data_5KAP # _model_server_result.job_id JAH2S7m1CxJkJEOzSb29UA _model_server_result.datetime_utc '2024-10-20 07:57:50' _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 5kap # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5KAP # _exptl.entry_id 5KAP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.198 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-(6-oxidanylidene-1~{H}-purin-9-yl)butylphosphonic acid' _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 5KAP _cell.length_a 45.106 _cell.length_b 93.893 _cell.length_c 109.784 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KAP _symmetry.cell_setting ? _symmetry.Int_Tables_number 17 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,N 1 1,2 B,I,J,K,L,M,O 2 1,3 # 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_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 93.893 0 3 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 109.784 # 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 I 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 OE1 GLU 119 A GLU 113 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc2 A OD2 ASP 120 A ASP 114 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc3 A OD1 ASP 179 A ASP 173 1_555 G MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc4 D O4 SO4 . A SO4 302 1_555 G MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc5 B OE2 GLU 119 B GLU 113 1_555 K MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc6 B OD1 ASP 120 B ASP 114 1_555 K MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc7 B OD1 ASP 179 B ASP 173 1_555 L MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc8 B O GLN 182 B GLN 176 1_555 M MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc9 B OG SER 183 B SER 177 1_555 M MG MG . B MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc10 J O4 SO4 . B SO4 302 1_555 L MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? # _chem_comp.formula 'C9 H13 N4 O4 P' _chem_comp.formula_weight 272.198 _chem_comp.id 6RH _chem_comp.mon_nstd_flag . _chem_comp.name '4-(6-oxidanylidene-1~{H}-purin-9-yl)butylphosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9-(4-(phosphonobutil)hypoxanthine # 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 C09 N08 6RH doub 1 n y C09 N10 6RH sing 2 n y N08 C07 6RH sing 3 n y C11 N10 6RH sing 4 n n C11 C12 6RH sing 5 n n N10 C06 6RH sing 6 n y C07 C06 6RH doub 7 n y C07 C02 6RH sing 8 n n C06 N05 6RH sing 9 n n C14 C13 6RH sing 10 n n C14 P15 6RH sing 11 n n C13 C12 6RH sing 12 n n O01 C02 6RH doub 13 n n C02 N03 6RH sing 14 n n N05 C04 6RH doub 15 n n O16 P15 6RH doub 16 n n N03 C04 6RH sing 17 n n P15 O17 6RH sing 18 n n P15 O18 6RH sing 19 n n C11 H1 6RH sing 20 n n C11 H2 6RH sing 21 n n C13 H3 6RH sing 22 n n C13 H4 6RH sing 23 n n C14 H5 6RH sing 24 n n C14 H6 6RH sing 25 n n C12 H7 6RH sing 26 n n C12 H8 6RH sing 27 n n C04 H9 6RH sing 28 n n C09 H11 6RH sing 29 n n O17 H12 6RH sing 30 n n O18 H13 6RH sing 31 n n N03 H14 6RH sing 32 n n # _atom_sites.entry_id 5KAP _atom_sites.fract_transf_matrix[1][1] 0.02217 _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] 0.01065 _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] 0.009109 _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 6RH A 1 301 1 6RH 564 . D 3 SO4 A 1 302 2 SO4 SO4 . E 3 SO4 A 1 303 3 SO4 SO4 . F 4 MG A 1 304 3 MG MG . G 4 MG A 1 305 4 MG MG . H 4 MG A 1 306 7 MG MG . I 2 6RH B 1 301 2 6RH 564 . J 3 SO4 B 1 302 4 SO4 SO4 . K 4 MG B 1 303 1 MG MG . L 4 MG B 1 304 8 MG MG . M 4 MG B 1 305 10 MG MG . N 5 HOH A 1 401 4 HOH HOH . N 5 HOH A 2 402 7 HOH HOH . N 5 HOH A 3 403 2 HOH HOH . N 5 HOH A 4 404 9 HOH HOH . N 5 HOH A 5 405 11 HOH HOH . N 5 HOH A 6 406 1 HOH HOH . O 5 HOH B 1 401 13 HOH HOH . O 5 HOH B 2 402 12 HOH HOH . O 5 HOH B 3 403 14 HOH HOH . O 5 HOH B 4 404 15 HOH HOH . O 5 HOH B 5 405 3 HOH HOH . O 5 HOH B 6 406 5 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 C C11 6RH . . . C 2 -20.269 63.355 4.117 1 89.37 ? C11 6RH 301 A 1 HETATM 2 C C13 6RH . . . C 2 -18.049 63.099 5.341 1 97.79 ? C13 6RH 301 A 1 HETATM 3 C C14 6RH . . . C 2 -17.331 64.429 5.117 1 107.21 ? C14 6RH 301 A 1 HETATM 4 C C12 6RH . . . C 2 -19.561 63.276 5.469 1 91.99 ? C12 6RH 301 A 1 HETATM 5 O O01 6RH . . . C 2 -25.804 65.084 5.445 1 88.89 ? O01 6RH 301 A 1 HETATM 6 C C02 6RH . . . C 2 -24.949 64.269 5.535 1 85.17 ? C02 6RH 301 A 1 HETATM 7 N N03 6RH . . . C 2 -25.18 63.066 6.28 1 82.23 ? N03 6RH 301 A 1 HETATM 8 C C04 6RH . . . C 2 -24.127 62.075 6.384 1 80.19 ? C04 6RH 301 A 1 HETATM 9 N N05 6RH . . . C 2 -22.833 62.303 5.733 1 78.61 ? N05 6RH 301 A 1 HETATM 10 C C06 6RH . . . C 2 -22.597 63.551 4.961 1 83.34 ? C06 6RH 301 A 1 HETATM 11 C C07 6RH . . . C 2 -23.598 64.502 4.857 1 83.33 ? C07 6RH 301 A 1 HETATM 12 N N08 6RH . . . C 2 -23.11 65.503 4.117 1 82.12 ? N08 6RH 301 A 1 HETATM 13 C C09 6RH . . . C 2 -21.868 65.205 3.77 1 83.82 ? C09 6RH 301 A 1 HETATM 14 N N10 6RH . . . C 2 -21.548 64.025 4.276 1 87.39 ? N10 6RH 301 A 1 HETATM 15 P P15 6RH . . . C 2 -16.181 64.839 6.522 1 113.14 ? P15 6RH 301 A 1 HETATM 16 O O16 6RH . . . C 2 -15.033 65.674 6.006 1 113.29 -1 O16 6RH 301 A 1 HETATM 17 O O17 6RH . . . C 2 -15.645 63.566 7.133 1 114.59 -1 O17 6RH 301 A 1 HETATM 18 O O18 6RH . . . C 2 -16.936 65.621 7.57 1 110.28 ? O18 6RH 301 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 18 #