0.013441
0.007760
0.000000
0.000000
0.015520
0.000000
0.000000
0.000000
0.025773
0.00000
0.00000
0.00000
Holland, D.R.
Rubin, J.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
74.400
74.400
38.800
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
H2 O
18.015
WATER
non-polymer
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
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
C25 H38 N3 O10 P
571.557
4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID
non-polymer
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Med.Chem.
JMCMAR
0151
0022-2623
40
3719
3725
10.1021/jm970402q
9371236
Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand.
1997
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
72
779
Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
1993
10.2210/pdb1skj/pdb
pdb_00001skj
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
IMAGE PLATE
1994-07
MARRESEARCH
CU FILTER
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
12907.508
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
2.7.1.112
SH2 DOMAIN
N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD)
1
man
polymer
571.557
4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID
1
syn
non-polymer
18.015
water
61
nat
water
SRC SH2
no
no
GSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS
LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD
GSAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSS
LQQLVAYYSKHADGLCHRLTNVCPTSKEFIVTD
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Alpharetrovirus
SCHMIDT-RUPPIN STRAIN A
Escherichia
sample
JM 83
11886
Rous sarcoma virus
JM83
562
Escherichia coli
PGEX-KT
BACTERIUM
1
2.5
48.77
WAKSMAN AND KURIYAN SRC SH2 STRUCTURE
VAPOR DIFFUSION, HANGING DROP
6.0
20% PEG 6K, 0.1M ODIUM CACODYLATE PH 6, HANGING DROP EXPERIMENT, PROTEIN 29 MG/ ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 6.0, vapor diffusion - hanging drop
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Refinement description
1
0
1998-02-25
1
1
2008-03-03
1
2
2011-07-13
1
3
2023-08-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1997-09-18
REL
REL
UR2
4-[3-CARBOXYMETHYL-3-(4-PHOSPHONOOXY-BENZYL)-UREIDO]-4-[(3-CYCLOHEXYL-PROPYL)-METHYL-CARBAMOYL]BUTYRIC ACID
HOH
water
G-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF
CLONING
: E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING
1SPS
PROTEIN MODEL FROM 1SPS
PDB
experimental model
UR2
1
2
UR2
UR2
113
A
HOH
1
3
HOH
HOH
114
A
HOH
2
3
HOH
HOH
115
A
HOH
3
3
HOH
HOH
116
A
HOH
4
3
HOH
HOH
117
A
HOH
5
3
HOH
HOH
118
A
HOH
7
3
HOH
HOH
119
A
HOH
9
3
HOH
HOH
120
A
HOH
10
3
HOH
HOH
121
A
HOH
11
3
HOH
HOH
122
A
HOH
12
3
HOH
HOH
123
A
HOH
13
3
HOH
HOH
124
A
HOH
16
3
HOH
HOH
125
A
HOH
19
3
HOH
HOH
126
A
HOH
21
3
HOH
HOH
127
A
HOH
22
3
HOH
HOH
128
A
HOH
23
3
HOH
HOH
129
A
HOH
24
3
HOH
HOH
130
A
HOH
25
3
HOH
HOH
131
A
HOH
26
3
HOH
HOH
132
A
HOH
27
3
HOH
HOH
133
A
HOH
28
3
HOH
HOH
134
A
HOH
30
3
HOH
HOH
135
A
HOH
31
3
HOH
HOH
136
A
HOH
32
3
HOH
HOH
137
A
HOH
33
3
HOH
HOH
138
A
HOH
36
3
HOH
HOH
139
A
HOH
37
3
HOH
HOH
140
A
HOH
38
3
HOH
HOH
141
A
HOH
39
3
HOH
HOH
142
A
HOH
40
3
HOH
HOH
143
A
HOH
41
3
HOH
HOH
144
A
HOH
42
3
HOH
HOH
145
A
HOH
44
3
HOH
HOH
146
A
HOH
45
3
HOH
HOH
147
A
HOH
48
3
HOH
HOH
148
A
HOH
49
3
HOH
HOH
149
A
HOH
51
3
HOH
HOH
150
A
HOH
52
3
HOH
HOH
151
A
HOH
53
3
HOH
HOH
152
A
HOH
55
3
HOH
HOH
153
A
HOH
60
3
HOH
HOH
154
A
HOH
63
3
HOH
HOH
155
A
HOH
65
3
HOH
HOH
156
A
HOH
67
3
HOH
HOH
157
A
HOH
68
3
HOH
HOH
158
A
HOH
69
3
HOH
HOH
159
A
HOH
71
3
HOH
HOH
160
A
HOH
74
3
HOH
HOH
161
A
HOH
77
3
HOH
HOH
162
A
HOH
80
3
HOH
HOH
163
A
HOH
85
3
HOH
HOH
164
A
HOH
88
3
HOH
HOH
165
A
HOH
89
3
HOH
HOH
166
A
HOH
93
3
HOH
HOH
167
A
HOH
94
3
HOH
HOH
168
A
HOH
96
3
HOH
HOH
169
A
HOH
97
3
HOH
HOH
170
A
HOH
98
3
HOH
HOH
171
A
HOH
106
3
HOH
HOH
172
A
HOH
116
3
HOH
HOH
173
A
HOH
117
3
HOH
HOH
174
A
n
1
0
A
n
2
1
A
n
3
2
A
GLU
3
n
4
GLU
3
A
GLU
4
n
5
GLU
4
A
TRP
5
n
6
TRP
5
A
TYR
6
n
7
TYR
6
A
PHE
7
n
8
PHE
7
A
GLY
8
n
9
GLY
8
A
LYS
9
n
10
LYS
9
A
ILE
10
n
11
ILE
10
A
THR
11
n
12
THR
11
A
ARG
12
n
13
ARG
12
A
ARG
13
n
14
ARG
13
A
GLU
14
n
15
GLU
14
A
SER
15
n
16
SER
15
A
GLU
16
n
17
GLU
16
A
ARG
17
n
18
ARG
17
A
LEU
18
n
19
LEU
18
A
LEU
19
n
20
LEU
19
A
LEU
20
n
21
LEU
20
A
ASN
21
n
22
ASN
21
A
PRO
22
n
23
PRO
22
A
GLU
23
n
24
GLU
23
A
ASN
24
n
25
ASN
24
A
PRO
25
n
26
PRO
25
A
ARG
26
n
27
ARG
26
A
GLY
27
n
28
GLY
27
A
THR
28
n
29
THR
28
A
PHE
29
n
30
PHE
29
A
LEU
30
n
31
LEU
30
A
VAL
31
n
32
VAL
31
A
ARG
32
n
33
ARG
32
A
GLU
33
n
34
GLU
33
A
SER
34
n
35
SER
34
A
GLU
35
n
36
GLU
35
A
THR
36
n
37
THR
36
A
THR
37
n
38
THR
37
A
LYS
38
n
39
LYS
38
A
GLY
39
n
40
GLY
39
A
ALA
40
n
41
ALA
40
A
TYR
41
n
42
TYR
41
A
CYS
42
n
43
CYS
42
A
LEU
43
n
44
LEU
43
A
SER
44
n
45
SER
44
A
VAL
45
n
46
VAL
45
A
SER
46
n
47
SER
46
A
ASP
47
n
48
ASP
47
A
PHE
48
n
49
PHE
48
A
ASP
49
n
50
ASP
49
A
ASN
50
n
51
ASN
50
A
ALA
51
n
52
ALA
51
A
LYS
52
n
53
LYS
52
A
GLY
53
n
54
GLY
53
A
LEU
54
n
55
LEU
54
A
ASN
55
n
56
ASN
55
A
VAL
56
n
57
VAL
56
A
LYS
57
n
58
LYS
57
A
HIS
58
n
59
HIS
58
A
TYR
59
n
60
TYR
59
A
LYS
60
n
61
LYS
60
A
ILE
61
n
62
ILE
61
A
ARG
62
n
63
ARG
62
A
LYS
63
n
64
LYS
63
A
LEU
64
n
65
LEU
64
A
ASP
65
n
66
ASP
65
A
SER
66
n
67
SER
66
A
GLY
67
n
68
GLY
67
A
GLY
68
n
69
GLY
68
A
PHE
69
n
70
PHE
69
A
TYR
70
n
71
TYR
70
A
ILE
71
n
72
ILE
71
A
THR
72
n
73
THR
72
A
SER
73
n
74
SER
73
A
ARG
74
n
75
ARG
74
A
THR
75
n
76
THR
75
A
GLN
76
n
77
GLN
76
A
PHE
77
n
78
PHE
77
A
SER
78
n
79
SER
78
A
SER
79
n
80
SER
79
A
LEU
80
n
81
LEU
80
A
GLN
81
n
82
GLN
81
A
GLN
82
n
83
GLN
82
A
LEU
83
n
84
LEU
83
A
VAL
84
n
85
VAL
84
A
ALA
85
n
86
ALA
85
A
TYR
86
n
87
TYR
86
A
TYR
87
n
88
TYR
87
A
SER
88
n
89
SER
88
A
LYS
89
n
90
LYS
89
A
HIS
90
n
91
HIS
90
A
ALA
91
n
92
ALA
91
A
ASP
92
n
93
ASP
92
A
GLY
93
n
94
GLY
93
A
LEU
94
n
95
LEU
94
A
CYS
95
n
96
CYS
95
A
HIS
96
n
97
HIS
96
A
ARG
97
n
98
ARG
97
A
LEU
98
n
99
LEU
98
A
THR
99
n
100
THR
99
A
ASN
100
n
101
ASN
100
A
VAL
101
n
102
VAL
101
A
CYS
102
n
103
CYS
102
A
PRO
103
n
104
PRO
103
A
THR
104
n
105
THR
104
A
n
106
105
A
n
107
106
A
n
108
107
A
n
109
108
A
n
110
109
A
n
111
110
A
n
112
111
A
n
113
112
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
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LEU
30
A
O
LEU
31
A
N
SER
44
A
N
SER
45
A
O
TYR
41
A
O
TYR
42
A
N
ILE
61
A
N
ILE
62
1
A
CB
GLU
3
A
CB
GLU
4
1
Y
1
A
CG
GLU
3
A
CG
GLU
4
1
Y
1
A
CD
GLU
3
A
CD
GLU
4
1
Y
1
A
OE1
GLU
3
A
OE1
GLU
4
1
Y
1
A
OE2
GLU
3
A
OE2
GLU
4
1
Y
1
A
CG
GLU
4
A
CG
GLU
5
1
Y
1
A
CD
GLU
4
A
CD
GLU
5
1
Y
1
A
OE1
GLU
4
A
OE1
GLU
5
1
Y
1
A
OE2
GLU
4
A
OE2
GLU
5
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
SER
1
A
SER
2
1
Y
1
A
ALA
2
A
ALA
3
1
Y
1
A
SER
105
A
SER
106
1
Y
1
A
LYS
106
A
LYS
107
1
Y
1
A
GLU
107
A
GLU
108
1
Y
1
A
PHE
108
A
PHE
109
1
Y
1
A
ILE
109
A
ILE
110
1
Y
1
A
VAL
110
A
VAL
111
1
Y
1
A
THR
111
A
THR
112
1
Y
1
A
ASP
112
A
ASP
113
1
Y
1
A
CA
THR
104
WRONG HAND
1
A
TYR
41
0.070
SIDE CHAIN
1
14.19
2.30
115.30
129.49
A
A
A
CA
CB
CG
LEU
LEU
LEU
30
30
30
N
1
A
GLU
4
-34.37
-30.75
1
A
SER
66
-95.70
39.39
1
A
THR
99
-117.09
-88.43
17.
0.2750000
0.2000000
0.2000000
2.0
8.
438
4253
10.
89.
RANDOM
1
R-FREE
2.4
MOLECULAR REPLACEMENT
PROTEIN MODEL FROM 1SPS
2.0
8.
61
881
0
0
820
0.014
2.9
28.6
2.7
0.2800000
0.2400000
2.51
53
445
8
10.
85.
25.5
2.4
25.
1SKJ
4694
2.
0.1090000
1
18.9
3.7
95.48
0.2760000
2.4
2.5
7.
3.5
96.9
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
data reduction
XDS
data scaling
XDS
phasing
X-PLOR
3.1
COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX
1
N
N
2
N
N
3
N
N
A
ARG
12
A
ARG
13
HELX_P
A
LEU
19
A
LEU
20
1
1
8
A
LEU
80
A
LEU
81
HELX_P
A
TYR
87
A
TYR
88
1
2
8
TYROSINE-PROTEIN KINASE
TYROSINE-PROTEIN KINASE, V-SRC SH2 DOMAIN, PHOSPHOTYROSINE RECOGNITION DOMAIN, PP60 SRC SH2 DOMAIN, PEPTIDOMIMETIC, UREIDO
SRC_RSVSA
UNP
1
1
P00524
MGSSKSKPKGPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGDFNTSDTVTSPQRAGALA
GGVTTFVALYDYESWIETDLSFKKGERLQIVNNTEGNWWLAHSVTTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESER
LLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHR
LTNVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHK
KLVQLYAVVSEEPIYIVIEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVC
KVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMGNGEVLDRVERGYR
MPCPPECPESLHDLMSQCWRRDPEERPTFEYLQAQLLPACVLEVAE
142
252
1SKJ
1
111
P00524
A
1
2
112
1
ILE
deletion
1SKJ
A
P00524
UNP
143
1
GLN
deletion
1SKJ
A
P00524
UNP
144
1
insertion
GLU
107
1SKJ
A
P00524
UNP
108
1
insertion
PHE
108
1SKJ
A
P00524
UNP
109
1
PRO
conflict
ILE
109
1SKJ
A
P00524
UNP
250
110
1
GLN
conflict
VAL
110
1SKJ
A
P00524
UNP
251
111
3
anti-parallel
anti-parallel
A
PHE
29
A
PHE
30
A
GLU
33
A
GLU
34
A
TYR
41
A
TYR
42
A
ASP
49
A
ASP
50
A
GLY
53
A
GLY
54
A
ILE
61
A
ILE
62
BINDING SITE FOR RESIDUE UR2 A 113
A
UR2
113
Software
16
A
PRO
22
A
PRO
23
16
4_674
A
ARG
26
A
ARG
27
16
4_674
A
ARG
32
A
ARG
33
16
1_555
A
SER
34
A
SER
35
16
1_555
A
GLU
35
A
GLU
36
16
1_555
A
THR
36
A
THR
37
16
1_555
A
CYS
42
A
CYS
43
16
1_555
A
HIS
58
A
HIS
59
16
1_555
A
TYR
59
A
TYR
60
16
1_555
A
LYS
60
A
LYS
61
16
1_555
A
ILE
71
A
ILE
72
16
1_555
A
ASP
92
A
ASP
93
16
1_555
A
GLY
93
A
GLY
94
16
1_555
A
HIS
96
A
HIS
97
16
4_674
A
HOH
133
C
HOH
16
4_674
A
HOH
153
C
HOH
16
1_555
169
P 61