data_8VP3 # _model_server_result.job_id Gim6NDVzBbnKaDzVr2aoCw _model_server_result.datetime_utc '2024-12-26 10:20:29' _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 8vp3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":801}' # _entry.id 8VP3 # _exptl.entry_id 8VP3 _exptl.method 'ELECTRON MICROSCOPY' # _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 2 _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 90 _cell.entry_id 8VP3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VP3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N 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 549 A THR 526 1_555 F MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 E O3B ADP . A ADP 801 1_555 F MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc3 C OG1 THR 549 B THR 526 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc4 C OE1 GLN 590 B GLN 567 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc5 H O3B ADP . B ADP 801 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? # _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 83 n n PB O2B ADP sing 84 n n PB O3B ADP sing 85 n n PB O3A ADP sing 86 n n O2B HOB2 ADP sing 87 n n O3B HOB3 ADP sing 88 n n PA O1A ADP doub 89 n n PA O2A ADP sing 90 n n PA O3A ADP sing 91 n n PA O5' ADP sing 92 n n O2A HOA2 ADP sing 93 n n O5' C5' ADP sing 94 n n C5' C4' ADP sing 95 n n C5' "H5'1" ADP sing 96 n n C5' "H5'2" ADP sing 97 n n C4' O4' ADP sing 98 n n C4' C3' ADP sing 99 n n C4' H4' ADP sing 100 n n O4' C1' ADP sing 101 n n C3' O3' ADP sing 102 n n C3' C2' ADP sing 103 n n C3' H3' ADP sing 104 n n O3' HO3' ADP sing 105 n n C2' O2' ADP sing 106 n n C2' C1' ADP sing 107 n n C2' H2' ADP sing 108 n n O2' HO2' ADP sing 109 n n C1' N9 ADP sing 110 n n C1' H1' ADP sing 111 n n N9 C8 ADP sing 112 n y N9 C4 ADP sing 113 n y C8 N7 ADP doub 114 n y C8 H8 ADP sing 115 n n N7 C5 ADP sing 116 n y C5 C6 ADP sing 117 n y C5 C4 ADP doub 118 n y C6 N6 ADP sing 119 n n C6 N1 ADP doub 120 n y N6 HN61 ADP sing 121 n n N6 HN62 ADP sing 122 n n N1 C2 ADP sing 123 n y C2 N3 ADP doub 124 n y C2 H2 ADP sing 125 n n N3 C4 ADP sing 126 n y # _atom_sites.entry_id 8VP3 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 E 3 ADP A 1 801 801 ADP ADP . F 4 MG A 1 802 802 MG MG . G 5 A1ACX A 1 803 803 A1ACX FAA . H 3 ADP B 1 801 801 ADP ADP . I 4 MG B 1 802 802 MG MG . J 6 POV B 1 803 803 POV EPC . # 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 3 119.98 105.176 70.992 1 119.67 ? PB ADP 801 B 1 HETATM 2 O O1B ADP . . . H 3 120.449 104.069 70.079 1 111.24 ? O1B ADP 801 B 1 HETATM 3 O O2B ADP . . . H 3 118.948 106.09 70.379 1 114.45 ? O2B ADP 801 B 1 HETATM 4 O O3B ADP . . . H 3 121.085 105.891 71.728 1 114.36 ? O3B ADP 801 B 1 HETATM 5 P PA ADP . . . H 3 119.935 103.456 73.2 1 110.67 ? PA ADP 801 B 1 HETATM 6 O O1A ADP . . . H 3 121.066 102.764 72.484 1 108.83 ? O1A ADP 801 B 1 HETATM 7 O O2A ADP . . . H 3 120.238 104.244 74.45 1 107.39 ? O2A ADP 801 B 1 HETATM 8 O O3A ADP . . . H 3 119.171 104.402 72.146 1 111.78 ? O3A ADP 801 B 1 HETATM 9 O O5' ADP . . . H 3 118.822 102.347 73.537 1 111.73 ? O5' ADP 801 B 1 HETATM 10 C C5' ADP . . . H 3 119.131 100.959 73.446 1 108.46 ? C5' ADP 801 B 1 HETATM 11 C C4' ADP . . . H 3 118.08 100.168 74.208 1 108.46 ? C4' ADP 801 B 1 HETATM 12 O O4' ADP . . . H 3 118.611 99.8 75.479 1 112.39 ? O4' ADP 801 B 1 HETATM 13 C C3' ADP . . . H 3 116.83 100.995 74.445 1 107.67 ? C3' ADP 801 B 1 HETATM 14 O O3' ADP . . . H 3 115.71 100.378 73.807 1 108.75 ? O3' ADP 801 B 1 HETATM 15 C C2' ADP . . . H 3 116.618 101.017 75.944 1 109.46 ? C2' ADP 801 B 1 HETATM 16 O O2' ADP . . . H 3 115.351 100.435 76.257 1 111.32 ? O2' ADP 801 B 1 HETATM 17 C C1' ADP . . . H 3 117.737 100.18 76.54 1 111.22 ? C1' ADP 801 B 1 HETATM 18 N N9 ADP . . . H 3 118.508 100.989 77.514 1 108.28 ? N9 ADP 801 B 1 HETATM 19 C C8 ADP . . . H 3 119.231 102.082 77.213 1 108.57 ? C8 ADP 801 B 1 HETATM 20 N N7 ADP . . . H 3 119.822 102.6 78.317 1 109.11 ? N7 ADP 801 B 1 HETATM 21 C C5 ADP . . . H 3 119.473 101.825 79.359 1 110.25 ? C5 ADP 801 B 1 HETATM 22 C C6 ADP . . . H 3 119.751 101.81 80.813 1 110.79 ? C6 ADP 801 B 1 HETATM 23 N N6 ADP . . . H 3 120.539 102.753 81.382 1 108.28 ? N6 ADP 801 B 1 HETATM 24 N N1 ADP . . . H 3 119.192 100.825 81.548 1 110.69 ? N1 ADP 801 B 1 HETATM 25 C C2 ADP . . . H 3 118.407 99.885 80.991 1 110.74 ? C2 ADP 801 B 1 HETATM 26 N N3 ADP . . . H 3 118.113 99.838 79.68 1 109.35 ? N3 ADP 801 B 1 HETATM 27 C C4 ADP . . . H 3 118.605 100.765 78.826 1 108.86 ? C4 ADP 801 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #