data_2YFZ # _model_server_result.job_id Ndf8ulVrBGaTWHY5p9hr8g _model_server_result.datetime_utc '2024-11-01 20:42:52' _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 2yfz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1141}' # _entry.id 2YFZ # _exptl.entry_id 2YFZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _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 2YFZ _cell.length_a 191.801 _cell.length_b 191.801 _cell.length_c 191.801 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YFZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 209 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 XYS BGC C1 O1 . O6 HO6 . sing 3 ? 2 4 3 GAL XYS C1 O1 . O2 HO2 . sing 4 ? 2 5 2 BGC BGC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B BGC 1 B 1 BGC A 1143 BGC 2 n B BGC 2 B 2 BGC A 1144 BGC 2 n B XYS 3 B 3 XYS A 1145 XYS 2 n B GAL 4 B 4 GAL A 1146 GAL 2 n B BGC 5 B 5 BGC A 1148 BGC # 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 covale ? covale1 B O4 BGC . B BGC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.314 ? covale ? covale2 B O4 BGC . B BGC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.314 ? covale ? covale3 B O6 BGC . B BGC 2 1_555 B C1 XYS . B XYS 3 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.257 ? covale ? covale4 B O6 BGC . B BGC 2 1_555 B C1 XYS . B XYS 3 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.257 ? covale ? covale5 B O4 BGC . B BGC 2 1_555 B C1 BGC . B BGC 5 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale6 B O4 BGC . B BGC 2 1_555 B C1 BGC . B BGC 5 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale7 B O2 XYS . B XYS 3 1_555 B C1 GAL . B GAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? metalc ? metalc1 A O LYS 27 A LYS 25 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc2 A OD1 ASP 30 A ASP 28 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc3 A O ASP 32 A ASP 30 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 A OG1 THR 35 A THR 33 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc5 A O THR 35 A THR 33 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc6 A O ALA 132 A ALA 130 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc7 A OE1 GLU 133 A GLU 131 1_555 C CA CA . A CA 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2YFZ _atom_sites.fract_transf_matrix[1][1] 0.005214 _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] 0.005214 _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] 0.005214 _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 C 3 CA A 1 1141 1141 CA CA . D 4 GOL A 1 1142 1142 GOL GOL . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2025 2025 HOH HOH . E 5 HOH A 25 2026 2026 HOH HOH . E 5 HOH A 26 2027 2027 HOH HOH . E 5 HOH A 27 2028 2028 HOH HOH . E 5 HOH A 28 2029 2029 HOH HOH . E 5 HOH A 29 2030 2030 HOH HOH . E 5 HOH A 30 2031 2031 HOH HOH . E 5 HOH A 31 2032 2032 HOH HOH . E 5 HOH A 32 2033 2033 HOH HOH . E 5 HOH A 33 2034 2034 HOH HOH . E 5 HOH A 34 2035 2035 HOH HOH . E 5 HOH A 35 2036 2036 HOH HOH . E 5 HOH A 36 2037 2037 HOH HOH . E 5 HOH A 37 2038 2038 HOH HOH . E 5 HOH A 38 2039 2039 HOH HOH . E 5 HOH A 39 2040 2040 HOH HOH . E 5 HOH A 40 2041 2041 HOH HOH . E 5 HOH A 41 2042 2042 HOH HOH . E 5 HOH A 42 2043 2043 HOH HOH . E 5 HOH A 43 2044 2044 HOH HOH . E 5 HOH A 44 2045 2045 HOH HOH . E 5 HOH A 45 2046 2046 HOH HOH . E 5 HOH A 46 2047 2047 HOH HOH . E 5 HOH A 47 2048 2048 HOH HOH . E 5 HOH A 48 2049 2049 HOH HOH . E 5 HOH A 49 2050 2050 HOH HOH . E 5 HOH A 50 2051 2051 HOH HOH . E 5 HOH A 51 2052 2052 HOH HOH . E 5 HOH A 52 2053 2053 HOH HOH . E 5 HOH A 53 2054 2054 HOH HOH . E 5 HOH A 54 2056 2056 HOH HOH . E 5 HOH A 55 2057 2057 HOH HOH . E 5 HOH A 56 2058 2058 HOH HOH . E 5 HOH A 57 2059 2059 HOH HOH . E 5 HOH A 58 2060 2060 HOH HOH . E 5 HOH A 59 2061 2061 HOH HOH . E 5 HOH A 60 2062 2062 HOH HOH . E 5 HOH A 61 2063 2063 HOH HOH . E 5 HOH A 62 2064 2064 HOH HOH . E 5 HOH A 63 2065 2065 HOH HOH . E 5 HOH A 64 2066 2066 HOH HOH . E 5 HOH A 65 2067 2067 HOH HOH . E 5 HOH A 66 2068 2068 HOH HOH . E 5 HOH A 67 2069 2069 HOH HOH . E 5 HOH A 68 2070 2070 HOH HOH . E 5 HOH A 69 2071 2071 HOH HOH . E 5 HOH A 70 2072 2072 HOH HOH . E 5 HOH A 71 2073 2073 HOH HOH . E 5 HOH A 72 2074 2074 HOH HOH . E 5 HOH A 73 2075 2075 HOH HOH . E 5 HOH A 74 2076 2076 HOH HOH . E 5 HOH A 75 2077 2077 HOH HOH . E 5 HOH A 76 2078 2078 HOH HOH . E 5 HOH A 77 2079 2079 HOH HOH . E 5 HOH A 78 2080 2080 HOH HOH . E 5 HOH A 79 2081 2081 HOH HOH . E 5 HOH A 80 2082 2082 HOH HOH . E 5 HOH A 81 2083 2083 HOH HOH . E 5 HOH A 82 2084 2084 HOH HOH . E 5 HOH A 83 2085 2085 HOH HOH . E 5 HOH A 84 2086 2086 HOH HOH . E 5 HOH A 85 2087 2087 HOH HOH . E 5 HOH A 86 2088 2088 HOH HOH . E 5 HOH A 87 2089 2089 HOH HOH . E 5 HOH A 88 2090 2090 HOH HOH . E 5 HOH A 89 2091 2091 HOH HOH . E 5 HOH A 90 2092 2092 HOH HOH . E 5 HOH A 91 2093 2093 HOH HOH . E 5 HOH A 92 2094 2094 HOH HOH . E 5 HOH A 93 2095 2095 HOH HOH . E 5 HOH A 94 2096 2096 HOH HOH . E 5 HOH A 95 2098 2098 HOH HOH . E 5 HOH A 96 2099 2099 HOH HOH . E 5 HOH A 97 2100 2100 HOH HOH . E 5 HOH A 98 2101 2101 HOH HOH . E 5 HOH A 99 2103 2103 HOH HOH . E 5 HOH A 100 2104 2104 HOH HOH . E 5 HOH A 101 2105 2105 HOH HOH . E 5 HOH A 102 2106 2106 HOH HOH . E 5 HOH A 103 2107 2107 HOH HOH . E 5 HOH A 104 2108 2108 HOH HOH . E 5 HOH A 105 2109 2109 HOH HOH . E 5 HOH A 106 2110 2110 HOH HOH . E 5 HOH A 107 2111 2111 HOH HOH . E 5 HOH A 108 2112 2112 HOH HOH . E 5 HOH A 109 2113 2113 HOH HOH . E 5 HOH A 110 2114 2114 HOH HOH . E 5 HOH A 111 2115 2115 HOH HOH . E 5 HOH A 112 2116 2116 HOH HOH . E 5 HOH A 113 2117 2117 HOH HOH . E 5 HOH A 114 2118 2118 HOH HOH . E 5 HOH A 115 2119 2119 HOH HOH . E 5 HOH A 116 2120 2120 HOH HOH . E 5 HOH A 117 2121 2121 HOH HOH . E 5 HOH A 118 2122 2122 HOH HOH . E 5 HOH A 119 2123 2123 HOH HOH . E 5 HOH A 120 2124 2124 HOH HOH . E 5 HOH A 121 2125 2125 HOH HOH . E 5 HOH A 122 2126 2126 HOH HOH . E 5 HOH A 123 2127 2127 HOH HOH . E 5 HOH A 124 2128 2128 HOH HOH . E 5 HOH A 125 2129 2129 HOH HOH . E 5 HOH A 126 2130 2130 HOH HOH . E 5 HOH A 127 2131 2131 HOH HOH . E 5 HOH A 128 2132 2132 HOH HOH . E 5 HOH A 129 2133 2133 HOH HOH . E 5 HOH A 130 2134 2134 HOH HOH . E 5 HOH A 131 2135 2135 HOH HOH . E 5 HOH A 132 2136 2136 HOH HOH . E 5 HOH A 133 2137 2137 HOH HOH . E 5 HOH A 134 2138 2138 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id C _atom_site.label_entity_id 3 _atom_site.Cartn_x 41.6 _atom_site.Cartn_y 6.147 _atom_site.Cartn_z 55.006 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 13.23 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 1141 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #