data_5D0N # _model_server_result.job_id yuPVyvB0QHnOdlrpD_cq4Q _model_server_result.datetime_utc '2024-12-08 11:53:05' _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 5d0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5D0N # _exptl.entry_id 5D0N _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 '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 5D0N _cell.length_a 175.342 _cell.length_b 175.342 _cell.length_c 175.342 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 207 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 3 2' # _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 _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' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 175.342 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 115 A CYS 128 1_555 A SG CYS 404 A CYS 417 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 152 A CYS 165 1_555 A SG CYS 158 A CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 B O1P AMP . A AMP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc2 B O3P AMP . A AMP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.965 ? metalc ? metalc3 B O5' AMP . A AMP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? # _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 5D0N _atom_sites.fract_transf_matrix[1][1] 0.005703 _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] 0.005703 _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] 0.005703 _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 B 2 AMP A 1 501 500 AMP AMP . C 3 MG A 1 502 1 MG MG . D 4 HOH A 1 601 2 HOH HOH . D 4 HOH A 2 602 23 HOH HOH . D 4 HOH A 3 603 4 HOH HOH . D 4 HOH A 4 604 20 HOH HOH . D 4 HOH A 5 605 8 HOH HOH . D 4 HOH A 6 606 24 HOH HOH . D 4 HOH A 7 607 30 HOH HOH . D 4 HOH A 8 608 17 HOH HOH . D 4 HOH A 9 609 3 HOH HOH . D 4 HOH A 10 610 13 HOH HOH . D 4 HOH A 11 611 28 HOH HOH . D 4 HOH A 12 612 9 HOH HOH . D 4 HOH A 13 613 5 HOH HOH . D 4 HOH A 14 614 19 HOH HOH . D 4 HOH A 15 615 29 HOH HOH . D 4 HOH A 16 616 12 HOH HOH . D 4 HOH A 17 617 14 HOH HOH . D 4 HOH A 18 618 10 HOH HOH . D 4 HOH A 19 619 21 HOH HOH . D 4 HOH A 20 620 11 HOH HOH . D 4 HOH A 21 621 26 HOH HOH . D 4 HOH A 22 622 18 HOH HOH . D 4 HOH A 23 623 27 HOH HOH . D 4 HOH A 24 624 7 HOH HOH . D 4 HOH A 25 625 22 HOH HOH . D 4 HOH A 26 626 25 HOH HOH . D 4 HOH A 27 627 15 HOH HOH . D 4 HOH A 28 628 1 HOH HOH . D 4 HOH A 29 629 6 HOH HOH . D 4 HOH A 30 630 16 HOH HOH . D 4 HOH A 31 631 32 HOH HOH . D 4 HOH A 32 632 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 . . . B 2 46.108 4.723 95.008 1 43.83 ? P AMP 501 A 1 HETATM 2 O O1P AMP . . . B 2 45.564 3.732 93.997 1 40.89 ? O1P AMP 501 A 1 HETATM 3 O O2P AMP . . . B 2 45.69 6.176 94.923 1 42.32 ? O2P AMP 501 A 1 HETATM 4 O O3P AMP . . . B 2 46.029 4.173 96.398 1 45.2 ? O3P AMP 501 A 1 HETATM 5 O O5' AMP . . . B 2 47.695 4.794 94.775 1 45.16 ? O5' AMP 501 A 1 HETATM 6 C C5' AMP . . . B 2 48.272 5.517 93.693 1 45.64 ? C5' AMP 501 A 1 HETATM 7 C C4' AMP . . . B 2 49.297 6.559 94.132 1 45.53 ? C4' AMP 501 A 1 HETATM 8 O O4' AMP . . . B 2 49.059 7.736 93.351 1 46.4 ? O4' AMP 501 A 1 HETATM 9 C C3' AMP . . . B 2 49.262 6.992 95.592 1 45.02 ? C3' AMP 501 A 1 HETATM 10 O O3' AMP . . . B 2 50.608 7.15 96.065 1 42.99 ? O3' AMP 501 A 1 HETATM 11 C C2' AMP . . . B 2 48.495 8.302 95.566 1 45.25 ? C2' AMP 501 A 1 HETATM 12 O O2' AMP . . . B 2 48.877 9.199 96.622 1 42.94 ? O2' AMP 501 A 1 HETATM 13 C C1' AMP . . . B 2 48.812 8.85 94.187 1 46.09 ? C1' AMP 501 A 1 HETATM 14 N N9 AMP . . . B 2 47.701 9.641 93.638 1 48.76 ? N9 AMP 501 A 1 HETATM 15 C C8 AMP . . . B 2 46.614 9.229 92.936 1 48.93 ? C8 AMP 501 A 1 HETATM 16 N N7 AMP . . . B 2 45.821 10.289 92.602 1 48.73 ? N7 AMP 501 A 1 HETATM 17 C C5 AMP . . . B 2 46.421 11.396 93.118 1 54.15 ? C5 AMP 501 A 1 HETATM 18 C C6 AMP . . . B 2 46.176 12.876 93.183 1 56.92 ? C6 AMP 501 A 1 HETATM 19 N N6 AMP . . . B 2 45.077 13.406 92.595 1 58.81 ? N6 AMP 501 A 1 HETATM 20 N N1 AMP . . . B 2 47.073 13.684 93.844 1 56.48 ? N1 AMP 501 A 1 HETATM 21 C C2 AMP . . . B 2 48.187 13.197 94.434 1 54.9 ? C2 AMP 501 A 1 HETATM 22 N N3 AMP . . . B 2 48.479 11.87 94.41 1 55.02 ? N3 AMP 501 A 1 HETATM 23 C C4 AMP . . . B 2 47.662 10.955 93.792 1 53.32 ? C4 AMP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #