data_1DMA # _model_server_result.job_id IbCH-ONTDkGDiTvMXXbiJg _model_server_result.datetime_utc '2025-03-04 17:26:54' _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 1dma # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 1DMA # _exptl.entry_id 1DMA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 1DMA _cell.length_a 87.51 _cell.length_b 87.51 _cell.length_c 134.08 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DMA _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 1DMA _atom_sites.fract_transf_matrix[1][1] 0.011427 _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] 0.011427 _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] 0.007458 _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 NCA A 1 700 700 NCA NCA . D 2 NCA B 1 700 700 NCA NCA . E 3 AMP B 1 701 701 AMP AMP . F 4 HOH A 1 1 1 HOH HOH . F 4 HOH A 2 2 2 HOH HOH . F 4 HOH A 3 5 5 HOH HOH . F 4 HOH A 4 6 6 HOH HOH . F 4 HOH A 5 8 8 HOH HOH . F 4 HOH A 6 13 13 HOH HOH . F 4 HOH A 7 14 14 HOH HOH . F 4 HOH A 8 15 15 HOH HOH . F 4 HOH A 9 16 16 HOH HOH . F 4 HOH A 10 17 17 HOH HOH . F 4 HOH A 11 18 18 HOH HOH . F 4 HOH A 12 19 19 HOH HOH . F 4 HOH A 13 20 20 HOH HOH . F 4 HOH A 14 21 21 HOH HOH . F 4 HOH A 15 29 29 HOH HOH . F 4 HOH A 16 30 30 HOH HOH . F 4 HOH A 17 32 32 HOH HOH . F 4 HOH A 18 33 33 HOH HOH . G 4 HOH B 1 3 3 HOH HOH . G 4 HOH B 2 4 4 HOH HOH . G 4 HOH B 3 7 7 HOH HOH . G 4 HOH B 4 9 9 HOH HOH . G 4 HOH B 5 10 10 HOH HOH . G 4 HOH B 6 11 11 HOH HOH . G 4 HOH B 7 12 12 HOH HOH . G 4 HOH B 8 22 22 HOH HOH . G 4 HOH B 9 23 23 HOH HOH . G 4 HOH B 10 24 24 HOH HOH . G 4 HOH B 11 25 25 HOH HOH . G 4 HOH B 12 26 26 HOH HOH . G 4 HOH B 13 27 27 HOH HOH . G 4 HOH B 14 28 28 HOH HOH . G 4 HOH B 15 31 31 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 P AMP . . . E 3 24.365 82.299 8.554 1 32.06 ? P AMP 701 B 1 HETATM 2 O O1P AMP . . . E 3 23.961 82 7.163 1 36.48 ? O1P AMP 701 B 1 HETATM 3 O O2P AMP . . . E 3 24.754 81.11 9.426 1 32.99 ? O2P AMP 701 B 1 HETATM 4 O O3P AMP . . . E 3 23.192 83.286 9.17 1 38.56 ? O3P AMP 701 B 1 HETATM 5 O O5' AMP . . . E 3 25.524 83.472 8.389 1 27.53 ? O5' AMP 701 B 1 HETATM 6 C C5' AMP . . . E 3 25.755 83.933 7.051 1 21.73 ? C5' AMP 701 B 1 HETATM 7 C C4' AMP . . . E 3 25.184 85.296 6.838 1 20.84 ? C4' AMP 701 B 1 HETATM 8 O O4' AMP . . . E 3 26.123 86.053 7.59 1 20.28 ? O4' AMP 701 B 1 HETATM 9 C C3' AMP . . . E 3 25.363 85.91 5.499 1 25.1 ? C3' AMP 701 B 1 HETATM 10 O O3' AMP . . . E 3 24.552 87.073 5.409 1 32.58 ? O3' AMP 701 B 1 HETATM 11 C C2' AMP . . . E 3 26.793 86.383 5.482 1 24.67 ? C2' AMP 701 B 1 HETATM 12 O O2' AMP . . . E 3 26.919 87.458 4.576 1 31.74 ? O2' AMP 701 B 1 HETATM 13 C C1' AMP . . . E 3 26.909 86.966 6.841 1 21.24 ? C1' AMP 701 B 1 HETATM 14 N N9 AMP . . . E 3 28.304 86.929 7.322 1 20.36 ? N9 AMP 701 B 1 HETATM 15 C C8 AMP . . . E 3 28.88 87.873 8.062 1 13.42 ? C8 AMP 701 B 1 HETATM 16 N N7 AMP . . . E 3 30.05 87.378 8.489 1 20.96 ? N7 AMP 701 B 1 HETATM 17 C C5 AMP . . . E 3 30.159 86.146 7.997 1 17.92 ? C5 AMP 701 B 1 HETATM 18 C C6 AMP . . . E 3 31.321 85.394 7.942 1 17.49 ? C6 AMP 701 B 1 HETATM 19 N N6 AMP . . . E 3 32.459 85.884 8.428 1 22.29 ? N6 AMP 701 B 1 HETATM 20 N N1 AMP . . . E 3 31.318 84.284 7.196 1 14.37 ? N1 AMP 701 B 1 HETATM 21 C C2 AMP . . . E 3 30.237 83.937 6.504 1 18.19 ? C2 AMP 701 B 1 HETATM 22 N N3 AMP . . . E 3 29.138 84.683 6.526 1 22.18 ? N3 AMP 701 B 1 HETATM 23 C C4 AMP . . . E 3 29.078 85.827 7.251 1 19.58 ? C4 AMP 701 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 971 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #