data_1QVI # _model_server_result.job_id lkJP7q7KvbszWLShr4efow _model_server_result.datetime_utc '2025-06-28 11:18:59' _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 1qvi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1999}' # _entry.id 1QVI # _exptl.entry_id 1QVI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 114.5 _cell.angle_gamma 90 _cell.entry_id 1QVI _cell.length_a 51.375 _cell.length_b 285.623 _cell.length_c 59.831 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QVI _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,K _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 6 _struct_asym.id F _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 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 D MG MG . A MG 1997 1_555 E O1 VO4 . A VO4 1998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 D MG MG . A MG 1997 1_555 F O1B ADP . A ADP 1999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc4 E V VO4 . A VO4 1998 1_555 F O3B ADP . A ADP 1999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc5 B OD2 ASP 30 Y ASP 30 1_555 G MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? metalc ? metalc6 B OD1 ASP 30 Y ASP 30 1_555 G MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc7 B OD1 ASP 32 Y ASP 32 1_555 G MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc8 B O PHE 34 Y PHE 34 1_555 G MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc9 B OD1 ASP 39 Y ASP 39 1_555 G MG MG . Y MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc10 C OD1 ASP 19 Z ASP 19 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc11 C O ASP 19 Z ASP 19 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc12 C OD2 ASP 22 Z ASP 22 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? metalc ? metalc13 C O GLY 23 Z GLY 23 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc14 C OD2 ASP 25 Z ASP 25 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc15 C O ALA 27 Z ALA 27 1_555 H CA CA . Z CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? # _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 1QVI _atom_sites.fract_transf_matrix[1][1] 0.019465 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008871 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003501 _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] 0.018368 _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 1997 1997 MG MG . E 5 VO4 A 1 1998 1998 VO4 VO4 . F 6 ADP A 1 1999 1999 ADP ADP . G 4 MG Y 1 502 502 MG MG . H 7 CA Z 1 503 503 CA CA . I 8 HOH A 1 2000 1 HOH TIP . I 8 HOH A 2 2001 3 HOH TIP . I 8 HOH A 3 2002 4 HOH TIP . I 8 HOH A 4 2003 5 HOH TIP . I 8 HOH A 5 2004 6 HOH TIP . I 8 HOH A 6 2005 7 HOH TIP . I 8 HOH A 7 2006 8 HOH TIP . I 8 HOH A 8 2007 10 HOH TIP . I 8 HOH A 9 2008 11 HOH TIP . I 8 HOH A 10 2009 12 HOH TIP . I 8 HOH A 11 2010 13 HOH TIP . I 8 HOH A 12 2011 14 HOH TIP . I 8 HOH A 13 2012 15 HOH TIP . I 8 HOH A 14 2013 17 HOH TIP . I 8 HOH A 15 2014 19 HOH TIP . I 8 HOH A 16 2015 20 HOH TIP . I 8 HOH A 17 2016 21 HOH TIP . I 8 HOH A 18 2017 22 HOH TIP . I 8 HOH A 19 2018 23 HOH TIP . I 8 HOH A 20 2019 24 HOH TIP . I 8 HOH A 21 2020 25 HOH TIP . I 8 HOH A 22 2021 26 HOH TIP . I 8 HOH A 23 2022 27 HOH TIP . I 8 HOH A 24 2023 28 HOH TIP . I 8 HOH A 25 2024 29 HOH TIP . I 8 HOH A 26 2025 30 HOH TIP . I 8 HOH A 27 2026 31 HOH TIP . I 8 HOH A 28 2027 33 HOH TIP . I 8 HOH A 29 2028 34 HOH TIP . I 8 HOH A 30 2029 37 HOH TIP . I 8 HOH A 31 2030 38 HOH TIP . I 8 HOH A 32 2031 39 HOH TIP . I 8 HOH A 33 2032 40 HOH TIP . I 8 HOH A 34 2033 41 HOH TIP . I 8 HOH A 35 2034 42 HOH TIP . I 8 HOH A 36 2035 43 HOH TIP . I 8 HOH A 37 2036 44 HOH TIP . I 8 HOH A 38 2037 45 HOH TIP . I 8 HOH A 39 2038 46 HOH TIP . I 8 HOH A 40 2039 48 HOH TIP . I 8 HOH A 41 2040 49 HOH TIP . I 8 HOH A 42 2041 50 HOH TIP . I 8 HOH A 43 2042 52 HOH TIP . J 8 HOH Y 1 503 18 HOH TIP . J 8 HOH Y 2 504 51 HOH TIP . K 8 HOH Z 1 504 2 HOH TIP . K 8 HOH Z 2 505 9 HOH TIP . K 8 HOH Z 3 506 16 HOH TIP . K 8 HOH Z 4 507 32 HOH TIP . K 8 HOH Z 5 508 35 HOH TIP . K 8 HOH Z 6 509 36 HOH TIP . K 8 HOH Z 7 510 47 HOH TIP . # 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 . . . F 6 -15.561 -9.854 57.448 1 20.03 ? PB ADP 1999 A 1 HETATM 2 O O1B ADP . . . F 6 -15.204 -9.794 58.848 1 23.44 ? O1B ADP 1999 A 1 HETATM 3 O O2B ADP . . . F 6 -15.912 -8.473 56.812 1 11.51 ? O2B ADP 1999 A 1 HETATM 4 O O3B ADP . . . F 6 -15.623 -11.063 56.651 1 15.11 ? O3B ADP 1999 A 1 HETATM 5 P PA ADP . . . F 6 -12.467 -9.434 57.731 1 22.74 ? PA ADP 1999 A 1 HETATM 6 O O1A ADP . . . F 6 -12.59 -8.386 58.735 1 25.51 ? O1A ADP 1999 A 1 HETATM 7 O O2A ADP . . . F 6 -12.234 -10.71 58.467 1 19.83 ? O2A ADP 1999 A 1 HETATM 8 O O3A ADP . . . F 6 -13.905 -9.767 56.943 1 2.43 ? O3A ADP 1999 A 1 HETATM 9 O O5' ADP . . . F 6 -11.148 -9.595 56.943 1 32.23 ? O5' ADP 1999 A 1 HETATM 10 C C5' ADP . . . F 6 -11.175 -10.151 55.649 1 22.07 ? C5' ADP 1999 A 1 HETATM 11 C C4' ADP . . . F 6 -9.624 -10.431 55.485 1 27.61 ? C4' ADP 1999 A 1 HETATM 12 O O4' ADP . . . F 6 -8.942 -9.386 54.824 1 28.76 ? O4' ADP 1999 A 1 HETATM 13 C C3' ADP . . . F 6 -8.791 -10.612 56.864 1 20.82 ? C3' ADP 1999 A 1 HETATM 14 O O3' ADP . . . F 6 -8.649 -11.974 57.33 1 20.01 ? O3' ADP 1999 A 1 HETATM 15 C C2' ADP . . . F 6 -7.449 -9.951 56.634 1 28.32 ? C2' ADP 1999 A 1 HETATM 16 O O2' ADP . . . F 6 -6.369 -10.842 56.288 1 30.08 ? O2' ADP 1999 A 1 HETATM 17 C C1' ADP . . . F 6 -7.79 -8.913 55.587 1 26.04 ? C1' ADP 1999 A 1 HETATM 18 N N9 ADP . . . F 6 -8.105 -7.554 56.19 1 21.55 ? N9 ADP 1999 A 1 HETATM 19 C C8 ADP . . . F 6 -9.324 -6.961 56.262 1 24.93 ? C8 ADP 1999 A 1 HETATM 20 N N7 ADP . . . F 6 -9.216 -5.786 56.851 1 25.69 ? N7 ADP 1999 A 1 HETATM 21 C C5 ADP . . . F 6 -7.963 -5.594 57.155 1 21.35 ? C5 ADP 1999 A 1 HETATM 22 C C6 ADP . . . F 6 -7.23 -4.581 57.79 1 28.48 ? C6 ADP 1999 A 1 HETATM 23 N N6 ADP . . . F 6 -7.842 -3.468 58.202 1 21.65 ? N6 ADP 1999 A 1 HETATM 24 N N1 ADP . . . F 6 -5.864 -4.713 57.964 1 28.88 ? N1 ADP 1999 A 1 HETATM 25 C C2 ADP . . . F 6 -5.19 -5.816 57.559 1 29.77 ? C2 ADP 1999 A 1 HETATM 26 N N3 ADP . . . F 6 -5.892 -6.808 56.949 1 25.36 ? N3 ADP 1999 A 1 HETATM 27 C C4 ADP . . . F 6 -7.245 -6.744 56.749 1 16.86 ? C4 ADP 1999 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 27 #