data_2HCB # _model_server_result.job_id CWKpS4IvIWDgFQSirplp6g _model_server_result.datetime_utc '2025-03-09 02:37:07' _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 2hcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":700}' # _entry.id 2HCB # _exptl.entry_id 2HCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _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 2HCB _cell.length_a 99.076 _cell.length_b 117.714 _cell.length_c 200.994 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HCB _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 _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 F N N ? 3 H N N ? 3 J N N ? 3 L 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 50 A THR 126 1_555 E MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? metalc ? metalc2 A OD2 ASP 105 A ASP 181 1_555 E MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc3 E MG MG . A MG 400 1_555 F O1G ACP . A ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc4 E MG MG . A MG 400 1_555 F O2B ACP . A ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc5 B OG1 THR 50 B THR 126 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 G MG MG . B MG 401 1_555 H O3G ACP . B ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc7 C OG1 THR 50 C THR 126 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 C OD1 ASP 105 C ASP 181 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? metalc ? metalc9 I MG MG . C MG 402 1_555 J O3G ACP . C ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc10 D OG1 THR 50 D THR 126 1_555 K MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc11 K MG MG . D MG 403 1_555 L O3G ACP . D ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc12 K MG MG . D MG 403 1_555 L O1B ACP . D ACP 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 2HCB _atom_sites.fract_transf_matrix[1][1] 0.010093 _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] 0.008495 _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] 0.004975 _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 2 MG A 1 400 400 MG MG . F 3 ACP A 1 700 700 ACP ABG . G 2 MG B 1 401 401 MG MG . H 3 ACP B 1 700 700 ACP ABG . I 2 MG C 1 402 402 MG MG . J 3 ACP C 1 700 700 ACP ABG . K 2 MG D 1 403 403 MG MG . L 3 ACP D 1 700 700 ACP ABG . # 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 PG ACP . . . F 3 -8.04 -28.914 16.634 1 34.99 ? PG ACP 700 A 1 HETATM 2 O O1G ACP . . . F 3 -8.459 -27.492 16.894 1 36.77 ? O1G ACP 700 A 1 HETATM 3 O O2G ACP . . . F 3 -6.674 -29.243 17.173 1 35.04 ? O2G ACP 700 A 1 HETATM 4 O O3G ACP . . . F 3 -9.115 -29.914 16.953 1 35.05 ? O3G ACP 700 A 1 HETATM 5 P PB ACP . . . F 3 -8.793 -27.717 14.077 1 36.4 ? PB ACP 700 A 1 HETATM 6 O O1B ACP . . . F 3 -10.269 -28.038 14.225 1 35.58 ? O1B ACP 700 A 1 HETATM 7 O O2B ACP . . . F 3 -8.272 -26.404 14.611 1 34.46 ? O2B ACP 700 A 1 HETATM 8 C C3B ACP . . . F 3 -7.845 -29.041 14.851 1 34.93 ? C3B ACP 700 A 1 HETATM 9 P PA ACP . . . F 3 -7.354 -26.817 11.856 1 33.3 ? PA ACP 700 A 1 HETATM 10 O O1A ACP . . . F 3 -8.092 -25.586 11.4 1 34.59 ? O1A ACP 700 A 1 HETATM 11 O O2A ACP . . . F 3 -6.204 -26.701 12.837 1 31.95 ? O2A ACP 700 A 1 HETATM 12 O O3A ACP . . . F 3 -8.463 -27.779 12.498 1 35.21 ? O3A ACP 700 A 1 HETATM 13 O O5' ACP . . . F 3 -6.87 -27.622 10.552 1 32.69 ? O5' ACP 700 A 1 HETATM 14 C C5' ACP . . . F 3 -5.534 -28.122 10.486 1 33.75 ? C5' ACP 700 A 1 HETATM 15 C C4' ACP . . . F 3 -4.915 -27.849 9.12 1 34.92 ? C4' ACP 700 A 1 HETATM 16 O O4' ACP . . . F 3 -5.769 -28.35 8.088 1 34.81 ? O4' ACP 700 A 1 HETATM 17 C C3' ACP . . . F 3 -4.71 -26.356 8.861 1 35.99 ? C3' ACP 700 A 1 HETATM 18 O O3' ACP . . . F 3 -3.384 -26.118 8.355 1 35.95 ? O3' ACP 700 A 1 HETATM 19 C C2' ACP . . . F 3 -5.742 -25.977 7.812 1 36.02 ? C2' ACP 700 A 1 HETATM 20 O O2' ACP . . . F 3 -5.203 -25.124 6.794 1 35.8 ? O2' ACP 700 A 1 HETATM 21 C C1' ACP . . . F 3 -6.158 -27.299 7.197 1 35.78 ? C1' ACP 700 A 1 HETATM 22 N N9 ACP . . . F 3 -7.618 -27.307 6.969 1 36.05 ? N9 ACP 700 A 1 HETATM 23 C C8 ACP . . . F 3 -8.569 -27.739 7.832 1 36.94 ? C8 ACP 700 A 1 HETATM 24 N N7 ACP . . . F 3 -9.81 -27.618 7.28 1 37.04 ? N7 ACP 700 A 1 HETATM 25 C C5 ACP . . . F 3 -9.642 -27.098 6.051 1 36.01 ? C5 ACP 700 A 1 HETATM 26 C C6 ACP . . . F 3 -10.533 -26.706 4.954 1 35.96 ? C6 ACP 700 A 1 HETATM 27 N N6 ACP . . . F 3 -11.872 -26.865 5.079 1 36.26 ? N6 ACP 700 A 1 HETATM 28 N N1 ACP . . . F 3 -9.962 -26.189 3.839 1 36 ? N1 ACP 700 A 1 HETATM 29 C C2 ACP . . . F 3 -8.623 -26.038 3.726 1 35.33 ? C2 ACP 700 A 1 HETATM 30 N N3 ACP . . . F 3 -7.756 -26.369 4.695 1 34.26 ? N3 ACP 700 A 1 HETATM 31 C C4 ACP . . . F 3 -8.205 -26.893 5.854 1 35.36 ? C4 ACP 700 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #