data_7EBG # _model_server_result.job_id G2Nik4qLHZo_XuC0vRDT4g _model_server_result.datetime_utc '2025-07-07 09:36:40' _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 7ebg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":504}' # _entry.id 7EBG # _exptl.entry_id 7EBG _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 90 _cell.angle_beta 101.185 _cell.angle_gamma 90 _cell.entry_id 7EBG _cell.length_a 69.965 _cell.length_b 67.441 _cell.length_c 78.605 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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 5 _struct_asym.id H _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 B OD1 ASN 251 B ASN 258 1_555 G MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc2 F O2 SO4 . B SO4 502 1_555 G MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 G MG MG . B MG 503 1_555 H O3B ADP . B ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc4 G MG MG . B MG 503 1_555 H O2A ADP . B ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc5 G MG MG . B MG 503 1_555 H O3A ADP . B ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc6 G MG MG . B MG 503 1_555 J O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc7 G MG MG . B MG 503 1_555 J O HOH . B HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? # _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 7EBG _atom_sites.fract_transf_matrix[1][1] 0.014293 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002826 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014828 _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] 0.012968 _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 2 SO4 A 1 501 1000 SO4 SO4 . D 3 J0L A 1 502 5000 J0L MOL . E 2 SO4 B 1 501 1000 SO4 SO4 . F 2 SO4 B 1 502 1001 SO4 SO4 . G 4 MG B 1 503 2000 MG MG . H 5 ADP B 1 504 2001 ADP ADP . I 6 HOH A 1 601 6073 HOH HOH . I 6 HOH A 2 602 6054 HOH HOH . I 6 HOH A 3 603 6075 HOH HOH . I 6 HOH A 4 604 6046 HOH HOH . I 6 HOH A 5 605 6061 HOH HOH . I 6 HOH A 6 606 6014 HOH HOH . I 6 HOH A 7 607 6013 HOH HOH . I 6 HOH A 8 608 6039 HOH HOH . I 6 HOH A 9 609 6036 HOH HOH . I 6 HOH A 10 610 6026 HOH HOH . I 6 HOH A 11 611 6064 HOH HOH . I 6 HOH A 12 612 6047 HOH HOH . I 6 HOH A 13 613 6001 HOH HOH . I 6 HOH A 14 614 6009 HOH HOH . I 6 HOH A 15 615 6045 HOH HOH . I 6 HOH A 16 616 6034 HOH HOH . I 6 HOH A 17 617 6002 HOH HOH . I 6 HOH A 18 618 6008 HOH HOH . I 6 HOH A 19 619 6028 HOH HOH . I 6 HOH A 20 620 6042 HOH HOH . I 6 HOH A 21 621 6057 HOH HOH . I 6 HOH A 22 622 6005 HOH HOH . I 6 HOH A 23 623 6019 HOH HOH . I 6 HOH A 24 624 6021 HOH HOH . I 6 HOH A 25 625 6032 HOH HOH . I 6 HOH A 26 626 6040 HOH HOH . I 6 HOH A 27 627 6011 HOH HOH . I 6 HOH A 28 628 6053 HOH HOH . I 6 HOH A 29 629 6038 HOH HOH . I 6 HOH A 30 630 6000 HOH HOH . I 6 HOH A 31 631 6033 HOH HOH . I 6 HOH A 32 632 6012 HOH HOH . I 6 HOH A 33 633 6035 HOH HOH . I 6 HOH A 34 634 6044 HOH HOH . I 6 HOH A 35 635 6023 HOH HOH . I 6 HOH A 36 636 6010 HOH HOH . I 6 HOH A 37 637 6060 HOH HOH . I 6 HOH A 38 638 6051 HOH HOH . I 6 HOH A 39 639 6006 HOH HOH . I 6 HOH A 40 640 6067 HOH HOH . I 6 HOH A 41 641 6063 HOH HOH . I 6 HOH A 42 642 6015 HOH HOH . I 6 HOH A 43 643 6020 HOH HOH . I 6 HOH A 44 644 6062 HOH HOH . I 6 HOH A 45 645 6049 HOH HOH . I 6 HOH A 46 646 6004 HOH HOH . I 6 HOH A 47 647 6052 HOH HOH . I 6 HOH A 48 648 6031 HOH HOH . I 6 HOH A 49 649 6030 HOH HOH . I 6 HOH A 50 650 6003 HOH HOH . I 6 HOH A 51 651 6050 HOH HOH . I 6 HOH A 52 652 6068 HOH HOH . I 6 HOH A 53 653 6025 HOH HOH . I 6 HOH A 54 654 6018 HOH HOH . I 6 HOH A 55 655 6027 HOH HOH . I 6 HOH A 56 656 6029 HOH HOH . I 6 HOH A 57 657 6048 HOH HOH . I 6 HOH A 58 658 6007 HOH HOH . I 6 HOH A 59 659 6069 HOH HOH . I 6 HOH A 60 660 6024 HOH HOH . I 6 HOH A 61 661 6072 HOH HOH . I 6 HOH A 62 662 6066 HOH HOH . I 6 HOH A 63 663 6055 HOH HOH . I 6 HOH A 64 664 6071 HOH HOH . I 6 HOH A 65 665 6058 HOH HOH . I 6 HOH A 66 666 6074 HOH HOH . I 6 HOH A 67 667 6016 HOH HOH . I 6 HOH A 68 668 6056 HOH HOH . I 6 HOH A 69 669 6065 HOH HOH . I 6 HOH A 70 670 6059 HOH HOH . I 6 HOH A 71 671 6043 HOH HOH . I 6 HOH A 72 672 6041 HOH HOH . I 6 HOH A 73 673 6037 HOH HOH . I 6 HOH A 74 674 6070 HOH HOH . I 6 HOH A 75 675 6017 HOH HOH . J 6 HOH B 1 601 6062 HOH HOH . J 6 HOH B 2 602 6037 HOH HOH . J 6 HOH B 3 603 6066 HOH HOH . J 6 HOH B 4 604 6016 HOH HOH . J 6 HOH B 5 605 6073 HOH HOH . J 6 HOH B 6 606 6072 HOH HOH . J 6 HOH B 7 607 6080 HOH HOH . J 6 HOH B 8 608 6067 HOH HOH . J 6 HOH B 9 609 6046 HOH HOH . J 6 HOH B 10 610 6096 HOH HOH . J 6 HOH B 11 611 6011 HOH HOH . J 6 HOH B 12 612 6050 HOH HOH . J 6 HOH B 13 613 6017 HOH HOH . J 6 HOH B 14 614 6055 HOH HOH . J 6 HOH B 15 615 6087 HOH HOH . J 6 HOH B 16 616 6033 HOH HOH . J 6 HOH B 17 617 6077 HOH HOH . J 6 HOH B 18 618 6048 HOH HOH . J 6 HOH B 19 619 6001 HOH HOH . J 6 HOH B 20 620 6083 HOH HOH . J 6 HOH B 21 621 6081 HOH HOH . J 6 HOH B 22 622 6012 HOH HOH . J 6 HOH B 23 623 6049 HOH HOH . J 6 HOH B 24 624 6051 HOH HOH . J 6 HOH B 25 625 6004 HOH HOH . J 6 HOH B 26 626 6042 HOH HOH . J 6 HOH B 27 627 6047 HOH HOH . J 6 HOH B 28 628 6024 HOH HOH . J 6 HOH B 29 629 6086 HOH HOH . J 6 HOH B 30 630 6022 HOH HOH . J 6 HOH B 31 631 6026 HOH HOH . J 6 HOH B 32 632 6034 HOH HOH . J 6 HOH B 33 633 6006 HOH HOH . J 6 HOH B 34 634 6005 HOH HOH . J 6 HOH B 35 635 6069 HOH HOH . J 6 HOH B 36 636 6032 HOH HOH . J 6 HOH B 37 637 6030 HOH HOH . J 6 HOH B 38 638 6084 HOH HOH . J 6 HOH B 39 639 6036 HOH HOH . J 6 HOH B 40 640 6000 HOH HOH . J 6 HOH B 41 641 6025 HOH HOH . J 6 HOH B 42 642 6043 HOH HOH . J 6 HOH B 43 643 6028 HOH HOH . J 6 HOH B 44 644 6003 HOH HOH . J 6 HOH B 45 645 6027 HOH HOH . J 6 HOH B 46 646 6053 HOH HOH . J 6 HOH B 47 647 6022 HOH HOH . J 6 HOH B 48 648 6044 HOH HOH . J 6 HOH B 49 649 6071 HOH HOH . J 6 HOH B 50 650 6015 HOH HOH . J 6 HOH B 51 651 6007 HOH HOH . J 6 HOH B 52 652 6065 HOH HOH . J 6 HOH B 53 653 6088 HOH HOH . J 6 HOH B 54 654 6038 HOH HOH . J 6 HOH B 55 655 6057 HOH HOH . J 6 HOH B 56 656 6056 HOH HOH . J 6 HOH B 57 657 6078 HOH HOH . J 6 HOH B 58 658 6052 HOH HOH . J 6 HOH B 59 659 6089 HOH HOH . J 6 HOH B 60 660 6010 HOH HOH . J 6 HOH B 61 661 6021 HOH HOH . J 6 HOH B 62 662 6097 HOH HOH . J 6 HOH B 63 663 6023 HOH HOH . J 6 HOH B 64 664 6029 HOH HOH . J 6 HOH B 65 665 6008 HOH HOH . J 6 HOH B 66 666 6002 HOH HOH . J 6 HOH B 67 667 6095 HOH HOH . J 6 HOH B 68 668 6014 HOH HOH . J 6 HOH B 69 669 6094 HOH HOH . J 6 HOH B 70 670 6013 HOH HOH . J 6 HOH B 71 671 6041 HOH HOH . J 6 HOH B 72 672 6060 HOH HOH . J 6 HOH B 73 673 6059 HOH HOH . J 6 HOH B 74 674 6031 HOH HOH . J 6 HOH B 75 675 6018 HOH HOH . J 6 HOH B 76 676 6054 HOH HOH . J 6 HOH B 77 677 6079 HOH HOH . J 6 HOH B 78 678 6092 HOH HOH . J 6 HOH B 79 679 6074 HOH HOH . J 6 HOH B 80 680 6009 HOH HOH . J 6 HOH B 81 681 6064 HOH HOH . J 6 HOH B 82 682 6093 HOH HOH . J 6 HOH B 83 683 6082 HOH HOH . J 6 HOH B 84 684 6085 HOH HOH . J 6 HOH B 85 685 6039 HOH HOH . J 6 HOH B 86 686 6040 HOH HOH . J 6 HOH B 87 687 6075 HOH HOH . J 6 HOH B 88 688 6063 HOH HOH . J 6 HOH B 89 689 6035 HOH HOH . J 6 HOH B 90 690 6058 HOH HOH . J 6 HOH B 91 691 6045 HOH HOH . J 6 HOH B 92 692 6091 HOH HOH . J 6 HOH B 93 693 6070 HOH HOH . J 6 HOH B 94 694 6019 HOH HOH . J 6 HOH B 95 695 6020 HOH HOH . J 6 HOH B 96 696 6090 HOH HOH . J 6 HOH B 97 697 6076 HOH HOH . J 6 HOH B 98 698 6068 HOH HOH . J 6 HOH B 99 699 6061 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 . . . H 5 14.081 8.644 11.678 0.91 33.11 ? PB ADP 504 B 1 HETATM 2 O O1B ADP . . . H 5 13.328 8.413 10.392 0.91 36.66 ? O1B ADP 504 B 1 HETATM 3 O O2B ADP . . . H 5 15.568 8.399 11.592 0.91 36.51 -1 O2B ADP 504 B 1 HETATM 4 O O3B ADP . . . H 5 13.707 9.923 12.392 0.91 33.51 ? O3B ADP 504 B 1 HETATM 5 P PA ADP . . . H 5 12.116 7.512 13.359 0.91 30.97 ? PA ADP 504 B 1 HETATM 6 O O1A ADP . . . H 5 11.73 6.088 13.685 0.91 32.29 ? O1A ADP 504 B 1 HETATM 7 O O2A ADP . . . H 5 12.121 8.563 14.444 0.91 31.47 -1 O2A ADP 504 B 1 HETATM 8 O O3A ADP . . . H 5 13.577 7.494 12.685 0.91 37.68 ? O3A ADP 504 B 1 HETATM 9 O O5' ADP . . . H 5 11.133 8.012 12.187 0.91 30.8 ? O5' ADP 504 B 1 HETATM 10 C C5' ADP . . . H 5 10.771 7.104 11.153 0.91 33.24 ? C5' ADP 504 B 1 HETATM 11 C C4' ADP . . . H 5 9.928 7.805 10.098 0.91 37.79 ? C4' ADP 504 B 1 HETATM 12 O O4' ADP . . . H 5 8.632 8.136 10.61 0.91 35.16 ? O4' ADP 504 B 1 HETATM 13 C C3' ADP . . . H 5 10.554 9.109 9.617 0.91 35.96 ? C3' ADP 504 B 1 HETATM 14 O O3' ADP . . . H 5 11.38 8.9 8.472 0.91 41.85 ? O3' ADP 504 B 1 HETATM 15 C C2' ADP . . . H 5 9.36 9.997 9.315 0.91 33.51 ? C2' ADP 504 B 1 HETATM 16 O O2' ADP . . . H 5 9.074 10.033 7.915 0.91 29.92 ? O2' ADP 504 B 1 HETATM 17 C C1' ADP . . . H 5 8.187 9.378 10.058 0.91 31.56 ? C1' ADP 504 B 1 HETATM 18 N N9 ADP . . . H 5 7.76 10.295 11.138 0.91 34.12 ? N9 ADP 504 B 1 HETATM 19 C C8 ADP . . . H 5 7.986 10.111 12.453 0.91 30.06 ? C8 ADP 504 B 1 HETATM 20 N N7 ADP . . . H 5 7.461 11.133 13.177 0.91 28.32 ? N7 ADP 504 B 1 HETATM 21 C C5 ADP . . . H 5 6.893 11.989 12.312 0.91 27.6 ? C5 ADP 504 B 1 HETATM 22 C C6 ADP . . . H 5 6.167 13.269 12.408 0.91 24.55 ? C6 ADP 504 B 1 HETATM 23 N N6 ADP . . . H 5 5.953 13.833 13.61 0.91 25.16 ? N6 ADP 504 B 1 HETATM 24 N N1 ADP . . . H 5 5.731 13.845 11.267 0.91 22.69 ? N1 ADP 504 B 1 HETATM 25 C C2 ADP . . . H 5 5.946 13.283 10.063 0.91 29.82 ? C2 ADP 504 B 1 HETATM 26 N N3 ADP . . . H 5 6.6 12.117 9.905 0.91 30.46 ? N3 ADP 504 B 1 HETATM 27 C C4 ADP . . . H 5 7.088 11.435 10.969 0.91 31.42 ? C4 ADP 504 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #