data_9B03 # _model_server_result.job_id Iut6a5VuHjcb22cUF68Zhg _model_server_result.datetime_utc '2025-04-13 19:59:15' _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 9b03 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":401}' # _entry.id 9B03 # _exptl.entry_id 9B03 _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 6 _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 9B03 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B03 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,L,M,N,O,P,Q,R,S,T _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 I N N ? 3 K N N ? 3 M N N ? 3 O N N ? 3 Q N N ? 3 S 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 covale ? covale1 A C GLU 68 A GLU 72 1_555 A N HIC 69 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C HIC 69 A HIC 73 1_555 A N GLY 70 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 B C GLU 68 B GLU 72 1_555 B N HIC 69 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 B C HIC 69 B HIC 73 1_555 B N GLY 70 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 C C GLU 68 C GLU 72 1_555 C N HIC 69 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 C C HIC 69 C HIC 73 1_555 C N GLY 70 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 D C GLU 68 D GLU 72 1_555 D N HIC 69 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale8 D C HIC 69 D HIC 73 1_555 D N GLY 70 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 E C GLU 68 E GLU 72 1_555 E N HIC 69 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale10 E C HIC 69 E HIC 73 1_555 E N GLY 70 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 F C GLU 68 F GLU 72 1_555 F N HIC 69 F HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale12 F C HIC 69 F HIC 73 1_555 F N GLY 70 F GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 I O1B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc2 I O3B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc3 I O1A ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc4 M O1B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc5 M O3B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc6 Q O1A ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? metalc ? metalc7 S O1B ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc8 S O3B ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc9 S O1A ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc10 S O3A ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? # _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 9B03 _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 I 3 ADP A 1 401 401 ADP ADP . J 4 MG A 1 402 402 MG MG . K 3 ADP B 1 401 401 ADP ADP . L 4 MG B 1 402 402 MG MG . M 3 ADP C 1 401 401 ADP ADP . N 4 MG C 1 402 402 MG MG . O 3 ADP D 1 401 401 ADP ADP . P 4 MG D 1 402 402 MG MG . Q 3 ADP E 1 401 401 ADP ADP . R 4 MG E 1 402 402 MG MG . S 3 ADP F 1 401 401 ADP ADP . T 4 MG F 1 402 402 MG MG . # 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 . . . Q 3 167.917 143.17 123.198 1 128.96 ? PB ADP 401 E 1 HETATM 2 O O1B ADP . . . Q 3 168.803 142.573 122.132 1 111.87 ? O1B ADP 401 E 1 HETATM 3 O O2B ADP . . . Q 3 168.335 142.991 124.656 1 111.05 ? O2B ADP 401 E 1 HETATM 4 O O3B ADP . . . Q 3 167.469 144.573 122.875 1 100.02 ? O3B ADP 401 E 1 HETATM 5 P PA ADP . . . Q 3 166.439 141.025 122.145 1 94.62 ? PA ADP 401 E 1 HETATM 6 O O1A ADP . . . Q 3 166.401 141.416 120.688 1 93.94 ? O1A ADP 401 E 1 HETATM 7 O O2A ADP . . . Q 3 167.439 140.022 122.665 1 103.58 ? O2A ADP 401 E 1 HETATM 8 O O3A ADP . . . Q 3 166.545 142.355 123.042 1 111.59 ? O3A ADP 401 E 1 HETATM 9 O O5' ADP . . . Q 3 164.98 140.565 122.615 1 91.7 ? O5' ADP 401 E 1 HETATM 10 C C5' ADP . . . Q 3 164.83 140.236 123.989 1 100.11 ? C5' ADP 401 E 1 HETATM 11 C C4' ADP . . . Q 3 163.538 140.848 124.499 1 93.41 ? C4' ADP 401 E 1 HETATM 12 O O4' ADP . . . Q 3 162.465 139.983 124.142 1 99.29 ? O4' ADP 401 E 1 HETATM 13 C C3' ADP . . . Q 3 163.543 140.985 126.008 1 96.59 ? C3' ADP 401 E 1 HETATM 14 O O3' ADP . . . Q 3 163.482 142.368 126.362 1 104.45 ? O3' ADP 401 E 1 HETATM 15 C C2' ADP . . . Q 3 162.296 140.279 126.49 1 98.2 ? C2' ADP 401 E 1 HETATM 16 O O2' ADP . . . Q 3 161.385 141.253 127 1 100.02 ? O2' ADP 401 E 1 HETATM 17 C C1' ADP . . . Q 3 161.695 139.596 125.274 1 101.53 ? C1' ADP 401 E 1 HETATM 18 N N9 ADP . . . Q 3 161.796 138.129 125.472 1 101.09 ? N9 ADP 401 E 1 HETATM 19 C C8 ADP . . . Q 3 162.941 137.444 125.648 1 99.57 ? C8 ADP 401 E 1 HETATM 20 N N7 ADP . . . Q 3 162.703 136.12 125.818 1 97.54 ? N7 ADP 401 E 1 HETATM 21 C C5 ADP . . . Q 3 161.372 135.943 125.754 1 99.21 ? C5 ADP 401 E 1 HETATM 22 C C6 ADP . . . Q 3 160.442 134.796 125.869 1 107.91 ? C6 ADP 401 E 1 HETATM 23 N N6 ADP . . . Q 3 160.902 133.536 126.063 1 106.58 ? N6 ADP 401 E 1 HETATM 24 N N1 ADP . . . Q 3 159.119 135.045 125.735 1 108.97 ? N1 ADP 401 E 1 HETATM 25 C C2 ADP . . . Q 3 158.645 136.287 125.528 1 99.62 ? C2 ADP 401 E 1 HETATM 26 N N3 ADP . . . Q 3 159.431 137.374 125.429 1 96.19 ? N3 ADP 401 E 1 HETATM 27 C C4 ADP . . . Q 3 160.777 137.27 125.527 1 97.62 ? C4 ADP 401 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #