data_5XJB # _model_server_result.job_id B-BpTXk5qj5XMoVpo6DyVg _model_server_result.datetime_utc '2024-10-20 08:08:24' _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 5xjb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 5XJB # _exptl.entry_id 5XJB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 5XJB _cell.length_a 89.452 _cell.length_b 166.593 _cell.length_c 75.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XJB _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 2 C N N ? 2 F 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 OG1 THR 185 A THR 351 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 A OG SER 297 A SER 463 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc3 C O2B ADP . A ADP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc4 B OG1 THR 185 B THR 351 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc5 B OG SER 298 B SER 464 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc6 F O1B ADP . B ADP 601 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 5XJB _atom_sites.fract_transf_matrix[1][1] 0.011179 _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] 0.006003 _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] 0.013245 _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 2 ADP A 1 601 1 ADP ADP . D 3 BEF A 1 602 1 BEF BEF . E 4 MG A 1 603 1 MG MG . F 2 ADP B 1 601 2 ADP ADP . G 3 BEF B 1 602 2 BEF BEF . H 4 MG B 1 603 2 MG MG . I 5 HOH A 1 701 4 HOH HOH . I 5 HOH A 2 702 1 HOH HOH . I 5 HOH A 3 703 2 HOH HOH . J 5 HOH B 1 701 5 HOH HOH . J 5 HOH B 2 702 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 P PB ADP . . . F 2 68.901 10.096 50.696 1 68.84 ? PB ADP 601 B 1 HETATM 2 O O1B ADP . . . F 2 69.805 11.187 50.169 1 75.24 ? O1B ADP 601 B 1 HETATM 3 O O2B ADP . . . F 2 67.429 10.327 50.427 1 69.22 ? O2B ADP 601 B 1 HETATM 4 O O3B ADP . . . F 2 69.258 9.588 52.072 1 67.96 ? O3B ADP 601 B 1 HETATM 5 P PA ADP . . . F 2 70.293 8.797 48.683 1 77.47 ? PA ADP 601 B 1 HETATM 6 O O1A ADP . . . F 2 69.682 9.333 47.402 1 68.12 ? O1A ADP 601 B 1 HETATM 7 O O2A ADP . . . F 2 71.597 9.379 49.194 1 84.79 ? O2A ADP 601 B 1 HETATM 8 O O3A ADP . . . F 2 69.199 8.798 49.842 1 73.22 ? O3A ADP 601 B 1 HETATM 9 O O5' ADP . . . F 2 70.484 7.206 48.656 1 75.32 ? O5' ADP 601 B 1 HETATM 10 C C5' ADP . . . F 2 71.503 6.87 47.769 1 86.57 ? C5' ADP 601 B 1 HETATM 11 C C4' ADP . . . F 2 71.881 5.412 47.795 1 90.76 ? C4' ADP 601 B 1 HETATM 12 O O4' ADP . . . F 2 70.791 4.523 47.494 1 91.05 ? O4' ADP 601 B 1 HETATM 13 C C3' ADP . . . F 2 72.882 5.335 46.657 1 97.9 ? C3' ADP 601 B 1 HETATM 14 O O3' ADP . . . F 2 73.882 4.36 46.967 1 102.68 ? O3' ADP 601 B 1 HETATM 15 C C2' ADP . . . F 2 71.984 5.014 45.472 1 99.34 ? C2' ADP 601 B 1 HETATM 16 O O2' ADP . . . F 2 72.721 4.324 44.458 1 119.98 ? O2' ADP 601 B 1 HETATM 17 C C1' ADP . . . F 2 70.797 4.233 46.079 1 95.65 ? C1' ADP 601 B 1 HETATM 18 N N9 ADP . . . F 2 69.509 4.634 45.436 1 86.34 ? N9 ADP 601 B 1 HETATM 19 C C8 ADP . . . F 2 68.677 5.579 45.925 1 84.92 ? C8 ADP 601 B 1 HETATM 20 N N7 ADP . . . F 2 67.593 5.746 45.133 1 81.66 ? N7 ADP 601 B 1 HETATM 21 C C5 ADP . . . F 2 67.714 4.89 44.109 1 84.83 ? C5 ADP 601 B 1 HETATM 22 C C6 ADP . . . F 2 66.885 4.574 42.92 1 90.71 ? C6 ADP 601 B 1 HETATM 23 N N6 ADP . . . F 2 65.711 5.255 42.741 1 93 ? N6 ADP 601 B 1 HETATM 24 N N1 ADP . . . F 2 67.349 3.614 42.068 1 84.15 ? N1 ADP 601 B 1 HETATM 25 C C2 ADP . . . F 2 68.519 2.977 42.302 1 80.8 ? C2 ADP 601 B 1 HETATM 26 N N3 ADP . . . F 2 69.308 3.233 43.372 1 75.89 ? N3 ADP 601 B 1 HETATM 27 C C4 ADP . . . F 2 68.976 4.159 44.301 1 79.79 ? C4 ADP 601 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #