data_3LDY # _model_server_result.job_id uaX-fofPrnp0nGillCYp6A _model_server_result.datetime_utc '2025-03-31 10:55:33' _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 3ldy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":144}' # _entry.id 3LDY # _exptl.entry_id 3LDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 65.409 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZINC ION' _entity.pdbx_number_of_molecules 2 _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 3LDY _cell.length_a 36.908 _cell.length_b 115.788 _cell.length_c 114.689 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 PISA trimeric 3 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1,2 A,B,C,D,E,F,G,H 2 1 # 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 36.908 0 57.3445 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N 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 metalc ? metalc1 A SG CYS 4 A CYS 4 1_555 E ZN ZN . A ZN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc2 A SG CYS 7 A CYS 7 1_555 E ZN ZN . A ZN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc3 A SG CYS 24 A CYS 24 1_555 E ZN ZN . A ZN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc4 A SG CYS 27 A CYS 27 1_555 E ZN ZN . A ZN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc5 A SG CYS 63 A CYS 63 1_555 D ZN ZN . A ZN 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc6 A SG CYS 66 A CYS 66 1_555 D ZN ZN . A ZN 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc7 A OD1 ASP 92 A ASP 92 1_555 F CA CA . A CA 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc8 A SG CYS 109 A CYS 109 1_555 D ZN ZN . A ZN 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc9 A SG CYS 112 A CYS 112 1_555 D ZN ZN . A ZN 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc10 A OD1 ASN 113 A ASN 113 1_555 F CA CA . A CA 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc11 F CA CA . A CA 145 1_555 G O HOH . A HOH 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc12 F CA CA . A CA 145 1_555 G O HOH . A HOH 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc13 F CA CA . A CA 145 1_555 C O3' DT 2 C DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc14 F CA CA . A CA 145 1_555 C OP1 DT 3 C DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 B DG 1 1_555 C N3 DC 10 C DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 B DG 1 1_555 C O2 DC 10 C DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 B DG 1 1_555 C N4 DC 10 C DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 B DA 2 1_555 C N3 DT 9 C DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 B DA 2 1_555 C O4 DT 9 C DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 3 B DG 3 1_555 C N3 DC 8 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 3 B DG 3 1_555 C O2 DC 8 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 3 B DG 3 1_555 C N4 DC 8 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 4 B DG 4 1_555 C N3 DC 7 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 4 B DG 4 1_555 C O2 DC 7 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 4 B DG 4 1_555 C N4 DC 7 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 5 B DC 5 1_555 C N1 DG 6 C DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 5 B DC 5 1_555 C O6 DG 6 C DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 5 B DC 5 1_555 C N2 DG 6 C DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DT 6 B DT 6 1_555 C N1 DA 4 C DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 6 B DT 6 1_555 C N6 DA 4 C DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog17 B N3 DT 7 B DT 7 1_555 C O4 DT 3 C DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog18 B O2 DT 7 B DT 7 1_555 C N3 DT 3 C DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog19 B N6 DA 8 B DA 8 1_555 C N1 DA 1 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog20 B N7 DA 8 B DA 8 1_555 C N6 DA 1 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Zn 2' _chem_comp.formula_weight 65.409 _chem_comp.id ZN _chem_comp.mon_nstd_flag . _chem_comp.name 'ZINC ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3LDY _atom_sites.fract_transf_matrix[1][1] 0.027094 _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] 0.008636 _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] 0.008719 _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 D 4 ZN A 1 143 1 ZN ZN . E 4 ZN A 1 144 2 ZN ZN . F 5 CA A 1 145 3 CA CA . G 6 HOH A 1 146 1 HOH HOH . G 6 HOH A 2 147 2 HOH HOH . G 6 HOH A 3 148 4 HOH HOH . G 6 HOH A 4 149 5 HOH HOH . G 6 HOH A 5 150 6 HOH HOH . G 6 HOH A 6 151 7 HOH HOH . G 6 HOH A 7 152 8 HOH HOH . G 6 HOH A 8 153 9 HOH HOH . G 6 HOH A 9 154 10 HOH HOH . G 6 HOH A 10 155 11 HOH HOH . G 6 HOH A 11 156 12 HOH HOH . G 6 HOH A 12 157 13 HOH HOH . G 6 HOH A 13 158 14 HOH HOH . G 6 HOH A 14 159 15 HOH HOH . G 6 HOH A 15 160 16 HOH HOH . G 6 HOH A 16 161 17 HOH HOH . G 6 HOH A 17 162 18 HOH HOH . G 6 HOH A 18 163 19 HOH HOH . G 6 HOH A 19 164 20 HOH HOH . G 6 HOH A 20 165 21 HOH HOH . G 6 HOH A 21 166 22 HOH HOH . G 6 HOH A 22 167 23 HOH HOH . G 6 HOH A 23 168 24 HOH HOH . G 6 HOH A 24 169 25 HOH HOH . G 6 HOH A 25 170 26 HOH HOH . G 6 HOH A 26 171 27 HOH HOH . G 6 HOH A 27 172 28 HOH HOH . G 6 HOH A 28 173 29 HOH HOH . G 6 HOH A 29 174 30 HOH HOH . G 6 HOH A 30 175 31 HOH HOH . G 6 HOH A 31 176 32 HOH HOH . G 6 HOH A 32 177 33 HOH HOH . G 6 HOH A 33 178 34 HOH HOH . G 6 HOH A 34 179 35 HOH HOH . G 6 HOH A 35 180 36 HOH HOH . G 6 HOH A 36 181 37 HOH HOH . G 6 HOH A 37 182 38 HOH HOH . G 6 HOH A 38 183 39 HOH HOH . G 6 HOH A 39 184 40 HOH HOH . G 6 HOH A 40 185 41 HOH HOH . G 6 HOH A 41 186 42 HOH HOH . G 6 HOH A 42 187 43 HOH HOH . G 6 HOH A 43 188 44 HOH HOH . G 6 HOH A 44 189 45 HOH HOH . G 6 HOH A 45 190 46 HOH HOH . G 6 HOH A 46 191 47 HOH HOH . G 6 HOH A 47 192 48 HOH HOH . G 6 HOH A 48 193 49 HOH HOH . G 6 HOH A 49 194 50 HOH HOH . G 6 HOH A 50 195 51 HOH HOH . G 6 HOH A 51 196 52 HOH HOH . G 6 HOH A 52 197 53 HOH HOH . G 6 HOH A 53 198 54 HOH HOH . G 6 HOH A 54 199 55 HOH HOH . G 6 HOH A 55 200 56 HOH HOH . G 6 HOH A 56 201 57 HOH HOH . G 6 HOH A 57 202 58 HOH HOH . G 6 HOH A 58 203 59 HOH HOH . G 6 HOH A 59 204 60 HOH HOH . G 6 HOH A 60 205 61 HOH HOH . G 6 HOH A 61 206 62 HOH HOH . G 6 HOH A 62 207 63 HOH HOH . G 6 HOH A 63 208 64 HOH HOH . G 6 HOH A 64 209 65 HOH HOH . G 6 HOH A 65 210 66 HOH HOH . G 6 HOH A 66 211 67 HOH HOH . G 6 HOH A 67 212 68 HOH HOH . G 6 HOH A 68 213 69 HOH HOH . G 6 HOH A 69 214 70 HOH HOH . G 6 HOH A 70 215 71 HOH HOH . G 6 HOH A 71 216 72 HOH HOH . G 6 HOH A 72 217 73 HOH HOH . G 6 HOH A 73 218 74 HOH HOH . G 6 HOH A 74 219 75 HOH HOH . G 6 HOH A 75 220 76 HOH HOH . G 6 HOH A 76 221 77 HOH HOH . G 6 HOH A 77 222 78 HOH HOH . G 6 HOH A 78 223 79 HOH HOH . G 6 HOH A 79 224 80 HOH HOH . G 6 HOH A 80 225 81 HOH HOH . G 6 HOH A 81 226 82 HOH HOH . G 6 HOH A 82 227 83 HOH HOH . G 6 HOH A 83 228 84 HOH HOH . G 6 HOH A 84 229 85 HOH HOH . G 6 HOH A 85 230 86 HOH HOH . G 6 HOH A 86 231 87 HOH HOH . G 6 HOH A 87 232 88 HOH HOH . G 6 HOH A 88 233 89 HOH HOH . H 6 HOH C 1 3 3 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol ZN _atom_site.label_atom_id ZN _atom_site.label_comp_id ZN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 4 _atom_site.Cartn_x 22.939 _atom_site.Cartn_y 39.541 _atom_site.Cartn_z 57.902 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 24.64 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id ZN _atom_site.auth_comp_id ZN _atom_site.auth_seq_id 144 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #