data_4HNA # _model_server_result.job_id 7_6MZEzMBjakYQ2UFDBOdg _model_server_result.datetime_utc '2024-11-15 10:14:27' _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 4hna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 4HNA # _exptl.entry_id 4HNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 9 _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 90 _cell.entry_id 4HNA _cell.length_a 77.05 _cell.length_b 160.54 _cell.length_c 174.95 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HNA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 _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 9 _struct_asym.id J _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 E O1G GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 E O1B GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc3 G O2B GDP . B GDP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc4 G O3B GDP . B GDP 501 1_555 I AL ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 H MG MG . B MG 502 1_555 I F3 ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc6 D OG1 THR 92 K THR 92 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc7 D OG SER 202 K SER 202 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc8 J O2B ADP . K ADP 401 1_555 K MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc9 J O3B ADP . K ADP 401 1_555 L AL ALF . K ALF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc10 K MG MG . K MG 402 1_555 L F4 ALF . K ALF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc11 K MG MG . K MG 402 1_555 M O HOH . K HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc12 K MG MG . K MG 402 1_555 M O HOH . K HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? # _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 4HNA _atom_sites.fract_transf_matrix[1][1] 0.012979 _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] 0.006229 _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] 0.005716 _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 5 GTP A 1 600 600 GTP GTP . F 6 MG A 1 601 601 MG MG . G 7 GDP B 1 501 600 GDP GDP . H 6 MG B 1 502 601 MG MG . I 8 ALF B 1 503 650 ALF ALF . J 9 ADP K 1 401 600 ADP ADP . K 6 MG K 1 402 601 MG MG . L 8 ALF K 1 403 650 ALF ALF . M 10 HOH K 1 501 610 HOH HOH . M 10 HOH K 2 502 611 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 . . . J 9 12.92 81.846 33.766 1 59.4 ? PB ADP 401 K 1 HETATM 2 O O1B ADP . . . J 9 14.181 81.081 33.894 1 60.31 ? O1B ADP 401 K 1 HETATM 3 O O2B ADP . . . J 9 13.014 82.79 32.562 1 59.18 ? O2B ADP 401 K 1 HETATM 4 O O3B ADP . . . J 9 11.702 80.863 33.542 1 55.74 ? O3B ADP 401 K 1 HETATM 5 P PA ADP . . . J 9 13.2 84.163 35.581 1 56.32 ? PA ADP 401 K 1 HETATM 6 O O1A ADP . . . J 9 12.078 85.109 35.405 1 57.57 ? O1A ADP 401 K 1 HETATM 7 O O2A ADP . . . J 9 14.371 84.625 34.763 1 57.88 ? O2A ADP 401 K 1 HETATM 8 O O3A ADP . . . J 9 12.732 82.702 35.11 1 57.6 ? O3A ADP 401 K 1 HETATM 9 O O5' ADP . . . J 9 13.65 84.138 37.084 1 55.7 ? O5' ADP 401 K 1 HETATM 10 C C5' ADP . . . J 9 12.719 83.821 38.129 1 58.65 ? C5' ADP 401 K 1 HETATM 11 C C4' ADP . . . J 9 13.076 84.614 39.36 1 62.24 ? C4' ADP 401 K 1 HETATM 12 O O4' ADP . . . J 9 14.405 84.268 39.81 1 63.91 ? O4' ADP 401 K 1 HETATM 13 C C3' ADP . . . J 9 13.028 86.137 39.25 1 60.22 ? C3' ADP 401 K 1 HETATM 14 O O3' ADP . . . J 9 12.328 86.663 40.373 1 60.22 ? O3' ADP 401 K 1 HETATM 15 C C2' ADP . . . J 9 14.509 86.524 39.143 1 58.88 ? C2' ADP 401 K 1 HETATM 16 O O2' ADP . . . J 9 14.783 87.866 39.53 1 56.19 ? O2' ADP 401 K 1 HETATM 17 C C1' ADP . . . J 9 15.176 85.437 39.998 1 62.67 ? C1' ADP 401 K 1 HETATM 18 N N9 ADP . . . J 9 16.544 85.103 39.614 1 62.6 ? N9 ADP 401 K 1 HETATM 19 C C8 ADP . . . J 9 16.923 84.408 38.496 1 62.81 ? C8 ADP 401 K 1 HETATM 20 N N7 ADP . . . J 9 18.22 84.281 38.358 1 63.25 ? N7 ADP 401 K 1 HETATM 21 C C5 ADP . . . J 9 18.733 84.917 39.477 1 64.35 ? C5 ADP 401 K 1 HETATM 22 C C6 ADP . . . J 9 20.053 85.106 39.94 1 67.15 ? C6 ADP 401 K 1 HETATM 23 N N6 ADP . . . J 9 21.142 84.72 39.261 1 69.05 ? N6 ADP 401 K 1 HETATM 24 N N1 ADP . . . J 9 20.215 85.731 41.131 1 65.57 ? N1 ADP 401 K 1 HETATM 25 C C2 ADP . . . J 9 19.13 86.149 41.792 1 63.8 ? C2 ADP 401 K 1 HETATM 26 N N3 ADP . . . J 9 17.843 86.047 41.443 1 62.48 ? N3 ADP 401 K 1 HETATM 27 C C4 ADP . . . J 9 17.711 85.418 40.268 1 62.7 ? C4 ADP 401 K 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #