data_5KHI # _model_server_result.job_id KWtdR4CFMCZ5DDcwdLOhuQ _model_server_result.datetime_utc '2024-11-25 05:26:56' _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 5khi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5KHI # _exptl.entry_id 5KHI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.191 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "Purine riboside-3',5'-cyclic 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 5KHI _cell.length_a 96.278 _cell.length_b 96.278 _cell.length_c 46.763 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KHI _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 96.278 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 48.139 -48.139 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 48.139 48.139 0 # _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 covale ? covale1 A C ASN 68 A ASN 507 1_555 A N CSX 69 A CSX 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C CSX 69 A CSX 508 1_555 A N ARG 70 A ARG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? # _chem_comp.formula 'C10 H11 N4 O6 P' _chem_comp.formula_weight 314.191 _chem_comp.id 6SX _chem_comp.mon_nstd_flag . _chem_comp.name "Purine riboside-3',5'-cyclic monophosphate" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms cPuMP # 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 O2P P 6SX doub 1 n n N7 C8 6SX doub 2 n y N7 C5 6SX sing 3 n y C8 N9 6SX sing 4 n y C6 C5 6SX doub 5 n y C6 N1 6SX sing 6 n y C5 C4 6SX sing 7 n y P O1P 6SX sing 8 n n P O3' 6SX sing 9 n n P O5' 6SX sing 10 n n O3' C3' 6SX sing 11 n n C3' C2' 6SX sing 12 n n C3' C4' 6SX sing 13 n n N1 C2 6SX doub 14 n y N9 C4 6SX sing 15 n y N9 C1' 6SX sing 16 n n C2' C1' 6SX sing 17 n n C2' O2' 6SX sing 18 n n C4 N3 6SX doub 19 n y O5' C5' 6SX sing 20 n n C5' C4' 6SX sing 21 n n C1' O4' 6SX sing 22 n n C4' O4' 6SX sing 23 n n C2 N3 6SX sing 24 n y C2 H1 6SX sing 25 n n C6 H2 6SX sing 26 n n O1P H3 6SX sing 27 n n C3' H4 6SX sing 28 n n C4' H5 6SX sing 29 n n C5' H6 6SX sing 30 n n C5' H7 6SX sing 31 n n C2' H8 6SX sing 32 n n O2' H9 6SX sing 33 n n C1' H10 6SX sing 34 n n C8 H11 6SX sing 35 n n # _atom_sites.entry_id 5KHI _atom_sites.fract_transf_matrix[1][1] 0.010387 _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] 0.010387 _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] 0.021384 _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 6SX A 1 701 1 6SX PMP . C 3 HOH A 1 801 30 HOH HOH . C 3 HOH A 2 802 29 HOH HOH . C 3 HOH A 3 803 48 HOH HOH . C 3 HOH A 4 804 11 HOH HOH . C 3 HOH A 5 805 17 HOH HOH . C 3 HOH A 6 806 49 HOH HOH . C 3 HOH A 7 807 47 HOH HOH . C 3 HOH A 8 808 28 HOH HOH . C 3 HOH A 9 809 25 HOH HOH . C 3 HOH A 10 810 14 HOH HOH . C 3 HOH A 11 811 41 HOH HOH . C 3 HOH A 12 812 10 HOH HOH . C 3 HOH A 13 813 9 HOH HOH . C 3 HOH A 14 814 5 HOH HOH . C 3 HOH A 15 815 4 HOH HOH . C 3 HOH A 16 816 7 HOH HOH . C 3 HOH A 17 817 50 HOH HOH . C 3 HOH A 18 818 1 HOH HOH . C 3 HOH A 19 819 19 HOH HOH . C 3 HOH A 20 820 31 HOH HOH . C 3 HOH A 21 821 46 HOH HOH . C 3 HOH A 22 822 22 HOH HOH . C 3 HOH A 23 823 8 HOH HOH . C 3 HOH A 24 824 16 HOH HOH . C 3 HOH A 25 825 42 HOH HOH . C 3 HOH A 26 826 20 HOH HOH . C 3 HOH A 27 827 13 HOH HOH . C 3 HOH A 28 828 40 HOH HOH . C 3 HOH A 29 829 23 HOH HOH . C 3 HOH A 30 830 36 HOH HOH . C 3 HOH A 31 831 51 HOH HOH . C 3 HOH A 32 832 35 HOH HOH . C 3 HOH A 33 833 45 HOH HOH . C 3 HOH A 34 834 26 HOH HOH . C 3 HOH A 35 835 34 HOH HOH . C 3 HOH A 36 836 39 HOH HOH . C 3 HOH A 37 837 6 HOH HOH . C 3 HOH A 38 838 15 HOH HOH . C 3 HOH A 39 839 18 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 N N1 6SX . . . B 2 11.845 2.329 55.028 1 64.71 ? N1 6SX 701 A 1 HETATM 2 C C2 6SX . . . B 2 12.639 1.867 56.032 1 69.61 ? C2 6SX 701 A 1 HETATM 3 C C4 6SX . . . B 2 14.46 3.074 55.22 1 58.25 ? C4 6SX 701 A 1 HETATM 4 C C5 6SX . . . B 2 13.614 3.591 54.124 1 63.59 ? C5 6SX 701 A 1 HETATM 5 C C6 6SX . . . B 2 12.284 3.168 54.07 1 58.9 ? C6 6SX 701 A 1 HETATM 6 P P 6SX . . . B 2 21.156 4.312 54.3 1 49.98 ? P 6SX 701 A 1 HETATM 7 O O1P 6SX . . . B 2 22.537 3.765 54.344 1 46.15 ? O1P 6SX 701 A 1 HETATM 8 O O2P 6SX . . . B 2 20.625 5.037 53.117 1 51.37 ? O2P 6SX 701 A 1 HETATM 9 O O3' 6SX . . . B 2 20.105 3.1 54.52 1 43.92 ? O3' 6SX 701 A 1 HETATM 10 C C3' 6SX . . . B 2 18.828 3.568 54.766 1 45.09 ? C3' 6SX 701 A 1 HETATM 11 C C4' 6SX . . . B 2 18.824 4.459 55.978 1 47.69 ? C4' 6SX 701 A 1 HETATM 12 C C5' 6SX . . . B 2 19.642 5.719 55.847 1 47.67 ? C5' 6SX 701 A 1 HETATM 13 O O5' 6SX . . . B 2 20.96 5.273 55.557 1 48.64 ? O5' 6SX 701 A 1 HETATM 14 C C2' 6SX . . . B 2 17.831 2.521 55.193 1 49.83 ? C2' 6SX 701 A 1 HETATM 15 O O2' 6SX . . . B 2 18.435 1.547 56.044 1 49.33 ? O2' 6SX 701 A 1 HETATM 16 C C1' 6SX . . . B 2 16.82 3.376 55.921 1 52.05 ? C1' 6SX 701 A 1 HETATM 17 O O4' 6SX . . . B 2 17.429 4.629 56.18 1 50.01 ? O4' 6SX 701 A 1 HETATM 18 N N9 6SX . . . B 2 15.653 3.616 55.044 1 62.14 ? N9 6SX 701 A 1 HETATM 19 N N7 6SX . . . B 2 14.398 4.4 53.382 1 61.21 ? N7 6SX 701 A 1 HETATM 20 C C8 6SX . . . B 2 15.633 4.405 53.946 1 63.21 ? C8 6SX 701 A 1 HETATM 21 N N3 6SX . . . B 2 13.935 2.223 56.137 1 68.12 ? N3 6SX 701 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 21 #