data_4OI0 # _model_server_result.job_id 8efT33wRb8SC_qR09NZlMw _model_server_result.datetime_utc '2024-11-25 10:58:14' _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 4oi0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4OI0 # _exptl.entry_id 4OI0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 4OI0 _cell.length_a 100.71 _cell.length_b 100.71 _cell.length_c 40.4 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OI0 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J _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 3 _struct_asym.id C _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 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc2 C O2B ADP . A ADP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc3 D MG MG . A MG 502 1_555 I O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc4 D MG MG . A MG 502 1_555 I O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc5 D MG MG . A MG 502 1_555 I O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? # _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 4OI0 _atom_sites.fract_transf_matrix[1][1] 0.00993 _atom_sites.fract_transf_matrix[1][2] 0.005733 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011466 _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] 0.024752 _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 3 ADP A 1 501 1 ADP ADP . D 4 MG A 1 502 2 MG MG . E 5 ALF A 1 503 3 ALF ALF . F 6 SAR A 1 504 10 SAR SAR . G 6 SAR A 1 505 11 SAR SAR . H 7 2PE A 1 506 12 2PE 2PE . I 8 HOH A 1 601 1 HOH HOH . I 8 HOH A 2 602 2 HOH HOH . I 8 HOH A 3 603 3 HOH HOH . I 8 HOH A 4 604 4 HOH HOH . I 8 HOH A 5 605 5 HOH HOH . I 8 HOH A 6 606 6 HOH HOH . I 8 HOH A 7 607 7 HOH HOH . I 8 HOH A 8 608 8 HOH HOH . I 8 HOH A 9 609 9 HOH HOH . I 8 HOH A 10 610 10 HOH HOH . I 8 HOH A 11 611 12 HOH HOH . I 8 HOH A 12 612 13 HOH HOH . I 8 HOH A 13 613 14 HOH HOH . I 8 HOH A 14 614 15 HOH HOH . I 8 HOH A 15 615 16 HOH HOH . I 8 HOH A 16 616 17 HOH HOH . I 8 HOH A 17 617 18 HOH HOH . I 8 HOH A 18 618 19 HOH HOH . I 8 HOH A 19 619 20 HOH HOH . I 8 HOH A 20 620 21 HOH HOH . I 8 HOH A 21 621 22 HOH HOH . I 8 HOH A 22 622 23 HOH HOH . I 8 HOH A 23 623 24 HOH HOH . I 8 HOH A 24 624 26 HOH HOH . I 8 HOH A 25 625 27 HOH HOH . I 8 HOH A 26 626 28 HOH HOH . I 8 HOH A 27 627 29 HOH HOH . I 8 HOH A 28 628 30 HOH HOH . I 8 HOH A 29 629 31 HOH HOH . I 8 HOH A 30 630 32 HOH HOH . I 8 HOH A 31 631 33 HOH HOH . I 8 HOH A 32 632 34 HOH HOH . I 8 HOH A 33 633 35 HOH HOH . I 8 HOH A 34 634 36 HOH HOH . I 8 HOH A 35 635 37 HOH HOH . I 8 HOH A 36 636 38 HOH HOH . I 8 HOH A 37 637 39 HOH HOH . I 8 HOH A 38 638 40 HOH HOH . I 8 HOH A 39 639 41 HOH HOH . I 8 HOH A 40 640 42 HOH HOH . I 8 HOH A 41 641 43 HOH HOH . I 8 HOH A 42 642 44 HOH HOH . I 8 HOH A 43 643 45 HOH HOH . I 8 HOH A 44 644 46 HOH HOH . I 8 HOH A 45 645 47 HOH HOH . I 8 HOH A 46 646 48 HOH HOH . I 8 HOH A 47 647 49 HOH HOH . I 8 HOH A 48 648 50 HOH HOH . I 8 HOH A 49 649 51 HOH HOH . I 8 HOH A 50 650 52 HOH HOH . I 8 HOH A 51 651 53 HOH HOH . I 8 HOH A 52 652 54 HOH HOH . I 8 HOH A 53 653 55 HOH HOH . I 8 HOH A 54 654 56 HOH HOH . I 8 HOH A 55 655 57 HOH HOH . I 8 HOH A 56 656 58 HOH HOH . I 8 HOH A 57 657 59 HOH HOH . I 8 HOH A 58 658 60 HOH HOH . I 8 HOH A 59 659 61 HOH HOH . I 8 HOH A 60 660 62 HOH HOH . I 8 HOH A 61 661 63 HOH HOH . I 8 HOH A 62 662 64 HOH HOH . I 8 HOH A 63 663 65 HOH HOH . I 8 HOH A 64 664 66 HOH HOH . I 8 HOH A 65 665 67 HOH HOH . I 8 HOH A 66 666 68 HOH HOH . I 8 HOH A 67 667 69 HOH HOH . I 8 HOH A 68 668 70 HOH HOH . I 8 HOH A 69 669 71 HOH HOH . I 8 HOH A 70 670 72 HOH HOH . I 8 HOH A 71 671 73 HOH HOH . I 8 HOH A 72 672 74 HOH HOH . I 8 HOH A 73 673 75 HOH HOH . I 8 HOH A 74 674 76 HOH HOH . I 8 HOH A 75 675 77 HOH HOH . I 8 HOH A 76 676 78 HOH HOH . I 8 HOH A 77 677 79 HOH HOH . I 8 HOH A 78 678 80 HOH HOH . I 8 HOH A 79 679 81 HOH HOH . I 8 HOH A 80 680 82 HOH HOH . I 8 HOH A 81 681 83 HOH HOH . I 8 HOH A 82 682 84 HOH HOH . I 8 HOH A 83 683 85 HOH HOH . I 8 HOH A 84 684 86 HOH HOH . I 8 HOH A 85 685 87 HOH HOH . I 8 HOH A 86 686 88 HOH HOH . I 8 HOH A 87 687 89 HOH HOH . I 8 HOH A 88 688 90 HOH HOH . I 8 HOH A 89 689 91 HOH HOH . I 8 HOH A 90 690 92 HOH HOH . I 8 HOH A 91 691 93 HOH HOH . I 8 HOH A 92 692 94 HOH HOH . I 8 HOH A 93 693 95 HOH HOH . I 8 HOH A 94 694 96 HOH HOH . I 8 HOH A 95 695 97 HOH HOH . I 8 HOH A 96 696 98 HOH HOH . I 8 HOH A 97 697 99 HOH HOH . I 8 HOH A 98 698 100 HOH HOH . I 8 HOH A 99 699 101 HOH HOH . I 8 HOH A 100 700 102 HOH HOH . I 8 HOH A 101 701 103 HOH HOH . I 8 HOH A 102 702 104 HOH HOH . I 8 HOH A 103 703 105 HOH HOH . I 8 HOH A 104 704 106 HOH HOH . I 8 HOH A 105 705 107 HOH HOH . I 8 HOH A 106 706 108 HOH HOH . I 8 HOH A 107 707 109 HOH HOH . I 8 HOH A 108 708 110 HOH HOH . I 8 HOH A 109 709 111 HOH HOH . I 8 HOH A 110 710 112 HOH HOH . I 8 HOH A 111 711 113 HOH HOH . I 8 HOH A 112 712 114 HOH HOH . I 8 HOH A 113 713 115 HOH HOH . I 8 HOH A 114 714 116 HOH HOH . I 8 HOH A 115 715 117 HOH HOH . I 8 HOH A 116 716 118 HOH HOH . I 8 HOH A 117 717 119 HOH HOH . I 8 HOH A 118 718 120 HOH HOH . I 8 HOH A 119 719 121 HOH HOH . I 8 HOH A 120 720 122 HOH HOH . I 8 HOH A 121 721 123 HOH HOH . I 8 HOH A 122 722 124 HOH HOH . I 8 HOH A 123 723 125 HOH HOH . I 8 HOH A 124 724 126 HOH HOH . I 8 HOH A 125 725 127 HOH HOH . I 8 HOH A 126 726 128 HOH HOH . I 8 HOH A 127 727 129 HOH HOH . I 8 HOH A 128 728 130 HOH HOH . I 8 HOH A 129 729 131 HOH HOH . I 8 HOH A 130 730 132 HOH HOH . I 8 HOH A 131 731 133 HOH HOH . I 8 HOH A 132 732 134 HOH HOH . I 8 HOH A 133 733 135 HOH HOH . J 8 HOH B 1 101 11 HOH HOH . J 8 HOH B 2 102 25 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 . . . C 3 -10.165 22.243 9.711 1 18.08 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . C 3 -10.941 21.047 10.205 1 17.5 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . C 3 -10.787 22.891 8.491 1 18.17 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . C 3 -9.867 23.203 10.83 1 18.64 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . C 3 -8.101 22.003 7.74 1 19.72 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . C 3 -7.803 23.478 7.601 1 20.2 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . C 3 -8.886 21.328 6.658 1 19.15 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . C 3 -8.73 21.709 9.197 1 17.48 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . C 3 -6.698 21.264 7.797 1 22.52 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . C 3 -5.789 21.588 8.842 1 24.74 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . C 3 -4.38 21.659 8.264 1 25.72 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . C 3 -3.928 20.371 7.824 1 25.81 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . C 3 -4.309 22.562 7.053 1 26.37 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . C 3 -3.167 23.399 7.241 1 28.77 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . C 3 -4.141 21.654 5.846 1 26.56 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . C 3 -3.286 22.195 4.834 1 28.33 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . C 3 -3.49 20.432 6.459 1 25.36 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . C 3 -3.889 19.167 5.837 1 23.89 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . C 3 -5.149 18.686 5.765 1 23.63 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . C 3 -5.163 17.473 5.164 1 22.42 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . C 3 -3.89 17.182 4.853 1 21.7 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . C 3 -3.198 16.06 4.224 1 21.06 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . C 3 -3.894 14.997 3.772 1 22.61 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . C 3 -1.859 16.136 4.101 1 23.89 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . C 3 -1.144 17.187 4.539 1 22.21 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . C 3 -1.723 18.245 5.133 1 22.57 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . C 3 -3.056 18.291 5.315 1 22.02 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #