data_5LDO # _model_server_result.job_id G5uQQjTlMj9D9GaMS3IvkA _model_server_result.datetime_utc '2024-10-14 16:25:43' _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 5ldo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5LDO # _exptl.entry_id 5LDO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _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 114.95 _cell.angle_gamma 90 _cell.entry_id 5LDO _cell.length_a 63.41 _cell.length_b 88.35 _cell.length_c 73.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LDO _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F 1 1 B 2 1 C 3 1 D 4 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 2 _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 3AM _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "3'-AMP" # 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 O1P P 3AM doub 1 n n P O2P 3AM sing 2 n n P O3P 3AM sing 3 n n P O3' 3AM sing 4 n n O2' C2' 3AM sing 5 n n C2' C3' 3AM sing 6 n n C2' C1' 3AM sing 7 n n C3' O3' 3AM sing 8 n n C3' C4' 3AM sing 9 n n C1' O4' 3AM sing 10 n n C1' N9 3AM sing 11 n n O4' C4' 3AM sing 12 n n C4' C5' 3AM sing 13 n n C5' O5' 3AM sing 14 n n N9 C8 3AM sing 15 n y N9 C4 3AM sing 16 n y C8 N7 3AM doub 17 n y N7 C5 3AM sing 18 n y C5 C6 3AM doub 19 n y C5 C4 3AM sing 20 n y C6 N6 3AM sing 21 n n C6 N1 3AM sing 22 n y C4 N3 3AM doub 23 n y N3 C2 3AM sing 24 n y C2 N1 3AM doub 25 n y O2P HO2P 3AM sing 26 n n O3P HO3P 3AM sing 27 n n O2' HO2' 3AM sing 28 n n C2' H2' 3AM sing 29 n n C3' H3' 3AM sing 30 n n C1' H1' 3AM sing 31 n n C4' H4' 3AM sing 32 n n C5' H5' 3AM sing 33 n n C5' "H5'A" 3AM sing 34 n n O5' HO5' 3AM sing 35 n n C8 H8 3AM sing 36 n n N6 HN6 3AM sing 37 n n N6 HN6A 3AM sing 38 n n C2 H2 3AM sing 39 n n # _atom_sites.entry_id 5LDO _atom_sites.fract_transf_matrix[1][1] 0.01577 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007338 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011319 _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] 0.014911 _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 3AM A 1 201 1 3AM 3AM . F 3 HOH A 1 301 3 HOH HOH . F 3 HOH A 2 302 1 HOH HOH . F 3 HOH A 3 303 2 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 O O1P 3AM . . . E 2 85.339 -15.832 -1.379 1 49.93 ? O1P 3AM 201 A 1 HETATM 2 P P 3AM . . . E 2 85.168 -14.528 -0.635 1 63.18 ? P 3AM 201 A 1 HETATM 3 O O2P 3AM . . . E 2 83.789 -14.458 -0.025 1 63.57 ? O2P 3AM 201 A 1 HETATM 4 O O3P 3AM . . . E 2 86.211 -14.432 0.443 1 52.14 ? O3P 3AM 201 A 1 HETATM 5 O O2' 3AM . . . E 2 83.088 -12.448 -2.596 1 57.15 ? O2' 3AM 201 A 1 HETATM 6 C C2' 3AM . . . E 2 84.165 -12.648 -3.558 1 66.96 ? C2' 3AM 201 A 1 HETATM 7 C C3' 3AM . . . E 2 85.138 -13.596 -3.038 1 77.84 ? C3' 3AM 201 A 1 HETATM 8 O O3' 3AM . . . E 2 85.34 -13.347 -1.634 1 74.97 ? O3' 3AM 201 A 1 HETATM 9 C C1' 3AM . . . E 2 84.936 -11.405 -3.74 1 72.64 ? C1' 3AM 201 A 1 HETATM 10 O O4' 3AM . . . E 2 86.353 -11.812 -4.023 1 72.93 ? O4' 3AM 201 A 1 HETATM 11 C C4' 3AM . . . E 2 86.402 -13.272 -3.733 1 74.37 ? C4' 3AM 201 A 1 HETATM 12 C C5' 3AM . . . E 2 86.507 -14.04 -4.993 1 62.75 ? C5' 3AM 201 A 1 HETATM 13 O O5' 3AM . . . E 2 87.042 -15.325 -4.724 1 55.46 ? O5' 3AM 201 A 1 HETATM 14 N N9 3AM . . . E 2 84.458 -10.653 -4.817 1 78.72 ? N9 3AM 201 A 1 HETATM 15 C C8 3AM . . . E 2 83.907 -11.14 -5.977 1 71.7 ? C8 3AM 201 A 1 HETATM 16 N N7 3AM . . . E 2 83.574 -10.117 -6.785 1 68.59 ? N7 3AM 201 A 1 HETATM 17 C C5 3AM . . . E 2 83.902 -8.918 -6.178 1 68.22 ? C5 3AM 201 A 1 HETATM 18 C C6 3AM . . . E 2 83.792 -7.589 -6.535 1 70.23 ? C6 3AM 201 A 1 HETATM 19 N N6 3AM . . . E 2 83.225 -7.227 -7.794 1 62.81 ? N6 3AM 201 A 1 HETATM 20 C C4 3AM . . . E 2 84.472 -9.23 -4.916 1 74.15 ? C4 3AM 201 A 1 HETATM 21 N N3 3AM . . . E 2 84.885 -8.231 -4.108 1 68.78 ? N3 3AM 201 A 1 HETATM 22 C C2 3AM . . . E 2 84.76 -6.922 -4.491 1 72.66 ? C2 3AM 201 A 1 HETATM 23 N N1 3AM . . . E 2 84.221 -6.619 -5.685 1 78.93 ? N1 3AM 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #