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