data_5O7D # _model_server_result.job_id XMj59vsSeXiEeJyNSV2T9w _model_server_result.datetime_utc '2024-11-12 21:51:19' _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 5o7d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5O7D # _exptl.entry_id 5O7D _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 97.32 _cell.angle_gamma 90 _cell.entry_id 5O7D _cell.length_a 36.05 _cell.length_b 106.68 _cell.length_c 50.69 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _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 5O7D _atom_sites.fract_transf_matrix[1][1] 0.027739 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003562 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009374 _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] 0.01989 _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 1 501 1 ADP ADP . C 3 HOH A 1 601 24 HOH HOH . C 3 HOH A 2 602 30 HOH HOH . C 3 HOH A 3 603 59 HOH HOH . C 3 HOH A 4 604 13 HOH HOH . C 3 HOH A 5 605 51 HOH HOH . C 3 HOH A 6 606 58 HOH HOH . C 3 HOH A 7 607 36 HOH HOH . C 3 HOH A 8 608 34 HOH HOH . C 3 HOH A 9 609 28 HOH HOH . C 3 HOH A 10 610 11 HOH HOH . C 3 HOH A 11 611 61 HOH HOH . C 3 HOH A 12 612 5 HOH HOH . C 3 HOH A 13 613 40 HOH HOH . C 3 HOH A 14 614 17 HOH HOH . C 3 HOH A 15 615 21 HOH HOH . C 3 HOH A 16 616 29 HOH HOH . C 3 HOH A 17 617 26 HOH HOH . C 3 HOH A 18 618 7 HOH HOH . C 3 HOH A 19 619 35 HOH HOH . C 3 HOH A 20 620 25 HOH HOH . C 3 HOH A 21 621 14 HOH HOH . C 3 HOH A 22 622 8 HOH HOH . C 3 HOH A 23 623 15 HOH HOH . C 3 HOH A 24 624 10 HOH HOH . C 3 HOH A 25 625 41 HOH HOH . C 3 HOH A 26 626 12 HOH HOH . C 3 HOH A 27 627 1 HOH HOH . C 3 HOH A 28 628 53 HOH HOH . C 3 HOH A 29 629 2 HOH HOH . C 3 HOH A 30 630 20 HOH HOH . C 3 HOH A 31 631 38 HOH HOH . C 3 HOH A 32 632 48 HOH HOH . C 3 HOH A 33 633 46 HOH HOH . C 3 HOH A 34 634 6 HOH HOH . C 3 HOH A 35 635 23 HOH HOH . C 3 HOH A 36 636 31 HOH HOH . C 3 HOH A 37 637 45 HOH HOH . C 3 HOH A 38 638 9 HOH HOH . C 3 HOH A 39 639 4 HOH HOH . C 3 HOH A 40 640 3 HOH HOH . C 3 HOH A 41 641 47 HOH HOH . C 3 HOH A 42 642 37 HOH HOH . C 3 HOH A 43 643 49 HOH HOH . C 3 HOH A 44 644 60 HOH HOH . C 3 HOH A 45 645 22 HOH HOH . C 3 HOH A 46 646 54 HOH HOH . C 3 HOH A 47 647 42 HOH HOH . C 3 HOH A 48 648 32 HOH HOH . C 3 HOH A 49 649 50 HOH HOH . C 3 HOH A 50 650 16 HOH HOH . C 3 HOH A 51 651 27 HOH HOH . C 3 HOH A 52 652 18 HOH HOH . C 3 HOH A 53 653 43 HOH HOH . C 3 HOH A 54 654 19 HOH HOH . C 3 HOH A 55 655 57 HOH HOH . C 3 HOH A 56 656 52 HOH HOH . C 3 HOH A 57 657 33 HOH HOH . C 3 HOH A 58 658 44 HOH HOH . C 3 HOH A 59 659 56 HOH HOH . C 3 HOH A 60 660 55 HOH HOH . C 3 HOH A 61 661 39 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 12.111 2.825 23.12 1 69.39 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 12.644 2.144 21.871 1 58.21 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 13.061 3.833 23.746 1 68.68 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 11.455 1.904 24.137 1 63.51 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 9.64 3.112 21.794 1 43.66 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 9.334 3.852 20.5 1 39.49 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 9.73 1.598 21.779 1 45.27 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 10.909 3.75 22.545 1 50.62 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 8.467 3.452 22.838 1 39.93 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 7.17 3.711 22.317 1 34.28 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 6.267 3.691 23.521 1 32.01 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 6.498 4.891 24.251 1 29.62 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 4.784 3.651 23.178 1 30.01 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 4.238 2.369 23.49 1 30.29 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 4.177 4.748 24.018 1 27.72 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 3.006 4.29 24.685 1 27.19 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 5.306 5.087 24.984 1 26.6 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 5.265 6.466 25.503 1 24.13 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 5.052 7.622 24.845 1 23.31 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 5.064 8.672 25.704 1 21.38 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 5.309 8.175 26.925 1 20.9 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 5.453 8.702 28.292 1 20.49 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 5.354 10.025 28.537 1 19.55 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 5.691 7.809 29.289 1 18.74 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 5.796 6.483 29.081 1 19.83 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 5.669 5.941 27.854 1 21.08 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 5.446 6.723 26.78 1 22.15 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #