data_5XJW # _model_server_result.job_id V8zqtiA954pNOmajL4o-7g _model_server_result.datetime_utc '2025-02-27 01:36:47' _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 5xjw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":108}' # _entry.id 5XJW # _exptl.entry_id 5XJW _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 5XJW _cell.length_a 48.309 _cell.length_b 48.309 _cell.length_c 83.636 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XJW _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 2 1 DDA DDA C1 O1 . O3 HO3 . sing 2 ? 2 3 2 ERI DDA C1 O1 . O3 HO3 . sing 3 ? 3 2 1 1GL 2GL C1 O1 . O3 HO3 . 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 DDA 1 C 1 DDA C 57 CDR 2 n C DDA 2 C 2 DDA C 58 CDR 2 n C ERI 3 C 3 ERI C 59 ERI 3 n D 2GL 1 D 1 2GL C 61 ARI 3 n D 1GL 2 D 2 1GL C 60 1GL 3 n E 2GL 1 E 1 2GL C 55 ARI 3 n E 1GL 2 E 2 1GL C 54 1GL 2 n F DDA 1 F 1 DDA C 63 CDR 2 n F DDA 2 F 2 DDA C 64 CDR 2 n F ERI 3 F 3 ERI C 65 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 2GL . D 2GL 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale2 G C2 CPH . A CPH 106 1_555 F O1 DDA . F DDA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale3 J C2 CPH . B CPH 103 1_555 C O1 DDA . C DDA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale4 J C6 CPH . B CPH 103 1_555 E O1 2GL . E 2GL 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale5 C O3 DDA . C DDA 1 1_555 C C1 DDA . C DDA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 sing covale ? covale6 C O3 DDA . C DDA 2 1_555 C C1 ERI . C ERI 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale7 D O3 2GL . D 2GL 1 1_555 D C1 1GL . D 1GL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 sing covale ? covale8 E O3 2GL . E 2GL 1 1_555 E C1 1GL . E 1GL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale9 F O3 DDA . F DDA 1 1_555 F C1 DDA . F DDA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale10 F O3 DDA . F DDA 2 1_555 F C1 ERI . F ERI 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing metalc ? metalc1 A N7 DG 8 A DG 8 1_555 I CO CO . A CO 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc2 G O1 CPH . A CPH 106 1_555 H CO CO . A CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc3 G O9 CPH . A CPH 106 1_555 H CO CO . A CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 H CO CO . A CO 107 1_555 L O HOH . A HOH 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc5 H CO CO . A CO 107 1_555 J O1 CPH . B CPH 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc6 H CO CO . A CO 107 1_555 J O9 CPH . B CPH 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc7 H CO CO . A CO 107 1_555 M O HOH . B HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc8 I CO CO . A CO 108 1_555 L O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc9 I CO CO . A CO 108 1_555 L O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc10 I CO CO . A CO 108 1_555 L O HOH . A HOH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc11 I CO CO . A CO 108 1_555 L O HOH . A HOH 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc12 I CO CO . A CO 108 1_555 L O HOH . A HOH 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc13 B N7 DG 8 B DG 21 1_555 K CO CO . B CO 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc14 K CO CO . B CO 107 1_555 M O HOH . B HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc15 K CO CO . B CO 107 1_555 M O HOH . B HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc16 K CO CO . B CO 107 1_555 M O HOH . B HOH 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc17 K CO CO . B CO 107 1_555 M O HOH . B HOH 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc18 K CO CO . B CO 107 1_555 M O HOH . B HOH 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? hydrog HOOGSTEEN hydrog1 A N3 DT 1 A DT 1 1_555 B N7 DA 13 B DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog2 A O4 DT 1 A DT 1 1_555 B N6 DA 13 B DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 DT 2 A DT 2 1_555 B N1 DA 12 B DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O4 DT 2 A DT 2 1_555 B N6 DA 12 B DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N3 DC 4 A DC 4 1_555 B N1 DG 11 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N4 DC 4 A DC 4 1_555 B O6 DG 11 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O2 DC 4 A DC 4 1_555 B N2 DG 11 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DG 5 A DG 5 1_555 B N3 DC 10 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N2 DG 5 A DG 5 1_555 B O2 DC 10 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O6 DG 5 A DG 5 1_555 B N4 DC 10 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DG 8 A DG 8 1_555 B N3 DC 9 B DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N2 DG 8 A DG 8 1_555 B O2 DC 9 B DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O6 DG 8 A DG 8 1_555 B N4 DC 9 B DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 DC 9 A DC 9 1_555 B N1 DG 8 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N4 DC 9 A DC 9 1_555 B O6 DG 8 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O2 DC 9 A DC 9 1_555 B N2 DG 8 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DC 10 A DC 10 1_555 B N1 DG 5 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DC 10 A DC 10 1_555 B O6 DG 5 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 DC 10 A DC 10 1_555 B N2 DG 5 B DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 11 A DG 11 1_555 B N3 DC 4 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 11 A DG 11 1_555 B O2 DC 4 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 11 A DG 11 1_555 B N4 DC 4 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 12 A DA 12 1_555 B N3 DT 2 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 12 A DA 12 1_555 B O4 DT 2 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog25 A N7 DA 13 A DA 13 1_555 B N3 DT 1 B DT 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 5XJW _atom_sites.fract_transf_matrix[1][1] 0.0207 _atom_sites.fract_transf_matrix[1][2] 0.011951 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023902 _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] 0.011957 _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 62 CPH CPH . H 5 CO A 1 107 600 CO CO . I 5 CO A 1 108 601 CO CO . J 4 CPH B 1 103 56 CPH CPH . K 5 CO B 1 107 602 CO CO . L 6 HOH A 1 201 116 HOH HOH . L 6 HOH A 2 202 103 HOH HOH . L 6 HOH A 3 203 241 HOH HOH . L 6 HOH A 4 204 105 HOH HOH . L 6 HOH A 5 205 219 HOH HOH . L 6 HOH A 6 206 100 HOH HOH . L 6 HOH A 7 207 104 HOH HOH . L 6 HOH A 8 208 156 HOH HOH . L 6 HOH A 9 209 112 HOH HOH . L 6 HOH A 10 210 186 HOH HOH . L 6 HOH A 11 211 115 HOH HOH . L 6 HOH A 12 212 170 HOH HOH . L 6 HOH A 13 213 102 HOH HOH . L 6 HOH A 14 214 125 HOH HOH . L 6 HOH A 15 215 204 HOH HOH . L 6 HOH A 16 216 157 HOH HOH . L 6 HOH A 17 217 175 HOH HOH . L 6 HOH A 18 218 106 HOH HOH . L 6 HOH A 19 219 163 HOH HOH . L 6 HOH A 20 220 178 HOH HOH . L 6 HOH A 21 221 215 HOH HOH . L 6 HOH A 22 222 184 HOH HOH . L 6 HOH A 23 223 220 HOH HOH . L 6 HOH A 24 224 195 HOH HOH . L 6 HOH A 25 225 192 HOH HOH . L 6 HOH A 26 226 203 HOH HOH . M 6 HOH B 1 201 113 HOH HOH . M 6 HOH B 2 202 109 HOH HOH . M 6 HOH B 3 203 101 HOH HOH . M 6 HOH B 4 204 110 HOH HOH . M 6 HOH B 5 205 180 HOH HOH . M 6 HOH B 6 206 134 HOH HOH . M 6 HOH B 7 207 127 HOH HOH . M 6 HOH B 8 208 108 HOH HOH . M 6 HOH B 9 209 126 HOH HOH . M 6 HOH B 10 210 114 HOH HOH . M 6 HOH B 11 211 171 HOH HOH . M 6 HOH B 12 212 193 HOH HOH . M 6 HOH B 13 213 107 HOH HOH . M 6 HOH B 14 214 189 HOH HOH . M 6 HOH B 15 215 158 HOH HOH . M 6 HOH B 16 216 145 HOH HOH . M 6 HOH B 17 217 121 HOH HOH . M 6 HOH B 18 218 153 HOH HOH . M 6 HOH B 19 219 133 HOH HOH . M 6 HOH B 20 220 185 HOH HOH . M 6 HOH B 21 221 140 HOH HOH . M 6 HOH B 22 222 111 HOH HOH . M 6 HOH B 23 223 194 HOH HOH . M 6 HOH B 24 224 237 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 I _atom_site.label_entity_id 5 _atom_site.Cartn_x -8.46 _atom_site.Cartn_y -16.844 _atom_site.Cartn_z 3.454 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 56.87 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 108 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #