data_9EMB # _model_server_result.job_id hMYapMHbc5Nz5iFj03NfUg _model_server_result.datetime_utc '2024-12-21 17:49:17' _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 9emb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 9EMB # _exptl.entry_id 9EMB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 9EMB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EMB _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? _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 ? 2 C N N ? 2 E N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 9EMB _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 C 2 AMP A 1 601 602 AMP AMP . D 3 PGW A 1 602 603 PGW PGW . E 2 AMP B 1 601 602 AMP AMP . F 3 PGW B 1 602 603 PGW PGW . # 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 P AMP . . . C 2 158.793 135.282 112.62 1 124.02 ? P AMP 601 A 1 HETATM 2 O O1P AMP . . . C 2 157.288 135.384 112.581 1 117.65 ? O1P AMP 601 A 1 HETATM 3 O O2P AMP . . . C 2 159.313 133.884 112.843 1 124.18 ? O2P AMP 601 A 1 HETATM 4 O O3P AMP . . . C 2 159.475 136.344 113.447 1 120.96 ? O3P AMP 601 A 1 HETATM 5 O O5' AMP . . . C 2 159.238 135.611 111.128 1 122.41 ? O5' AMP 601 A 1 HETATM 6 C C5' AMP . . . C 2 158.893 136.85 110.515 1 122.9 ? C5' AMP 601 A 1 HETATM 7 C C4' AMP . . . C 2 159.215 136.843 109.042 1 120.57 ? C4' AMP 601 A 1 HETATM 8 O O4' AMP . . . C 2 158.685 138.049 108.428 1 115.8 ? O4' AMP 601 A 1 HETATM 9 C C3' AMP . . . C 2 160.709 136.808 108.707 1 121 ? C3' AMP 601 A 1 HETATM 10 O O3' AMP . . . C 2 160.942 135.915 107.619 1 121.51 ? O3' AMP 601 A 1 HETATM 11 C C2' AMP . . . C 2 161.008 138.243 108.278 1 121.98 ? C2' AMP 601 A 1 HETATM 12 O O2' AMP . . . C 2 162.09 138.378 107.381 1 122.82 ? O2' AMP 601 A 1 HETATM 13 C C1' AMP . . . C 2 159.686 138.653 107.641 1 122.05 ? C1' AMP 601 A 1 HETATM 14 N N9 AMP . . . C 2 159.45 140.098 107.603 1 125.69 ? N9 AMP 601 A 1 HETATM 15 C C8 AMP . . . C 2 159.644 140.972 108.609 1 127.46 ? C8 AMP 601 A 1 HETATM 16 N N7 AMP . . . C 2 159.33 142.234 108.215 1 128.33 ? N7 AMP 601 A 1 HETATM 17 C C5 AMP . . . C 2 158.93 142.176 106.933 1 126.48 ? C5 AMP 601 A 1 HETATM 18 C C6 AMP . . . C 2 158.461 143.14 105.914 1 124.24 ? C6 AMP 601 A 1 HETATM 19 N N6 AMP . . . C 2 158.354 144.459 106.201 1 124.05 ? N6 AMP 601 A 1 HETATM 20 N N1 AMP . . . C 2 158.143 142.66 104.692 1 123.44 ? N1 AMP 601 A 1 HETATM 21 C C2 AMP . . . C 2 158.243 141.353 104.391 1 123.9 ? C2 AMP 601 A 1 HETATM 22 N N3 AMP . . . C 2 158.664 140.428 105.272 1 122.54 ? N3 AMP 601 A 1 HETATM 23 C C4 AMP . . . C 2 159.017 140.768 106.533 1 124.87 ? C4 AMP 601 A 1 HETATM 24 H "H5'1" AMP . . . C 2 159.439 137.66 111.002 1 122.72 ? "H5'1" AMP 601 A 1 HETATM 25 H "H5'2" AMP . . . C 2 157.825 137.036 110.652 1 121.95 ? "H5'2" AMP 601 A 1 HETATM 26 H H4' AMP . . . C 2 158.739 135.963 108.588 1 122.37 ? H4' AMP 601 A 1 HETATM 27 H H3' AMP . . . C 2 161.298 136.539 109.594 1 122.28 ? H3' AMP 601 A 1 HETATM 28 H HO3' AMP . . . C 2 161.888 135.885 107.423 1 123.16 ? HO3' AMP 601 A 1 HETATM 29 H H2' AMP . . . C 2 161.187 138.847 109.178 1 122.53 ? H2' AMP 601 A 1 HETATM 30 H HO2' AMP . . . C 2 162.903 138.083 107.812 1 123.39 ? HO2' AMP 601 A 1 HETATM 31 H H1' AMP . . . C 2 159.65 138.246 106.621 1 122.83 ? H1' AMP 601 A 1 HETATM 32 H H8 AMP . . . C 2 159.998 140.708 109.598 1 122.72 ? H8 AMP 601 A 1 HETATM 33 H HN61 AMP . . . C 2 158.032 145.105 105.496 1 122.55 ? HN61 AMP 601 A 1 HETATM 34 H HN62 AMP . . . C 2 158.597 144.796 107.121 1 122.21 ? HN62 AMP 601 A 1 HETATM 35 H H2 AMP . . . C 2 157.975 141.029 103.393 1 123.02 ? H2 AMP 601 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 35 #