data_5YZE # _model_server_result.job_id XsES_B2TkwANUvy6Pr-Vmw _model_server_result.datetime_utc '2025-02-27 01:24:09' _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 5yze # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":107}' # _entry.id 5YZE # _exptl.entry_id 5YZE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.933 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COBALT (II) ION' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5YZE _cell.length_a 46.401 _cell.length_b 46.401 _cell.length_c 73.822 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YZE _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 1 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,G,H,I,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 I N N ? 5 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 1 2 CDR CDR C3 H3 . O1 HO1 . sing 2 ? 2 2 3 CDR ERI C3 H3 . O1 HO1 . sing 3 ? 3 1 2 ARI 1GL C3 H3 . O1 HO1 . 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 C CDR 1 C 1 CDR A 101 CDR 2 n C CDR 2 C 2 CDR A 102 CDR 2 n C ERI 3 C 3 ERI A 103 ERI 3 n D ARI 1 D 1 ARI A 105 ARI 3 n D 1GL 2 D 2 1GL A 104 1GL 3 n E ARI 1 E 1 ARI B 102 ARI 3 n E 1GL 2 E 2 1GL B 101 1GL 2 n F CDR 1 F 1 CDR B 104 CDR 2 n F CDR 2 F 2 CDR B 105 CDR 2 n F ERI 3 F 3 ERI B 106 ERI # 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 G C6 CPH . A CPH 106 1_555 D O1 ARI . D ARI 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale2 G C2 CPH . A CPH 106 1_555 F O1 CDR . F CDR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale3 J C2 CPH . B CPH 103 1_555 C O1 CDR . C CDR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale4 J C6 CPH . B CPH 103 1_555 E O1 ARI . E ARI 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale5 C C3 CDR . C CDR 1 1_555 C O1 CDR . C CDR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale6 C C3 CDR . C CDR 2 1_555 C O1 ERI . C ERI 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale7 D C3 ARI . D ARI 1 1_555 D O1 1GL . D 1GL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale8 E C3 ARI . E ARI 1 1_555 E O1 1GL . E 1GL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale9 F C3 CDR . F CDR 1 1_555 F O1 CDR . F CDR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale10 F C3 CDR . F CDR 2 1_555 F O1 ERI . F ERI 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? metalc ? metalc1 A N7 DG 7 A DG 7 1_555 I CO CO . A CO 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc2 G O1 CPH . A CPH 106 1_555 H CO CO . A CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc3 G O9 CPH . A CPH 106 1_555 H CO CO . A CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc4 H CO CO . A CO 107 1_555 L O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc5 H CO CO . A CO 107 1_555 J O9 CPH . B CPH 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc6 H CO CO . A CO 107 1_555 J O1 CPH . B CPH 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc7 H CO CO . A CO 107 1_555 M O HOH . B HOH 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc8 I CO CO . A CO 108 1_555 L O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc9 I CO CO . A CO 108 1_555 L O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc10 I CO CO . A CO 108 1_555 L O HOH . A HOH 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc11 I CO CO . A CO 108 1_555 L O HOH . A HOH 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc12 I CO CO . A CO 108 1_555 L O HOH . A HOH 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc13 B N7 DG 7 B DG 18 1_555 K CO CO . B CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc14 K CO CO . B CO 107 1_555 M O HOH . B HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc15 K CO CO . B CO 107 1_555 M O HOH . B HOH 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc16 K CO CO . B CO 107 1_555 M O HOH . B HOH 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc17 K CO CO . B CO 107 1_555 M O HOH . B HOH 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc18 K CO CO . B CO 107 1_555 M O HOH . B HOH 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? hydrog WATSON-CRICK hydrog1 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 7 A DG 7 1_555 B N3 DC 8 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 7 A DG 7 1_555 B O2 DC 8 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 7 A DG 7 1_555 B N4 DC 8 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DC 8 A DC 8 1_555 B N1 DG 7 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 DC 8 A DC 8 1_555 B O6 DG 7 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 DC 8 A DC 8 1_555 B N2 DG 7 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Co 2' _chem_comp.formula_weight 58.933 _chem_comp.id CO _chem_comp.mon_nstd_flag . _chem_comp.name 'COBALT (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YZE _atom_sites.fract_transf_matrix[1][1] 0.021551 _atom_sites.fract_transf_matrix[1][2] 0.012443 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024885 _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] 0.013546 _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 G 4 CPH A 1 106 106 CPH CPH . H 5 CO A 1 107 107 CO CO . I 5 CO A 1 108 108 CO CO . J 4 CPH B 1 103 103 CPH CPH . K 5 CO B 1 107 107 CO CO . L 6 HOH A 1 201 201 HOH HOH . L 6 HOH A 2 202 202 HOH HOH . L 6 HOH A 3 203 203 HOH HOH . L 6 HOH A 4 204 204 HOH HOH . L 6 HOH A 5 205 205 HOH HOH . L 6 HOH A 6 206 206 HOH HOH . L 6 HOH A 7 207 207 HOH HOH . L 6 HOH A 8 208 208 HOH HOH . L 6 HOH A 9 209 209 HOH HOH . L 6 HOH A 10 210 210 HOH HOH . L 6 HOH A 11 211 211 HOH HOH . L 6 HOH A 12 212 212 HOH HOH . L 6 HOH A 13 213 213 HOH HOH . L 6 HOH A 14 214 214 HOH HOH . L 6 HOH A 15 215 215 HOH HOH . L 6 HOH A 16 216 216 HOH HOH . L 6 HOH A 17 217 217 HOH HOH . L 6 HOH A 18 218 218 HOH HOH . L 6 HOH A 19 219 219 HOH HOH . L 6 HOH A 20 220 220 HOH HOH . L 6 HOH A 21 221 221 HOH HOH . L 6 HOH A 22 222 222 HOH HOH . L 6 HOH A 23 223 223 HOH HOH . L 6 HOH A 24 224 224 HOH HOH . L 6 HOH A 25 225 225 HOH HOH . L 6 HOH A 26 226 226 HOH HOH . L 6 HOH A 27 227 227 HOH HOH . L 6 HOH A 28 228 228 HOH HOH . L 6 HOH A 29 229 229 HOH HOH . L 6 HOH A 30 230 230 HOH HOH . L 6 HOH A 31 231 231 HOH HOH . L 6 HOH A 32 232 232 HOH HOH . L 6 HOH A 33 233 233 HOH HOH . L 6 HOH A 34 234 234 HOH HOH . L 6 HOH A 35 235 235 HOH HOH . L 6 HOH A 36 236 236 HOH HOH . L 6 HOH A 37 237 237 HOH HOH . M 6 HOH B 1 201 201 HOH HOH . M 6 HOH B 2 202 202 HOH HOH . M 6 HOH B 3 203 203 HOH HOH . M 6 HOH B 4 204 204 HOH HOH . M 6 HOH B 5 205 205 HOH HOH . M 6 HOH B 6 206 206 HOH HOH . M 6 HOH B 7 207 207 HOH HOH . M 6 HOH B 8 208 208 HOH HOH . M 6 HOH B 9 209 209 HOH HOH . M 6 HOH B 10 210 210 HOH HOH . M 6 HOH B 11 211 211 HOH HOH . M 6 HOH B 12 212 212 HOH HOH . M 6 HOH B 13 213 213 HOH HOH . M 6 HOH B 14 214 214 HOH HOH . M 6 HOH B 15 215 215 HOH HOH . M 6 HOH B 16 216 216 HOH HOH . M 6 HOH B 17 217 217 HOH HOH . M 6 HOH B 18 218 218 HOH HOH . M 6 HOH B 19 219 219 HOH HOH . M 6 HOH B 20 220 220 HOH HOH . M 6 HOH B 21 221 221 HOH HOH . M 6 HOH B 22 222 222 HOH HOH . M 6 HOH B 23 223 223 HOH HOH . M 6 HOH B 24 224 224 HOH HOH . M 6 HOH B 25 225 225 HOH HOH . M 6 HOH B 26 226 226 HOH HOH . M 6 HOH B 27 227 227 HOH HOH . M 6 HOH B 28 228 228 HOH HOH . M 6 HOH B 29 229 229 HOH HOH . M 6 HOH B 30 230 230 HOH HOH . M 6 HOH B 31 231 231 HOH HOH . M 6 HOH B 32 232 232 HOH HOH . M 6 HOH B 33 233 233 HOH HOH . M 6 HOH B 34 234 234 HOH HOH . M 6 HOH B 35 235 235 HOH HOH . M 6 HOH B 36 236 236 HOH HOH . M 6 HOH B 37 237 237 HOH HOH . M 6 HOH B 38 238 238 HOH HOH . M 6 HOH B 39 239 239 HOH HOH . M 6 HOH B 40 240 240 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CO _atom_site.label_atom_id CO _atom_site.label_comp_id CO _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 5 _atom_site.Cartn_x 0.987 _atom_site.Cartn_y 13.385 _atom_site.Cartn_z 6.166 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.94 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 107 _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 10 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #