data_6JDB # _model_server_result.job_id nrQWaDjLhPyDxL5s_ppB7w _model_server_result.datetime_utc '2024-11-23 09:07:19' _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 6jdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6JDB # _exptl.entry_id 6JDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 301.188 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose _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 6JDB _cell.length_a 92.591 _cell.length_b 92.591 _cell.length_c 183.321 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 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 _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' 8_666 -y+1,-x+1,-z+1 0 -1 0 -1 0 0 0 0 -1 92.591 92.591 183.321 # _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 # 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 ND1 HIS 155 A HIS 156 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A SG CYS 165 A CYS 166 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc3 A SG CYS 167 A CYS 168 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 A SG CYS 172 A CYS 173 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? # _chem_comp.formula 'C8 H16 N O9 P' _chem_comp.formula_weight 301.188 _chem_comp.id BMX _chem_comp.mon_nstd_flag n _chem_comp.name 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE;N-acetyl-6-O-phosphono-alpha-D-mannosamine;2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose;2-acetamido-2-deoxy-6-O-phosphono-D-mannose;2-acetamido-2-deoxy-6-O-phosphono-mannose # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 O1 BMX sing 114 n n C1 C2 BMX sing 115 n n C1 O5 BMX sing 116 n n C2 N2 BMX sing 117 n n C2 C3 BMX sing 118 n n N2 C7 BMX sing 119 n n C7 O7 BMX doub 120 n n C7 C8 BMX sing 121 n n C3 O3 BMX sing 122 n n C3 C4 BMX sing 123 n n C4 O4 BMX sing 124 n n C4 C5 BMX sing 125 n n C5 C6 BMX sing 126 n n C5 O5 BMX sing 127 n n C6 O6 BMX sing 128 n n O6 P BMX sing 129 n n P O17 BMX doub 130 n n P O18 BMX sing 131 n n P O19 BMX sing 132 n n C1 H1 BMX sing 133 n n O1 HO1 BMX sing 134 n n C2 H2 BMX sing 135 n n N2 HN2 BMX sing 136 n n C3 H3 BMX sing 137 n n C8 H81 BMX sing 138 n n C8 H82 BMX sing 139 n n C8 H83 BMX sing 140 n n O3 HO3 BMX sing 141 n n C4 H4 BMX sing 142 n n O4 HO4 BMX sing 143 n n C5 H5 BMX sing 144 n n C6 H61 BMX sing 145 n n C6 H62 BMX sing 146 n n O18 H18 BMX sing 147 n n O19 H19 BMX sing 148 n n # _pdbx_chem_comp_identifier.comp_id BMX _pdbx_chem_comp_identifier.identifier a-D-ManpNAc6PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 6JDB _atom_sites.fract_transf_matrix[1][1] 0.0108 _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] 0.0108 _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] 0.005455 _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 ADP A 1 301 1 ADP ADP . C 3 BMX A 1 302 1 BMX BMX . D 4 ZN A 1 303 1 ZN ZN . E 5 HOH A 1 401 10 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 1 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 4 HOH HOH . E 5 HOH A 6 406 9 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 6 HOH HOH . E 5 HOH A 9 409 12 HOH HOH . E 5 HOH A 10 410 11 HOH HOH . E 5 HOH A 11 411 7 HOH HOH . E 5 HOH A 12 412 3 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 C C1 BMX . . . C 3 18.569 57.464 81.174 1 55.2 ? C1 BMX 302 A 1 HETATM 2 C C2 BMX . . . C 3 18.02 58.706 80.47 1 54.12 ? C2 BMX 302 A 1 HETATM 3 C C3 BMX . . . C 3 17.107 59.497 81.329 1 53.02 ? C3 BMX 302 A 1 HETATM 4 C C4 BMX . . . C 3 16.022 58.622 81.905 1 52.67 ? C4 BMX 302 A 1 HETATM 5 C C5 BMX . . . C 3 16.649 57.538 82.746 1 49.55 ? C5 BMX 302 A 1 HETATM 6 C C6 BMX . . . C 3 15.591 56.68 83.366 1 53.29 ? C6 BMX 302 A 1 HETATM 7 C C7 BMX . . . C 3 17.951 58.083 77.972 1 53.36 ? C7 BMX 302 A 1 HETATM 8 C C8 BMX . . . C 3 17.154 57.498 76.805 1 55.75 ? C8 BMX 302 A 1 HETATM 9 N N2 BMX . . . C 3 17.301 58.167 79.289 1 52.09 ? N2 BMX 302 A 1 HETATM 10 O O1 BMX . . . C 3 19.56 57.83 82 1 55.03 ? O1 BMX 302 A 1 HETATM 11 O O3 BMX . . . C 3 16.531 60.605 80.578 1 48.8 ? O3 BMX 302 A 1 HETATM 12 O O4 BMX . . . C 3 15.118 59.405 82.69 1 51.38 ? O4 BMX 302 A 1 HETATM 13 O O5 BMX . . . C 3 17.542 56.687 81.928 1 57.17 ? O5 BMX 302 A 1 HETATM 14 O O6 BMX . . . C 3 14.648 56.294 82.43 1 58.93 ? O6 BMX 302 A 1 HETATM 15 O O7 BMX . . . C 3 19.063 58.475 77.805 1 51.54 ? O7 BMX 302 A 1 HETATM 16 P P BMX . . . C 3 14.089 54.746 82.495 0.5 63.57 ? P BMX 302 A 1 HETATM 17 O O19 BMX . . . C 3 12.9 54.714 83.435 0.5 65.07 ? O19 BMX 302 A 1 HETATM 18 O O17 BMX . . . C 3 13.649 54.301 81.12 0.5 65.21 ? O17 BMX 302 A 1 HETATM 19 O O18 BMX . . . C 3 15.152 53.821 82.995 0.5 61.37 ? O18 BMX 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #