data_7ZBG # _model_server_result.job_id '_kKEPAwSVS4pV2l8qaaA4Q' _model_server_result.datetime_utc '2025-06-28 04:38:47' _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 7zbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7ZBG # _exptl.entry_id 7ZBG _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 7ZBG _cell.length_a 103.4 _cell.length_b 103.4 _cell.length_c 67.02 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 OD1 ASN 63 A ASN 107 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 B O1B ADP . A ADP 501 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 B O1A ADP . A ADP 501 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc4 G MG MG . A MG 506 1_555 I O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc5 G MG MG . A MG 506 1_555 I O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc6 G MG MG . A MG 506 1_555 I O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? # _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 7ZBG _atom_sites.fract_transf_matrix[1][1] 0.009671 _atom_sites.fract_transf_matrix[1][2] 0.005584 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011167 _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] 0.014921 _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 1 501 501 ADP ADP . C 3 SO4 A 1 502 1 SO4 SO4 . D 3 SO4 A 1 503 2 SO4 SO4 . E 3 SO4 A 1 504 3 SO4 SO4 . F 3 SO4 A 1 505 4 SO4 SO4 . G 4 MG A 1 506 3 MG MG . H 5 ITH A 1 507 5 ITH 00Z . I 6 HOH A 1 601 10 HOH HOH . I 6 HOH A 2 602 32 HOH HOH . I 6 HOH A 3 603 6 HOH HOH . I 6 HOH A 4 604 41 HOH HOH . I 6 HOH A 5 605 34 HOH HOH . I 6 HOH A 6 606 49 HOH HOH . I 6 HOH A 7 607 14 HOH HOH . I 6 HOH A 8 608 43 HOH HOH . I 6 HOH A 9 609 31 HOH HOH . I 6 HOH A 10 610 39 HOH HOH . I 6 HOH A 11 611 50 HOH HOH . I 6 HOH A 12 612 4 HOH HOH . I 6 HOH A 13 613 46 HOH HOH . I 6 HOH A 14 614 21 HOH HOH . I 6 HOH A 15 615 23 HOH HOH . I 6 HOH A 16 616 22 HOH HOH . I 6 HOH A 17 617 33 HOH HOH . I 6 HOH A 18 618 18 HOH HOH . I 6 HOH A 19 619 15 HOH HOH . I 6 HOH A 20 620 12 HOH HOH . I 6 HOH A 21 621 30 HOH HOH . I 6 HOH A 22 622 9 HOH HOH . I 6 HOH A 23 623 8 HOH HOH . I 6 HOH A 24 624 3 HOH HOH . I 6 HOH A 25 625 20 HOH HOH . I 6 HOH A 26 626 44 HOH HOH . I 6 HOH A 27 627 47 HOH HOH . I 6 HOH A 28 628 25 HOH HOH . I 6 HOH A 29 629 11 HOH HOH . I 6 HOH A 30 630 40 HOH HOH . I 6 HOH A 31 631 48 HOH HOH . I 6 HOH A 32 632 2 HOH HOH . I 6 HOH A 33 633 17 HOH HOH . I 6 HOH A 34 634 1 HOH HOH . I 6 HOH A 35 635 42 HOH HOH . I 6 HOH A 36 636 38 HOH HOH . I 6 HOH A 37 637 7 HOH HOH . I 6 HOH A 38 638 45 HOH HOH . I 6 HOH A 39 639 19 HOH HOH . I 6 HOH A 40 640 16 HOH HOH . I 6 HOH A 41 641 13 HOH HOH . I 6 HOH A 42 642 29 HOH HOH . I 6 HOH A 43 643 5 HOH HOH . I 6 HOH A 44 644 28 HOH HOH . I 6 HOH A 45 645 26 HOH HOH . I 6 HOH A 46 646 24 HOH HOH . I 6 HOH A 47 647 37 HOH HOH . I 6 HOH A 48 648 36 HOH HOH . I 6 HOH A 49 649 27 HOH HOH . I 6 HOH A 50 650 35 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 -12.263 -23.739 -13.777 1 26.97 0 PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 -11.946 -24.924 -14.688 1 28.55 0 O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 -12.696 -22.493 -14.533 1 26.76 0 O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 -13.138 -24.126 -12.64 1 28.81 0 O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 -9.45 -24.03 -13.183 1 28.97 0 PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 -9.641 -25.494 -13.489 1 26.37 0 O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 -8.656 -23.664 -11.974 1 29.81 0 O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 -10.901 -23.363 -13.091 1 23.83 0 O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 -8.835 -23.327 -14.455 1 25.8 0 O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 -8.557 -21.914 -14.576 1 29.78 0 C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 -8.856 -21.437 -15.982 1 28.5 0 C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 -7.776 -21.856 -16.851 1 32.86 0 O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 -10.097 -22.012 -16.665 1 29.43 0 C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 -11.272 -21.315 -16.302 1 26.01 0 O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 -9.762 -21.883 -18.155 1 28.06 0 C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 -10.061 -20.57 -18.561 1 29.61 0 O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 -8.251 -22.091 -18.168 1 30.74 0 C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 -7.772 -23.395 -18.575 1 28.18 0 N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 -7.386 -24.429 -17.757 1 32.49 0 C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 -6.93 -25.489 -18.401 1 27.46 0 N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 -7.016 -25.121 -19.728 1 25.16 0 C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 -6.742 -25.832 -20.912 1 26.07 0 C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 -6.227 -27.053 -20.91 1 30.37 0 N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 -6.919 -25.186 -22.093 1 29.26 0 N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 -7.377 -23.917 -22.056 1 29.07 0 C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 -7.716 -23.163 -20.995 1 29.53 0 N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 -7.504 -23.824 -19.847 1 28.61 0 C4 ADP 501 A 1 HETATM 28 H "H5'1" ADP . . . B 2 -7.607 -21.744 -14.367 1 28.5 0 "H5'1" ADP 501 A 1 HETATM 29 H "H5'2" ADP . . . B 2 -9.113 -21.409 -13.932 1 28.49 0 "H5'2" ADP 501 A 1 HETATM 30 H H4' ADP . . . B 2 -8.904 -20.457 -15.976 1 29.71 0 H4' ADP 501 A 1 HETATM 31 H H3' ADP . . . B 2 -10.192 -22.97 -16.427 1 28.3 0 H3' ADP 501 A 1 HETATM 32 H H2' ADP . . . B 2 -10.237 -22.566 -18.698 1 29.11 0 H2' ADP 501 A 1 HETATM 33 H H1' ADP . . . B 2 -7.86 -21.417 -18.77 1 30.09 0 H1' ADP 501 A 1 HETATM 34 H H8 ADP . . . B 2 -7.438 -24.385 -16.818 1 30.06 0 H8 ADP 501 A 1 HETATM 35 H HN61 ADP . . . B 2 -5.566 -27.247 -21.453 1 28.98 0 HN61 ADP 501 A 1 HETATM 36 H HN62 ADP . . . B 2 -6.55 -27.661 -20.366 1 28.98 0 HN62 ADP 501 A 1 HETATM 37 H H2 ADP . . . B 2 -7.509 -23.511 -22.899 1 29.19 0 H2 ADP 501 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #