data_8TBX # _model_server_result.job_id IAmbE1_iNBuFoF3AhNChkw _model_server_result.datetime_utc '2024-10-12 04:34:19' _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 8tbx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 8TBX # _exptl.entry_id 8TBX _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 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 8TBX _cell.length_a 50.708 _cell.length_b 71.517 _cell.length_c 138.496 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TBX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OG1 THR 54 A THR 53 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc2 A OE1 GLU 167 A GLU 371 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc3 A ND1 HIS 425 A HIS 629 1_555 D ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc4 A SG CYS 427 A CYS 631 1_555 D ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc5 A SG CYS 434 A CYS 638 1_555 D ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc6 A SG CYS 445 A CYS 649 1_555 D ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc7 B O2B ADP . A ADP 701 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? # _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 8TBX _atom_sites.fract_transf_matrix[1][1] 0.019721 _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] 0.013983 _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] 0.00722 _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 1 701 1000 ADP ADP . C 3 MG A 1 702 1 MG MG . D 4 ZN A 1 703 1 ZN ZN . E 5 HOH A 1 801 10 HOH HOH . E 5 HOH A 2 802 16 HOH HOH . E 5 HOH A 3 803 15 HOH HOH . E 5 HOH A 4 804 4 HOH HOH . E 5 HOH A 5 805 14 HOH HOH . E 5 HOH A 6 806 18 HOH HOH . E 5 HOH A 7 807 2 HOH HOH . E 5 HOH A 8 808 5 HOH HOH . E 5 HOH A 9 809 6 HOH HOH . E 5 HOH A 10 810 7 HOH HOH . E 5 HOH A 11 811 1 HOH HOH . E 5 HOH A 12 812 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 . . . B 2 7.674 1.106 18.672 1 43.65 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . B 2 8.431 0.595 17.494 1 47.53 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . B 2 8.305 0.727 20.005 1 47.99 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . B 2 7.394 2.574 18.573 1 47.61 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . B 2 5.355 -0.233 19.817 1 44.52 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . B 2 5.838 -1.586 20.232 1 48.23 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . B 2 5.259 0.834 20.875 1 44.98 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . B 2 6.247 0.338 18.611 1 46.16 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . B 2 3.98 -0.433 19.061 1 40.22 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . B 2 3.396 0.556 18.184 1 37.28 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . B 2 1.901 0.479 18.353 1 37.22 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . B 2 1.402 -0.704 17.672 1 34.19 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . B 2 1.429 0.346 19.81 1 38.67 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . B 2 0.193 1.012 20.005 1 45.28 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . B 2 1.314 -1.168 19.999 1 38.93 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . B 2 0.368 -1.581 20.961 1 35.32 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . B 2 0.86 -1.609 18.611 1 39.66 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . B 2 1.308 -2.953 18.283 1 42.21 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . B 2 2.519 -3.514 18.611 1 43.04 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . B 2 2.657 -4.74 18.176 1 42.42 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . B 2 1.452 -5.014 17.539 1 41.86 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . B 2 0.976 -6.163 16.879 1 42.39 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . B 2 1.7 -7.277 16.737 1 44.55 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . B 2 -0.277 -6.106 16.346 1 42.22 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . B 2 -0.988 -4.977 16.497 1 42.48 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . B 2 -0.644 -3.84 17.107 1 43.69 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . B 2 0.605 -3.921 17.608 1 42.82 ? C4 ADP 701 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #