data_2YGP # _model_server_result.job_id ySwe8MHyrYMVy_CXyplZgw _model_server_result.datetime_utc '2024-11-26 09:57:50' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2ygp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1213}' # _entry.id 2YGP # _exptl.entry_id 2YGP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 734.039 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2YGP _cell.length_a 50.76 _cell.length_b 134.241 _cell.length_c 60.193 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGP _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -50.76 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 109 A CYS 140 1_555 A SG CYS 146 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 151 A CYS 182 1_555 A SG CYS 161 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 155 A CYS 186 1_555 A SG CYS 167 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 169 A CYS 200 1_555 A SG CYS 178 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A C GLY 30 A GLY 61 1_555 A N MLY 31 A MLY 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C MLY 31 A MLY 62 1_555 A N MET 32 A MET 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale3 A C ARG 40 A ARG 71 1_555 A N MLY 41 A MLY 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 A C MLY 41 A MLY 72 1_555 A N ALA 42 A ALA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale5 A ND2 ASN 57 A ASN 88 1_555 C C1 NAG . A NAG 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 A C ASP 79 A ASP 110 1_555 A N MLY 80 A MLY 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale7 A C MLY 80 A MLY 111 1_555 A N GLY 81 A GLY 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale8 A C HIS 98 A HIS 129 1_555 A N MLY 99 A MLY 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 A C MLY 99 A MLY 130 1_555 A N ALA 100 A ALA 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale10 A C GLY 111 A GLY 142 1_555 A N MLY 112 A MLY 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C MLY 112 A MLY 143 1_555 A N GLN 113 A GLN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale12 A C LEU 134 A LEU 165 1_555 A N MLY 135 A MLY 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 A C MLY 135 A MLY 166 1_555 A N THR 136 A THR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? # _chem_comp.formula 'C40 H80 N O8 P' _chem_comp.formula_weight 734.039 _chem_comp.id PCF _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2YGP _atom_sites.fract_transf_matrix[1][1] 0.019701 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007449 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016613 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PCF A 1 1213 1213 PCF PCF . C 3 NAG A 1 1214 1214 NAG NAG . D 4 CA A 1 1215 1215 CA CA . E 5 SPD A 1 1216 1216 SPD SPD . F 6 HOH A 1 2001 2001 HOH HOH . F 6 HOH A 2 2002 2002 HOH HOH . F 6 HOH A 3 2003 2003 HOH HOH . F 6 HOH A 4 2004 2004 HOH HOH . F 6 HOH A 5 2005 2005 HOH HOH . F 6 HOH A 6 2006 2006 HOH HOH . F 6 HOH A 7 2007 2007 HOH HOH . F 6 HOH A 8 2008 2008 HOH HOH . F 6 HOH A 9 2009 2009 HOH HOH . F 6 HOH A 10 2010 2010 HOH HOH . F 6 HOH A 11 2011 2011 HOH HOH . F 6 HOH A 12 2012 2012 HOH HOH . F 6 HOH A 13 2013 2013 HOH HOH . F 6 HOH A 14 2014 2014 HOH HOH . F 6 HOH A 15 2015 2015 HOH HOH . F 6 HOH A 16 2016 2016 HOH HOH . F 6 HOH A 17 2017 2017 HOH HOH . F 6 HOH A 18 2018 2018 HOH HOH . F 6 HOH A 19 2019 2019 HOH HOH . F 6 HOH A 20 2020 2020 HOH HOH . F 6 HOH A 21 2021 2021 HOH HOH . F 6 HOH A 22 2022 2022 HOH HOH . F 6 HOH A 23 2023 2023 HOH HOH . F 6 HOH A 24 2024 2024 HOH HOH . F 6 HOH A 25 2025 2025 HOH HOH . F 6 HOH A 26 2026 2026 HOH HOH . F 6 HOH A 27 2027 2027 HOH HOH . F 6 HOH A 28 2028 2028 HOH HOH . F 6 HOH A 29 2029 2029 HOH HOH . F 6 HOH A 30 2030 2030 HOH HOH . F 6 HOH A 31 2031 2031 HOH HOH . F 6 HOH A 32 2032 2032 HOH HOH . F 6 HOH A 33 2033 2033 HOH HOH . F 6 HOH A 34 2034 2034 HOH HOH . F 6 HOH A 35 2035 2035 HOH HOH . F 6 HOH A 36 2036 2036 HOH HOH . F 6 HOH A 37 2037 2037 HOH HOH . F 6 HOH A 38 2038 2038 HOH HOH . F 6 HOH A 39 2039 2039 HOH HOH . F 6 HOH A 40 2040 2040 HOH HOH . F 6 HOH A 41 2041 2041 HOH HOH . F 6 HOH A 42 2042 2042 HOH HOH . F 6 HOH A 43 2043 2043 HOH HOH . F 6 HOH A 44 2044 2044 HOH HOH . F 6 HOH A 45 2045 2045 HOH HOH . F 6 HOH A 46 2046 2046 HOH HOH . F 6 HOH A 47 2047 2047 HOH HOH . F 6 HOH A 48 2048 2048 HOH HOH . F 6 HOH A 49 2049 2049 HOH HOH . F 6 HOH A 50 2050 2050 HOH HOH . F 6 HOH A 51 2051 2051 HOH HOH . F 6 HOH A 52 2052 2052 HOH HOH . F 6 HOH A 53 2053 2053 HOH HOH . F 6 HOH A 54 2054 2054 HOH HOH . F 6 HOH A 55 2055 2055 HOH HOH . F 6 HOH A 56 2056 2056 HOH HOH . F 6 HOH A 57 2057 2057 HOH HOH . F 6 HOH A 58 2058 2058 HOH HOH . F 6 HOH A 59 2059 2059 HOH HOH . F 6 HOH A 60 2060 2060 HOH HOH . F 6 HOH A 61 2061 2061 HOH HOH . F 6 HOH A 62 2062 2062 HOH HOH . F 6 HOH A 63 2063 2063 HOH HOH . F 6 HOH A 64 2064 2064 HOH HOH . F 6 HOH A 65 2065 2065 HOH HOH . F 6 HOH A 66 2066 2066 HOH HOH . F 6 HOH A 67 2067 2067 HOH HOH . F 6 HOH A 68 2068 2068 HOH HOH . F 6 HOH A 69 2069 2069 HOH HOH . F 6 HOH A 70 2070 2070 HOH HOH . F 6 HOH A 71 2071 2071 HOH HOH . F 6 HOH A 72 2072 2072 HOH HOH . F 6 HOH A 73 2073 2073 HOH HOH . F 6 HOH A 74 2074 2074 HOH HOH . F 6 HOH A 75 2075 2075 HOH HOH . F 6 HOH A 76 2076 2076 HOH HOH . F 6 HOH A 77 2077 2077 HOH HOH . F 6 HOH A 78 2078 2078 HOH HOH . F 6 HOH A 79 2079 2079 HOH HOH . F 6 HOH A 80 2080 2080 HOH HOH . F 6 HOH A 81 2081 2081 HOH HOH . F 6 HOH A 82 2082 2082 HOH HOH . F 6 HOH A 83 2083 2083 HOH HOH . F 6 HOH A 84 2084 2084 HOH HOH . F 6 HOH A 85 2085 2085 HOH HOH . F 6 HOH A 86 2086 2086 HOH HOH . F 6 HOH A 87 2087 2087 HOH HOH . F 6 HOH A 88 2088 2088 HOH HOH . F 6 HOH A 89 2089 2089 HOH HOH . F 6 HOH A 90 2090 2090 HOH HOH . F 6 HOH A 91 2091 2091 HOH HOH . F 6 HOH A 92 2092 2092 HOH HOH . F 6 HOH A 93 2093 2093 HOH HOH . F 6 HOH A 94 2094 2094 HOH HOH . F 6 HOH A 95 2095 2095 HOH HOH . F 6 HOH A 96 2096 2096 HOH HOH . F 6 HOH A 97 2097 2097 HOH HOH . F 6 HOH A 98 2098 2098 HOH HOH . F 6 HOH A 99 2099 2099 HOH HOH . F 6 HOH A 100 2100 2100 HOH HOH . F 6 HOH A 101 2101 2101 HOH HOH . F 6 HOH A 102 2102 2102 HOH HOH . F 6 HOH A 103 2103 2103 HOH HOH . F 6 HOH A 104 2104 2104 HOH HOH . F 6 HOH A 105 2105 2105 HOH HOH . F 6 HOH A 106 2106 2106 HOH HOH . F 6 HOH A 107 2107 2107 HOH HOH . F 6 HOH A 108 2108 2108 HOH HOH . F 6 HOH A 109 2109 2109 HOH HOH . F 6 HOH A 110 2110 2110 HOH HOH . F 6 HOH A 111 2111 2111 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N PCF . . . B 2 10.72 -14.043 14.329 1 99.27 ? N PCF 1213 A 1 HETATM 2 P P PCF . . . B 2 7.766 -10.961 15.184 1 95.28 ? P PCF 1213 A 1 HETATM 3 O O11 PCF . . . B 2 6.297 -10.972 14.616 1 155.35 ? O11 PCF 1213 A 1 HETATM 4 O O12 PCF . . . B 2 8.775 -11.162 14.112 1 94.6 ? O12 PCF 1213 A 1 HETATM 5 O O13 PCF . . . B 2 7.87 -12.346 15.936 1 123.98 ? O13 PCF 1213 A 1 HETATM 6 O O14 PCF . . . B 2 7.958 -9.786 16.08 1 87.1 ? O14 PCF 1213 A 1 HETATM 7 C C11 PCF . . . B 2 8.588 -13.373 15.256 1 118.87 ? C11 PCF 1213 A 1 HETATM 8 C C12 PCF . . . B 2 10.027 -12.957 15.009 1 106.04 ? C12 PCF 1213 A 1 HETATM 9 C C13 PCF . . . B 2 10.104 -14.116 13.017 1 97.54 ? C13 PCF 1213 A 1 HETATM 10 C C14 PCF . . . B 2 10.586 -15.272 15.083 1 101.68 ? C14 PCF 1213 A 1 HETATM 11 C C15 PCF . . . B 2 12.122 -13.694 14.217 1 99.87 ? C15 PCF 1213 A 1 HETATM 12 C C1 PCF . . . B 2 5.339 -10.048 15.012 1 161.86 ? C1 PCF 1213 A 1 HETATM 13 C C2 PCF . . . B 2 4.493 -10.833 15.956 1 149.27 ? C2 PCF 1213 A 1 HETATM 14 C C3 PCF . . . B 2 3.8 -9.865 16.86 1 157.65 ? C3 PCF 1213 A 1 HETATM 15 O O31 PCF . . . B 2 2.431 -10.124 16.782 1 174.21 ? O31 PCF 1213 A 1 HETATM 16 O O32 PCF . . . B 2 2.021 -7.978 17.231 1 182.4 ? O32 PCF 1213 A 1 HETATM 17 C C31 PCF . . . B 2 1.634 -9.116 17.374 1 161.95 ? C31 PCF 1213 A 1 HETATM 18 C C32 PCF . . . B 2 0.415 -9.482 18.154 1 138.62 ? C32 PCF 1213 A 1 HETATM 19 C C33 PCF . . . B 2 0.155 -10.97 18.135 1 108.03 ? C33 PCF 1213 A 1 HETATM 20 C C34 PCF . . . B 2 -1.019 -11.286 17.232 1 75.3 ? C34 PCF 1213 A 1 HETATM 21 C C35 PCF . . . B 2 -1.774 -12.541 17.618 1 53.14 ? C35 PCF 1213 A 1 HETATM 22 C C36 PCF . . . B 2 -3.217 -12.18 17.881 1 47.06 ? C36 PCF 1213 A 1 HETATM 23 C C37 PCF . . . B 2 -4.185 -13.082 17.17 1 38.89 ? C37 PCF 1213 A 1 HETATM 24 C C38 PCF . . . B 2 -4.151 -14.434 17.858 1 29.49 ? C38 PCF 1213 A 1 HETATM 25 C C39 PCF . . . B 2 -4.024 -15.613 16.922 1 39.21 ? C39 PCF 1213 A 1 HETATM 26 C C40 PCF . . . B 2 -2.981 -16.56 17.451 1 40.46 ? C40 PCF 1213 A 1 HETATM 27 C C41 PCF . . . B 2 -3.434 -17.994 17.564 1 44.71 ? C41 PCF 1213 A 1 HETATM 28 C C42 PCF . . . B 2 -4.17 -18.469 16.317 1 50.74 ? C42 PCF 1213 A 1 HETATM 29 C C43 PCF . . . B 2 -3.323 -19.271 15.345 1 46.24 ? C43 PCF 1213 A 1 HETATM 30 O O21 PCF . . . B 2 3.564 -11.674 15.261 1 127.1 ? O21 PCF 1213 A 1 HETATM 31 O O22 PCF . . . B 2 4.876 -13.046 16.405 1 112.09 ? O22 PCF 1213 A 1 HETATM 32 C C21 PCF . . . B 2 3.851 -12.99 15.751 1 108.26 ? C21 PCF 1213 A 1 HETATM 33 C C22 PCF . . . B 2 3.007 -14.216 15.475 1 78.58 ? C22 PCF 1213 A 1 HETATM 34 C C23 PCF . . . B 2 2.01 -14.493 16.579 1 55.49 ? C23 PCF 1213 A 1 HETATM 35 C C24 PCF . . . B 2 1.334 -15.865 16.506 1 44.88 ? C24 PCF 1213 A 1 HETATM 36 C C25 PCF . . . B 2 1.757 -16.717 17.674 1 44.48 ? C25 PCF 1213 A 1 HETATM 37 C C26 PCF . . . B 2 0.66 -17.619 18.188 1 38.02 ? C26 PCF 1213 A 1 HETATM 38 C C27 PCF . . . B 2 1.136 -19.055 18.267 1 41.47 ? C27 PCF 1213 A 1 HETATM 39 C C28 PCF . . . B 2 -0.02 -20.013 18.474 1 46.58 ? C28 PCF 1213 A 1 HETATM 40 C C29 PCF . . . B 2 -0.093 -21.029 17.351 1 42.57 ? C29 PCF 1213 A 1 HETATM 41 C C30 PCF . . . B 2 -1.051 -22.185 17.537 1 35.96 ? C30 PCF 1213 A 1 HETATM 42 C C47 PCF . . . B 2 -0.638 -23.361 16.678 1 30.94 ? C47 PCF 1213 A 1 HETATM 43 C C48 PCF . . . B 2 -1.564 -24.537 16.901 1 35.8 ? C48 PCF 1213 A 1 HETATM 44 C C49 PCF . . . B 2 -2.686 -24.779 15.89 1 36.93 ? C49 PCF 1213 A 1 HETATM 45 C C50 PCF . . . B 2 -2.389 -24.391 14.452 1 32.54 ? C50 PCF 1213 A 1 HETATM 46 C C51 PCF . . . B 2 -1.41 -25.278 13.704 1 31.79 ? C51 PCF 1213 A 1 HETATM 47 C C52 PCF . . . B 2 -1.651 -25.393 12.211 1 28.03 ? C52 PCF 1213 A 1 HETATM 48 C C44 PCF . . . B 2 -4.215 -20.17 14.486 1 44.29 ? C44 PCF 1213 A 1 HETATM 49 C C45 PCF . . . B 2 -5.063 -19.465 13.445 1 31.86 ? C45 PCF 1213 A 1 HETATM 50 C C46 PCF . . . B 2 -5.382 -20.299 12.215 1 31.51 ? C46 PCF 1213 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 50 #