0.019685
0.000000
0.000000
0.000000
0.019685
0.000000
0.000000
0.000000
0.011181
0.00000
0.00000
0.00000
Nioche, P.
Liu, W.-Q.
Broutin, I.
Charbonnier, F.
Latreille, M.-T.
Vidal, M.
Roques, B.
Garbay, C.
Ducruix, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
50.800
50.800
89.440
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
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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
315
1167
1177
10.1006/jmbi.2001.5299
11827484
Crystal structures of the SH2 domain of Grb2: highlight on the binding of a new high-affinity inhibitor.
2002
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
290
1
1999-06-21
SINGLE WAVELENGTH
M
x-ray
1
1.057
1.0
X31
EMBL/DESY, HAMBURG
1.057
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X31
11054.430
GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
SH2 Domain
1
man
polymer
1071.034
peptide: PSpYVNVQN
1
syn
polymer
18.015
water
90
nat
water
GRB2 ADAPTER PROTEIN
no
no
GSMAWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYH
RSTSVSRNQQIFLRDI
GSMAWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYH
RSTSVSRNQQIFLRDI
A
polypeptide(L)
no
yes
APS(PTR)VNVQN
APSYVNVQN
L
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
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
1
2.38
48.22
VAPOR DIFFUSION, HANGING DROP
6
ammonium phosphate, PEG400, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
diffrn_source
entity
pdbx_entity_src_syn
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Data collection
Data collection
Source and taxonomy
Structure summary
1
0
2002-03-13
1
1
2008-04-27
1
2
2011-07-13
1
3
2018-10-03
1
4
2018-10-10
_diffrn_source.pdbx_synchrotron_site
_entity.formula_weight
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
xray structure of Grb2 SH2 domain complexed with a doubly phosphorylated pseudopeptide
xray structure of Grb2 SH2 domain
RCSB
Y
RCSB
2001-09-13
REL
REL
HOH
water
This peptide was chemically synthesized.
32630
synthetic construct
sample
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2017
3
HOH
HOH
2017
L
HOH
2044
3
HOH
HOH
2044
L
HOH
2046
3
HOH
HOH
2046
L
HOH
2077
3
HOH
HOH
2077
L
HOH
2084
3
HOH
HOH
2084
L
GLY
56
n
1
GLY
56
A
SER
57
n
2
SER
57
A
MET
58
n
3
MET
58
A
ALA
59
n
4
ALA
59
A
TRP
60
n
5
TRP
60
A
PHE
61
n
6
PHE
61
A
PHE
62
n
7
PHE
62
A
GLY
63
n
8
GLY
63
A
LYS
64
n
9
LYS
64
A
ILE
65
n
10
ILE
65
A
PRO
66
n
11
PRO
66
A
ARG
67
n
12
ARG
67
A
ALA
68
n
13
ALA
68
A
LYS
69
n
14
LYS
69
A
ALA
70
n
15
ALA
70
A
GLU
71
n
16
GLU
71
A
GLU
72
n
17
GLU
72
A
MET
73
n
18
MET
73
A
LEU
74
n
19
LEU
74
A
SER
75
n
20
SER
75
A
LYS
76
n
21
LYS
76
A
GLN
77
n
22
GLN
77
A
ARG
78
n
23
ARG
78
A
HIS
79
n
24
HIS
79
A
ASP
80
n
25
ASP
80
A
GLY
81
n
26
GLY
81
A
ALA
82
n
27
ALA
82
A
PHE
83
n
28
PHE
83
A
LEU
84
n
29
LEU
84
A
ILE
85
n
30
ILE
85
A
ARG
86
n
31
ARG
86
A
GLU
87
n
32
GLU
87
A
SER
88
n
33
SER
88
A
GLU
89
n
34
GLU
89
A
SER
90
n
35
SER
90
A
ALA
91
n
36
ALA
91
A
PRO
92
n
37
PRO
92
A
GLY
93
n
38
GLY
93
A
ASP
94
n
39
ASP
94
A
PHE
95
n
40
PHE
95
A
SER
96
n
41
SER
96
A
LEU
97
n
42
LEU
97
A
SER
98
n
43
SER
98
A
VAL
99
n
44
VAL
99
A
LYS
100
n
45
LYS
100
A
PHE
101
n
46
PHE
101
A
GLY
102
n
47
GLY
102
A
ASN
103
n
48
ASN
103
A
ASP
104
n
49
ASP
104
A
VAL
105
n
50
VAL
105
A
GLN
106
n
51
GLN
106
A
HIS
107
n
52
HIS
107
A
PHE
108
n
53
PHE
108
A
LYS
109
n
54
LYS
109
A
VAL
110
n
55
VAL
110
A
LEU
111
n
56
LEU
111
A
ARG
112
n
57
ARG
112
A
ASP
113
n
58
ASP
113
A
GLY
114
n
59
GLY
114
A
ALA
115
n
60
ALA
115
A
GLY
116
n
61
GLY
116
A
LYS
117
n
62
LYS
117
A
TYR
118
n
63
TYR
118
A
PHE
119
n
64
PHE
119
A
LEU
120
n
65
LEU
120
A
TRP
121
n
66
TRP
121
A
VAL
122
n
67
VAL
122
A
VAL
123
n
68
VAL
123
A
LYS
124
n
69
LYS
124
A
PHE
125
n
70
PHE
125
A
ASN
126
n
71
ASN
126
A
SER
127
n
72
SER
127
A
LEU
128
n
73
LEU
128
A
ASN
129
n
74
ASN
129
A
GLU
130
n
75
GLU
130
A
LEU
131
n
76
LEU
131
A
VAL
132
n
77
VAL
132
A
ASP
133
n
78
ASP
133
A
TYR
134
n
79
TYR
134
A
HIS
135
n
80
HIS
135
A
ARG
136
n
81
ARG
136
A
SER
137
n
82
SER
137
A
THR
138
n
83
THR
138
A
SER
139
n
84
SER
139
A
VAL
140
n
85
VAL
140
A
SER
141
n
86
SER
141
A
ARG
142
n
87
ARG
142
A
ASN
143
n
88
ASN
143
A
GLN
144
n
89
GLN
144
A
GLN
145
n
90
GLN
145
A
ILE
146
n
91
ILE
146
A
PHE
147
n
92
PHE
147
A
LEU
148
n
93
LEU
148
A
ARG
149
n
94
ARG
149
A
ASP
150
n
95
ASP
150
A
ILE
151
n
96
ILE
151
A
ALA
1000
n
1
ALA
1000
L
PRO
1001
n
2
PRO
1001
L
SER
1002
n
3
SER
1002
L
PTR
1003
n
4
PTR
1003
L
VAL
1004
n
5
VAL
1004
L
ASN
1005
n
6
ASN
1005
L
VAL
1006
n
7
VAL
1006
L
GLN
1007
n
8
GLN
1007
L
ASN
1008
n
9
ASN
1008
L
author_and_software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
4
tetrameric
880
-8
6060
3490
-24
10400
L
PTR
1003
O-PHOSPHOTYROSINE
B
PTR
4
TYR
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
ARG
86
A
N
ARG
31
A
O
SER
96
A
O
SER
41
A
N
LEU
97
A
N
LEU
42
A
O
PHE
108
A
O
PHE
53
A
N
LEU
111
A
N
LEU
56
A
O
PHE
119
A
O
PHE
64
A
N
TYR
118
A
N
TYR
63
A
O
PHE
125
A
O
PHE
70
1
A
A
O
O
HOH
HOH
2025
2032
1.99
1
A
A
OE1
O
GLU
HOH
89
2057
2.16
A
1
4.21
0.50
120.30
124.51
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
67
67
67
N
1
-14.34
2.30
111.70
97.36
A
A
A
CD
CE
NZ
LYS
LYS
LYS
69
69
69
B
B
B
N
1
-3.02
0.50
120.30
117.28
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
142
142
142
N
1
A
A
CB
CG
GLU
GLU
71
71
-0.114
0.019
1.517
1.403
N
1
A
A
CB
CG1
VAL
VAL
99
99
-0.174
0.021
1.524
1.350
B
N
1
A
A
NE2
O
GLN
HOH
144
2028
2.17
B
1_555
5_645
1
A
ASP
113
-103.77
-168.39
1
A
TRP
121
-127.95
-69.72
1
A
VAL
122
-133.84
-37.86
1
L
PRO
1001
-53.37
179.82
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
bond-maz-ptr.param
bond-maz-ptr.top
19.6
0.00
0.00
0.00
0.00
0.00
0.00
0.2280000
0.007
0.1900000
1.55
8.00
993
17119
5.8
97.6
RANDOM
1238854.70
0.000000
1
RESTRAINED
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
Engh & Huber
0.20
0.16
5.00
0.14
0.12
1.55
8.00
90
947
0
0
857
0.035
2.9
25.7
2.03
1.80
1.50
2.84
2.00
2.25
2.00
3.35
2.50
0.3010000
0.024
0.2570000
1.65
156
2576
6
5.7
95.7
18.6
1.55
1JYR
17213
17122
0.0520000
1
99.7
phasing
AMoRE
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALEPACK
GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide
1
N
N
2
N
N
3
N
N
3
N
N
A
PRO
66
A
PRO
11
HELX_P
A
LYS
76
A
LYS
21
1
1
11
A
SER
127
A
SER
72
HELX_P
A
HIS
135
A
HIS
80
1
2
9
covale
1.293
L
SER
1002
B
C
SER
3
1_555
L
PTR
1003
B
N
PTR
4
1_555
covale
1.295
L
PTR
1003
B
C
PTR
4
1_555
L
VAL
1004
B
N
VAL
5
1_555
SIGNALING PROTEIN/INHIBITOR
receptor binding, regulatory, inhibitor, SIGNALING PROTEIN-INHIBITOR COMPLEX
GRB2_HUMAN
UNP
1
60
P62993
WFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTS
VSRNQQIFLRDI
1JYR
PDB
2
1JYR
APSYVNVQN
60
151
1JYR
60
151
P62993
A
1
5
96
1000
1008
1JYR
1000
1008
1JYR
L
2
1
9
1
CLONING ARTIFACT
GLY
56
1JYR
A
P62993
UNP
1
1
CLONING ARTIFACT
SER
57
1JYR
A
P62993
UNP
2
1
CLONING ARTIFACT
MET
58
1JYR
A
P62993
UNP
3
1
CLONING ARTIFACT
ALA
59
1JYR
A
P62993
UNP
4
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
PHE
83
A
PHE
28
A
GLU
87
A
GLU
32
A
PHE
95
A
PHE
40
A
PHE
101
A
PHE
46
A
ASP
104
A
ASP
49
A
LYS
109
A
LYS
54
A
LEU
111
A
LEU
56
A
ARG
112
A
ARG
57
A
TYR
118
A
TYR
63
A
PHE
119
A
PHE
64
A
LYS
124
A
LYS
69
A
PHE
125
A
PHE
70
BINDING SITE FOR CHAIN L OF PEPTIDE: PSPYVNVQN
Software
26
A
ARG
67
A
ARG
12
26
1_555
A
SER
75
A
SER
20
26
8_665
A
ARG
86
A
ARG
31
26
1_555
A
SER
88
A
SER
33
26
1_555
A
SER
90
A
SER
35
26
1_555
A
SER
96
A
SER
41
26
1_555
A
LYS
100
A
LYS
45
26
8_665
A
ASN
103
A
ASN
48
26
8_665
A
HIS
107
A
HIS
52
26
1_555
A
PHE
108
A
PHE
53
26
1_555
A
LYS
109
A
LYS
54
26
1_555
A
LEU
111
A
LEU
56
26
1_555
A
LEU
120
A
LEU
65
26
1_555
A
TRP
121
A
TRP
66
26
1_555
A
TYR
134
A
TYR
79
26
5_655
A
SER
137
A
SER
82
26
5_655
A
THR
138
A
THR
83
26
5_655
A
ARG
149
A
ARG
94
26
5_655
A
HOH
2036
C
HOH
26
8_665
A
HOH
2071
C
HOH
26
5_655
A
HOH
2081
C
HOH
26
8_665
A
HOH
2089
C
HOH
26
8_665
L
HOH
2017
D
HOH
26
1_555
L
HOH
2044
D
HOH
26
1_555
L
HOH
2046
D
HOH
26
1_555
L
HOH
2077
D
HOH
26
1_555
92
P 41 21 2