data_1U3G # _model_server_result.job_id hIFanZ8VZnb97sI4DQllZA _model_server_result.datetime_utc '2024-11-20 15:20:09' _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 1u3g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 1U3G # _exptl.entry_id 1U3G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 1U3G _cell.length_a 50.925 _cell.length_b 84.106 _cell.length_c 41.615 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U3G _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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,F _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 4 _struct_asym.id D _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 OD2 ASP 149 A ASP 124 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc2 A OD1 ASP 179 A ASP 154 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc3 D O3B ADP . A ADP 301 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc4 D O1A ADP . A ADP 301 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc5 C MG MG . A MG 401 1_555 F O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? # _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 1U3G _atom_sites.fract_transf_matrix[1][1] 0.019637 _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] 0.01189 _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] 0.02403 _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 PO4 A 1 201 201 PO4 PO4 . C 3 MG A 1 401 401 MG MG . D 4 ADP A 1 301 301 ADP ADP . E 5 THF A 1 501 501 THF THF . F 6 HOH A 1 601 601 HOH HOH . F 6 HOH A 2 602 602 HOH HOH . F 6 HOH A 3 603 603 HOH HOH . F 6 HOH A 4 604 604 HOH HOH . F 6 HOH A 5 605 605 HOH HOH . F 6 HOH A 6 606 606 HOH HOH . F 6 HOH A 7 607 607 HOH HOH . F 6 HOH A 8 608 608 HOH HOH . F 6 HOH A 9 609 609 HOH HOH . F 6 HOH A 10 610 610 HOH HOH . F 6 HOH A 11 611 611 HOH HOH . F 6 HOH A 12 612 612 HOH HOH . F 6 HOH A 13 613 613 HOH HOH . F 6 HOH A 14 614 614 HOH HOH . F 6 HOH A 15 615 615 HOH HOH . F 6 HOH A 16 616 616 HOH HOH . F 6 HOH A 17 617 617 HOH HOH . F 6 HOH A 18 618 618 HOH HOH . F 6 HOH A 19 619 619 HOH HOH . F 6 HOH A 20 620 620 HOH HOH . F 6 HOH A 21 621 621 HOH HOH . F 6 HOH A 22 622 622 HOH HOH . F 6 HOH A 23 623 623 HOH HOH . F 6 HOH A 24 624 624 HOH HOH . F 6 HOH A 25 625 625 HOH HOH . F 6 HOH A 26 626 626 HOH HOH . F 6 HOH A 27 627 627 HOH HOH . F 6 HOH A 28 628 628 HOH HOH . F 6 HOH A 29 629 629 HOH HOH . F 6 HOH A 30 630 630 HOH HOH . F 6 HOH A 31 631 631 HOH HOH . F 6 HOH A 32 632 632 HOH HOH . F 6 HOH A 33 633 633 HOH HOH . F 6 HOH A 34 634 634 HOH HOH . F 6 HOH A 35 635 635 HOH HOH . F 6 HOH A 36 636 636 HOH HOH . F 6 HOH A 37 637 637 HOH HOH . F 6 HOH A 38 638 638 HOH HOH . F 6 HOH A 39 639 639 HOH HOH . F 6 HOH A 40 640 640 HOH HOH . F 6 HOH A 41 641 641 HOH HOH . F 6 HOH A 42 642 642 HOH HOH . F 6 HOH A 43 643 643 HOH HOH . F 6 HOH A 44 644 644 HOH HOH . F 6 HOH A 45 645 645 HOH HOH . F 6 HOH A 46 646 646 HOH HOH . F 6 HOH A 47 647 647 HOH HOH . F 6 HOH A 48 648 648 HOH HOH . F 6 HOH A 49 649 649 HOH HOH . F 6 HOH A 50 650 650 HOH HOH . F 6 HOH A 51 651 651 HOH HOH . F 6 HOH A 52 652 652 HOH HOH . F 6 HOH A 53 653 653 HOH HOH . F 6 HOH A 54 654 654 HOH HOH . F 6 HOH A 55 655 655 HOH HOH . F 6 HOH A 56 656 656 HOH HOH . F 6 HOH A 57 657 657 HOH HOH . F 6 HOH A 58 658 658 HOH HOH . F 6 HOH A 59 659 659 HOH HOH . F 6 HOH A 60 660 660 HOH HOH . F 6 HOH A 61 661 661 HOH HOH . F 6 HOH A 62 662 662 HOH HOH . F 6 HOH A 63 663 663 HOH HOH . F 6 HOH A 64 664 664 HOH HOH . F 6 HOH A 65 665 665 HOH HOH . F 6 HOH A 66 666 666 HOH HOH . F 6 HOH A 67 667 667 HOH HOH . F 6 HOH A 68 668 668 HOH HOH . F 6 HOH A 69 669 669 HOH HOH . F 6 HOH A 70 670 670 HOH HOH . F 6 HOH A 71 671 671 HOH HOH . F 6 HOH A 72 672 672 HOH HOH . F 6 HOH A 73 673 673 HOH HOH . F 6 HOH A 74 674 674 HOH HOH . F 6 HOH A 75 675 675 HOH HOH . F 6 HOH A 76 676 676 HOH HOH . F 6 HOH A 77 677 677 HOH HOH . F 6 HOH A 78 678 678 HOH HOH . F 6 HOH A 79 679 679 HOH HOH . F 6 HOH A 80 680 680 HOH HOH . F 6 HOH A 81 681 681 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 . . . D 4 3.37 17.48 20.287 1 18.3 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . D 4 4.809 17.745 20.099 1 19.8 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . D 4 2.881 16.129 19.547 1 18.45 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . D 4 2.549 18.62 19.83 1 15.22 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . D 4 1.908 16.627 22.608 1 25.04 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . D 4 0.727 17.43 22.253 1 24.88 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . D 4 1.714 15.201 22.285 1 25.47 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . D 4 3.138 17.184 21.799 1 21.67 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . D 4 2.334 16.799 24.131 1 28.64 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . D 4 2.575 18.081 24.715 1 33.63 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . D 4 2.169 18.017 26.199 1 36.19 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . D 4 2.118 19.364 26.676 1 38.74 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . D 4 0.784 17.407 26.431 1 38.54 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . D 4 0.848 16.236 27.252 1 38.13 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . D 4 -0.072 18.463 27.129 1 40.23 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . D 4 -0.6 18.031 28.396 1 41.56 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . D 4 0.814 19.705 27.189 1 41.29 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . D 4 0.229 20.848 26.385 1 43.36 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . D 4 0.221 20.93 25.042 1 43.8 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . D 4 -0.369 22.062 24.664 1 44.53 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . D 4 -0.742 22.713 25.733 1 45.53 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . D 4 -1.391 23.928 25.981 1 46.19 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . D 4 -1.773 24.702 24.957 1 46.94 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . D 4 -1.638 24.331 27.274 1 46.87 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . D 4 -1.265 23.571 28.339 1 48.14 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . D 4 -0.635 22.392 28.111 1 46.99 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . D 4 -0.359 21.933 26.855 1 45.12 ? C4 ADP 301 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #