data_1B7T # _model_server_result.job_id 3zAQAWbaCUgXgjGSq229wg _model_server_result.datetime_utc '2024-10-18 14:28:01' _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 1b7t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":999}' # _entry.id 1B7T # _exptl.entry_id 1B7T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 89.1 _cell.angle_beta 90 _cell.angle_gamma 73.5 _cell.entry_id 1B7T _cell.length_a 51.7 _cell.length_b 58.9 _cell.length_c 138.9 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1B7T _symmetry.cell_setting triclinic _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 5 _struct_asym.id E _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 183 A THR 183 1_555 D MG MG . A MG 836 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc2 A OG SER 241 A SER 241 1_555 D MG MG . A MG 836 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc3 D MG MG . A MG 836 1_555 E O1B ADP . A ADP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc4 D MG MG . A MG 836 1_555 H O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc5 D MG MG . A MG 836 1_555 H O HOH . A HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 D MG MG . A MG 836 1_555 H O HOH . A HOH 1057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc7 B OD1 ASP 28 Y ASP 28 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc8 B OD1 ASP 30 Y ASP 30 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc9 B OD2 ASP 30 Y ASP 30 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc10 B OD1 ASP 32 Y ASP 32 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc11 B O PHE 34 Y PHE 34 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc12 B OD2 ASP 39 Y ASP 39 1_555 F MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc13 F MG MG . Y MG 502 1_555 I O HOH . Y HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc14 C O ASP 19 Z ASP 19 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc15 C OD1 ASP 19 Z ASP 19 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc16 C OD1 ASP 22 Z ASP 22 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc17 C O ASP 22 Z ASP 22 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.377 ? metalc ? metalc18 C O GLY 23 Z GLY 23 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc19 C OD1 ASP 25 Z ASP 25 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc20 C O ALA 27 Z ALA 27 1_555 G CA CA . Z CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc21 G CA CA . Z CA 501 1_555 J O HOH . Z HOH 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? # _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 1B7T _atom_sites.fract_transf_matrix[1][1] 0.019342 _atom_sites.fract_transf_matrix[1][2] -0.005729 _atom_sites.fract_transf_matrix[1][3] 0.000094 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017707 _atom_sites.fract_transf_matrix[2][3] -0.00029 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.0072 _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 D 4 MG A 1 836 503 MG MG . E 5 ADP A 1 999 999 ADP ADP . F 4 MG Y 1 502 502 MG MG . G 6 CA Z 1 501 501 CA CA . H 7 HOH A 1 1000 603 HOH HOH . H 7 HOH A 2 1001 604 HOH HOH . H 7 HOH A 3 1002 605 HOH HOH . H 7 HOH A 4 1003 606 HOH HOH . H 7 HOH A 5 1004 607 HOH HOH . H 7 HOH A 6 1005 608 HOH HOH . H 7 HOH A 7 1006 609 HOH HOH . H 7 HOH A 8 1007 610 HOH HOH . H 7 HOH A 9 1008 611 HOH HOH . H 7 HOH A 10 1009 612 HOH HOH . H 7 HOH A 11 1010 613 HOH HOH . H 7 HOH A 12 1011 614 HOH HOH . H 7 HOH A 13 1012 616 HOH HOH . H 7 HOH A 14 1013 618 HOH HOH . H 7 HOH A 15 1014 619 HOH HOH . H 7 HOH A 16 1015 620 HOH HOH . H 7 HOH A 17 1016 621 HOH HOH . H 7 HOH A 18 1017 623 HOH HOH . H 7 HOH A 19 1018 625 HOH HOH . H 7 HOH A 20 1019 650 HOH HOH . H 7 HOH A 21 1020 651 HOH HOH . H 7 HOH A 22 1021 654 HOH HOH . H 7 HOH A 23 1022 655 HOH HOH . H 7 HOH A 24 1023 656 HOH HOH . H 7 HOH A 25 1024 657 HOH HOH . H 7 HOH A 26 1025 658 HOH HOH . H 7 HOH A 27 1026 659 HOH HOH . H 7 HOH A 28 1027 660 HOH HOH . H 7 HOH A 29 1028 661 HOH HOH . H 7 HOH A 30 1029 662 HOH HOH . H 7 HOH A 31 1030 663 HOH HOH . H 7 HOH A 32 1031 664 HOH HOH . H 7 HOH A 33 1032 665 HOH HOH . H 7 HOH A 34 1033 666 HOH HOH . H 7 HOH A 35 1034 667 HOH HOH . H 7 HOH A 36 1035 670 HOH HOH . H 7 HOH A 37 1036 672 HOH HOH . H 7 HOH A 38 1037 673 HOH HOH . H 7 HOH A 39 1038 674 HOH HOH . H 7 HOH A 40 1039 675 HOH HOH . H 7 HOH A 41 1040 676 HOH HOH . H 7 HOH A 42 1041 677 HOH HOH . H 7 HOH A 43 1042 678 HOH HOH . H 7 HOH A 44 1043 679 HOH HOH . H 7 HOH A 45 1044 680 HOH HOH . H 7 HOH A 46 1045 681 HOH HOH . H 7 HOH A 47 1046 685 HOH HOH . H 7 HOH A 48 1047 686 HOH HOH . H 7 HOH A 49 1048 687 HOH HOH . H 7 HOH A 50 1049 688 HOH HOH . H 7 HOH A 51 1050 689 HOH HOH . H 7 HOH A 52 1051 690 HOH HOH . H 7 HOH A 53 1052 691 HOH HOH . H 7 HOH A 54 1053 692 HOH HOH . H 7 HOH A 55 1054 693 HOH HOH . H 7 HOH A 56 1055 694 HOH HOH . H 7 HOH A 57 1056 695 HOH HOH . H 7 HOH A 58 1057 696 HOH HOH . H 7 HOH A 59 1058 697 HOH HOH . H 7 HOH A 60 1059 698 HOH HOH . H 7 HOH A 61 1060 699 HOH HOH . H 7 HOH A 62 1061 700 HOH HOH . H 7 HOH A 63 1062 701 HOH HOH . H 7 HOH A 64 1063 702 HOH HOH . H 7 HOH A 65 1064 703 HOH HOH . H 7 HOH A 66 1065 704 HOH HOH . H 7 HOH A 67 1066 705 HOH HOH . H 7 HOH A 68 1067 706 HOH HOH . H 7 HOH A 69 1068 707 HOH HOH . H 7 HOH A 70 1069 750 HOH HOH . H 7 HOH A 71 1070 751 HOH HOH . H 7 HOH A 72 1071 752 HOH HOH . H 7 HOH A 73 1072 760 HOH HOH . H 7 HOH A 74 1073 770 HOH HOH . H 7 HOH A 75 1074 802 HOH HOH . H 7 HOH A 76 1075 804 HOH HOH . H 7 HOH A 77 1076 805 HOH HOH . H 7 HOH A 78 1077 806 HOH HOH . H 7 HOH A 79 1078 808 HOH HOH . H 7 HOH A 80 1079 809 HOH HOH . I 7 HOH Y 1 622 622 HOH HOH . I 7 HOH Y 2 762 762 HOH HOH . I 7 HOH Y 3 763 763 HOH HOH . I 7 HOH Y 4 764 764 HOH HOH . I 7 HOH Y 5 765 765 HOH HOH . I 7 HOH Y 6 766 766 HOH HOH . I 7 HOH Y 7 768 768 HOH HOH . I 7 HOH Y 8 769 769 HOH HOH . J 7 HOH Z 1 624 624 HOH HOH . J 7 HOH Z 2 653 653 HOH HOH . J 7 HOH Z 3 671 671 HOH HOH . J 7 HOH Z 4 682 682 HOH HOH . J 7 HOH Z 5 683 683 HOH HOH . J 7 HOH Z 6 753 753 HOH HOH . J 7 HOH Z 7 754 754 HOH HOH . J 7 HOH Z 8 755 755 HOH HOH . J 7 HOH Z 9 757 757 HOH HOH . J 7 HOH Z 10 758 758 HOH HOH . J 7 HOH Z 11 759 759 HOH HOH . J 7 HOH Z 12 761 761 HOH HOH . J 7 HOH Z 13 772 772 HOH HOH . J 7 HOH Z 14 773 773 HOH HOH . J 7 HOH Z 15 774 774 HOH HOH . J 7 HOH Z 16 775 775 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 . . . E 5 3.115 -4.65 -1.197 1 34.47 ? PB ADP 999 A 1 HETATM 2 O O1B ADP . . . E 5 1.799 -4.596 -1.908 1 15.49 ? O1B ADP 999 A 1 HETATM 3 O O2B ADP . . . E 5 2.995 -4.045 0.335 1 32.68 ? O2B ADP 999 A 1 HETATM 4 O O3B ADP . . . E 5 4.207 -3.963 -1.944 1 17.07 ? O3B ADP 999 A 1 HETATM 5 P PA ADP . . . E 5 2.631 -7.454 -1.386 1 18.16 ? PA ADP 999 A 1 HETATM 6 O O1A ADP . . . E 5 2.655 -7.498 -2.874 1 24.87 ? O1A ADP 999 A 1 HETATM 7 O O2A ADP . . . E 5 1.241 -7.335 -0.876 1 15.32 ? O2A ADP 999 A 1 HETATM 8 O O3A ADP . . . E 5 3.459 -6.167 -0.985 1 8.63 ? O3A ADP 999 A 1 HETATM 9 O O5' ADP . . . E 5 3.413 -8.705 -0.75 1 2 ? O5' ADP 999 A 1 HETATM 10 C C5' ADP . . . E 5 4.76 -8.886 -1.172 1 5.46 ? C5' ADP 999 A 1 HETATM 11 C C4' ADP . . . E 5 5.103 -10.376 -1.246 1 32.85 ? C4' ADP 999 A 1 HETATM 12 O O4' ADP . . . E 5 5.272 -10.933 0.064 1 27.87 ? O4' ADP 999 A 1 HETATM 13 C C3' ADP . . . E 5 4.081 -11.231 -1.949 1 40.13 ? C3' ADP 999 A 1 HETATM 14 O O3' ADP . . . E 5 4.397 -11.416 -3.336 1 33.84 ? O3' ADP 999 A 1 HETATM 15 C C2' ADP . . . E 5 4.14 -12.554 -1.212 1 43.77 ? C2' ADP 999 A 1 HETATM 16 O O2' ADP . . . E 5 5.108 -13.473 -1.751 1 46.93 ? O2' ADP 999 A 1 HETATM 17 C C1' ADP . . . E 5 4.478 -12.124 0.205 1 34.55 ? C1' ADP 999 A 1 HETATM 18 N N9 ADP . . . E 5 3.244 -11.927 1.076 1 34.38 ? N9 ADP 999 A 1 HETATM 19 C C8 ADP . . . E 5 2.678 -10.748 1.452 1 27.03 ? C8 ADP 999 A 1 HETATM 20 N N7 ADP . . . E 5 1.602 -10.988 2.219 1 26.85 ? N7 ADP 999 A 1 HETATM 21 C C5 ADP . . . E 5 1.466 -12.301 2.348 1 34.09 ? C5 ADP 999 A 1 HETATM 22 C C6 ADP . . . E 5 0.559 -13.174 3.009 1 35.91 ? C6 ADP 999 A 1 HETATM 23 N N6 ADP . . . E 5 -0.47 -12.679 3.729 1 28.37 ? N6 ADP 999 A 1 HETATM 24 N N1 ADP . . . E 5 0.733 -14.544 2.923 1 30.3 ? N1 ADP 999 A 1 HETATM 25 C C2 ADP . . . E 5 1.754 -15.094 2.208 1 36.38 ? C2 ADP 999 A 1 HETATM 26 N N3 ADP . . . E 5 2.626 -14.274 1.569 1 34.85 ? N3 ADP 999 A 1 HETATM 27 C C4 ADP . . . E 5 2.523 -12.907 1.608 1 33.93 ? C4 ADP 999 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #