data_4OI2 # _model_server_result.job_id 2xYbtkCnbX2ubfM0Qc7gZA _model_server_result.datetime_utc '2024-11-25 10:44:29' _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 4oi2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4OI2 # _exptl.entry_id 4OI2 _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 120 _cell.entry_id 4OI2 _cell.length_a 100.15 _cell.length_b 100.15 _cell.length_c 40.41 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OI2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _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,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 131 A THR 128 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc2 B O2B ADP . A ADP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc3 C MG MG . A MG 502 1_555 E O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc4 C MG MG . A MG 502 1_555 E O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc5 C MG MG . A MG 502 1_555 E O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc6 C MG MG . A MG 502 1_555 E O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _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 66 n n PB O2B ADP sing 67 n n PB O3B ADP sing 68 n n PB O3A ADP sing 69 n n O2B HOB2 ADP sing 70 n n O3B HOB3 ADP sing 71 n n PA O1A ADP doub 72 n n PA O2A ADP sing 73 n n PA O3A ADP sing 74 n n PA O5' ADP sing 75 n n O2A HOA2 ADP sing 76 n n O5' C5' ADP sing 77 n n C5' C4' ADP sing 78 n n C5' "H5'1" ADP sing 79 n n C5' "H5'2" ADP sing 80 n n C4' O4' ADP sing 81 n n C4' C3' ADP sing 82 n n C4' H4' ADP sing 83 n n O4' C1' ADP sing 84 n n C3' O3' ADP sing 85 n n C3' C2' ADP sing 86 n n C3' H3' ADP sing 87 n n O3' HO3' ADP sing 88 n n C2' O2' ADP sing 89 n n C2' C1' ADP sing 90 n n C2' H2' ADP sing 91 n n O2' HO2' ADP sing 92 n n C1' N9 ADP sing 93 n n C1' H1' ADP sing 94 n n N9 C8 ADP sing 95 n y N9 C4 ADP sing 96 n y C8 N7 ADP doub 97 n y C8 H8 ADP sing 98 n n N7 C5 ADP sing 99 n y C5 C6 ADP sing 100 n y C5 C4 ADP doub 101 n y C6 N6 ADP sing 102 n n C6 N1 ADP doub 103 n y N6 HN61 ADP sing 104 n n N6 HN62 ADP sing 105 n n N1 C2 ADP sing 106 n y C2 N3 ADP doub 107 n y C2 H2 ADP sing 108 n n N3 C4 ADP sing 109 n y # _atom_sites.entry_id 4OI2 _atom_sites.fract_transf_matrix[1][1] 0.009985 _atom_sites.fract_transf_matrix[1][2] 0.005765 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01153 _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] 0.024746 _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 MG A 1 502 2 MG MG . D 4 2PE A 1 503 1 2PE 2PE . E 5 HOH A 1 601 1 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 3 HOH HOH . E 5 HOH A 4 604 4 HOH HOH . E 5 HOH A 5 605 5 HOH HOH . E 5 HOH A 6 606 6 HOH HOH . E 5 HOH A 7 607 7 HOH HOH . E 5 HOH A 8 608 8 HOH HOH . E 5 HOH A 9 609 9 HOH HOH . E 5 HOH A 10 610 10 HOH HOH . E 5 HOH A 11 611 11 HOH HOH . E 5 HOH A 12 612 12 HOH HOH . E 5 HOH A 13 613 13 HOH HOH . E 5 HOH A 14 614 14 HOH HOH . E 5 HOH A 15 615 15 HOH HOH . E 5 HOH A 16 616 16 HOH HOH . E 5 HOH A 17 617 17 HOH HOH . E 5 HOH A 18 618 18 HOH HOH . E 5 HOH A 19 619 19 HOH HOH . E 5 HOH A 20 620 20 HOH HOH . E 5 HOH A 21 621 21 HOH HOH . E 5 HOH A 22 622 22 HOH HOH . E 5 HOH A 23 623 23 HOH HOH . E 5 HOH A 24 624 24 HOH HOH . E 5 HOH A 25 625 25 HOH HOH . E 5 HOH A 26 626 26 HOH HOH . E 5 HOH A 27 627 27 HOH HOH . E 5 HOH A 28 628 28 HOH HOH . E 5 HOH A 29 629 29 HOH HOH . E 5 HOH A 30 630 30 HOH HOH . E 5 HOH A 31 631 31 HOH HOH . E 5 HOH A 32 632 32 HOH HOH . E 5 HOH A 33 633 33 HOH HOH . E 5 HOH A 34 634 34 HOH HOH . E 5 HOH A 35 635 35 HOH HOH . E 5 HOH A 36 636 36 HOH HOH . E 5 HOH A 37 637 37 HOH HOH . E 5 HOH A 38 638 38 HOH HOH . E 5 HOH A 39 639 39 HOH HOH . E 5 HOH A 40 640 40 HOH HOH . E 5 HOH A 41 641 41 HOH HOH . E 5 HOH A 42 642 42 HOH HOH . E 5 HOH A 43 643 43 HOH HOH . E 5 HOH A 44 644 44 HOH HOH . E 5 HOH A 45 645 45 HOH HOH . E 5 HOH A 46 646 46 HOH HOH . E 5 HOH A 47 647 47 HOH HOH . E 5 HOH A 48 648 48 HOH HOH . E 5 HOH A 49 649 49 HOH HOH . E 5 HOH A 50 650 50 HOH HOH . E 5 HOH A 51 651 51 HOH HOH . E 5 HOH A 52 652 52 HOH HOH . E 5 HOH A 53 653 53 HOH HOH . E 5 HOH A 54 654 54 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 -9.56 22.099 9.275 1 27.36 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 -9.032 22.993 10.372 1 27.86 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 -10.249 22.833 8.149 1 27.1 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 -10.32 20.892 9.767 1 26.9 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 -7.628 21.916 7.197 1 26.72 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 -8.459 21.263 6.118 1 25.98 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 -7.431 23.412 7.205 1 26.85 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 -8.209 21.483 8.641 1 27.09 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 -6.187 21.205 7.188 1 26.96 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 -5.136 21.63 8.058 1 27.45 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 -3.808 21.551 7.312 1 28.02 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 -3.486 20.183 7.029 1 28.13 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 -3.873 22.282 5.978 1 28.15 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 -2.714 23.112 5.832 1 28.25 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 -3.882 21.188 4.933 1 28.16 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 -3.18 21.592 3.757 1 29.1 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 -3.189 20.033 5.637 1 28.16 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 -3.633 18.712 5.123 1 28.14 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 -4.9 18.281 4.968 1 28.28 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 -4.935 17.018 4.466 1 28.34 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 -3.66 16.621 4.297 1 28.08 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 -2.972 15.402 3.812 1 28.03 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 -3.671 14.322 3.39 1 27.9 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 -1.615 15.407 3.801 1 28.3 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 -0.894 16.471 4.208 1 28.1 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 -1.456 17.606 4.663 1 27.95 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 -2.806 17.741 4.731 1 28.12 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #