73
-67.48
90.76
6
A
ALA
2
-136.10
-44.65
6
A
SER
3
51.58
85.99
6
A
LYS
4
63.47
89.42
6
A
LYS
37
-141.71
27.27
6
A
LYS
40
70.17
-69.45
6
A
ASP
66
65.84
-87.99
6
A
LYS
67
-147.22
-7.47
6
A
LYS
68
69.45
115.99
7
A
LYS
4
-142.20
-75.27
7
A
SER
5
-145.77
-49.56
7
A
GLU
18
-141.62
-41.28
7
A
ARG
65
-140.68
-82.15
7
B
ASN
60
63.27
90.92
8
A
ALA
2
63.31
94.76
8
A
LEU
34
-76.37
-78.27
8
A
LYS
37
-94.51
-62.72
8
A
VAL
64
-82.47
49.48
8
A
LYS
68
63.21
94.33
8
A
HIS
69
-163.45
-79.66
8
A
THR
70
48.86
76.20
8
B
ALA
46
59.37
19.49
8
B
ARG
74
67.63
-66.54
9
A
LYS
37
-148.20
21.74
9
A
LYS
40
67.23
-64.96
9
A
ARG
65
-141.40
-89.93
9
A
ASP
66
-146.38
-158.84
9
A
LYS
67
77.97
-51.49
9
B
LYS
33
-82.72
-70.07
10
A
ASP
49
-62.85
-71.62
10
A
ARG
65
-169.48
76.46
10
A
LYS
67
52.15
76.83
10
B
LYS
33
-90.64
-64.89
10
B
PRO
37
-37.37
121.44
11
A
ALA
2
63.75
177.40
11
A
LEU
34
-94.07
-77.16
11
A
ASP
41
-140.70
-71.46
11
A
ARG
65
-99.88
-86.47
11
A
LYS
67
66.59
100.86
11
A
THR
70
46.60
-98.26
11
B
GLU
51
-68.95
-85.48
11
B
ASP
52
-179.07
-58.66
11
B
LEU
73
55.60
86.68
12
A
SER
3
78.12
168.17
12
A
LYS
4
-173.47
-75.16
12
A
LYS
6
71.27
148.56
12
A
ARG
65
160.25
-26.73
12
A
ASP
66
79.19
-0.38
12
A
THR
70
-169.62
-21.72
12
B
LEU
73
-73.95
26.42
12
B
ARG
74
64.00
103.91
13
A
ALA
2
68.21
100.82
13
A
ASP
41
-127.95
-52.82
13
A
ARG
65
-133.16
-65.08
13
A
ASP
66
171.19
116.23
13
A
LYS
67
59.25
177.41
13
B
ASN
60
64.89
68.50
14
A
SER
3
-81.11
35.66
14
A
SER
39
-125.00
-81.07
14
A
LYS
40
-175.79
-54.67
14
B
GLN
41
-68.09
99.71
14
B
LEU
73
-82.98
30.14
15
A
SER
3
65.82
172.58
15
A
LYS
4
-131.20
-48.41
15
A
SER
5
-139.89
-57.51
15
A
ASP
66
-160.12
-61.89
15
B
ASN
60
60.28
76.96
15
B
ARG
74
65.68
-67.57
16
A
SER
5
73.56
138.87
16
A
ASP
66
178.68
-84.23
16
A
LYS
67
-163.55
95.01
16
B
LYS
33
-91.02
-69.37
16
B
LEU
73
63.02
85.76
17
A
LEU
34
-98.16
-74.16
17
A
ASP
36
-122.00
-58.17
17
A
ASP
66
72.13
-37.80
17
B
LYS
33
-74.38
-77.48
17
B
ASN
60
60.91
67.98
17
B
ARG
74
58.41
87.49
18
A
LYS
4
-97.35
34.48
18
A
SER
5
48.05
90.58
18
A
LEU
34
-80.02
-74.73
18
A
ASP
36
-128.53
-62.85
18
A
ASP
41
-124.89
-51.67
18
A
ASP
66
-166.11
-12.72
18
A
LYS
67
76.65
161.19
18
A
HIS
69
-127.39
-90.00
18
B
ALA
46
58.69
18.47
19
A
SER
3
68.83
108.87
19
A
LYS
4
70.67
108.34
19
A
LEU
34
-92.52
-76.50
19
A
ASP
66
67.47
100.22
19
A
LYS
67
68.13
77.00
19
B
LEU
73
-55.05
100.33
20
A
ALA
2
-161.86
119.94
20
A
LYS
4
59.61
81.17
20
A
LYS
6
-89.82
35.50
20
A
LYS
7
64.39
133.28
20
A
ARG
65
-164.00
-50.38
20
A
HIS
69
-86.11
33.21
20
B
ARG
74
71.45
-69.18
Solution Structure of the Sla1 SH3-3-Ubiquitin Complex
1
N
N
2
N
N
B
ILE
23
B
ILE
23
HELX_P
B
LYS
33
B
LYS
33
1
1
11
SIGNALING PROTEIN
endocytosis, monoubiquitin signaling, ubiquitin-binding motif, SH3, ubiquitin, Actin-binding, Cytoplasm, Cytoskeleton, Phosphorylation, SH3 domain, DNA damage, DNA repair, Nucleus, Ubl conjugation, SIGNALING PROTEIN
SLA1_YEAST
UNP
1
350
P32790
MASKSKKRGIVQYDFMAESQDELTIKSGDKVYILDDKKSKDWWMCQLVDSGKSGLVPAQFIEPVRDKKHTE
UBIQ_YEAST
UNP
2
1
P61864
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
350
420
2JT4
1
71
P32790
A
1
1
71
1
76
2JT4
1
76
P61864
B
2
1
76
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
SER
53
A
SER
53
A
PRO
57
A
PRO
57
A
TRP
42
A
TRP
42
A
LEU
47
A
LEU
47
A
LYS
30
A
LYS
30
A
ASP
35
A
ASP
35
A
LYS
7
A
LYS
7
A
VAL
11
A
VAL
11
A
ILE
61
A
ILE
61
A
PRO
63
A
PRO
63
B
THR
12
B
THR
12
B
GLU
16
B
GLU
16
B
GLN
2
B
GLN
2
B
THR
7
B
THR
7
B
THR
66
B
THR
66
B
LEU
71
B
LEU
71
B
GLN
41
B
GLN
41
B
PHE
45
B
PHE
45
B
LYS
48
B
LYS
48
B
LEU
50
B
LEU
50