data_5KHK # _model_server_result.job_id RBPYDTzrfGC_iXI1HkmJaQ _model_server_result.datetime_utc '2024-11-26 08:38:56' _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 5khk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5KHK # _exptl.entry_id 5KHK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 329.206 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-Aminopurine 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 5KHK _cell.length_a 96.429 _cell.length_b 96.429 _cell.length_c 46.423 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KHK _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 96.429 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 48.2145 -48.2145 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 48.2145 48.2145 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _chem_comp.formula 'C10 H12 N5 O6 P' _chem_comp.formula_weight 329.206 _chem_comp.id 6SZ _chem_comp.mon_nstd_flag . _chem_comp.name "2-Aminopurine riboside-3',5'-cyclic monophosphate" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-NH2-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 N7 C8 6SZ doub 1 n y N7 C5 6SZ sing 2 n y O2A PA 6SZ doub 3 n n C6 C5 6SZ doub 4 n y C6 N1 6SZ sing 5 n y C8 N9 6SZ sing 6 n y C5 C4 6SZ sing 7 n y PA O1A 6SZ sing 8 n n PA O3' 6SZ sing 9 n n PA O5' 6SZ sing 10 n n O3' C3' 6SZ sing 11 n n C3' C2' 6SZ sing 12 n n C3' C4' 6SZ sing 13 n n N1 C2 6SZ doub 14 n y N9 C4 6SZ sing 15 n y N9 C1' 6SZ sing 16 n n C4 N3 6SZ doub 17 n y C2' C1' 6SZ sing 18 n n C2' O2' 6SZ sing 19 n n O5' C5' 6SZ sing 20 n n C1' O4' 6SZ sing 21 n n C2 N3 6SZ sing 22 n y C2 N2 6SZ sing 23 n n C5' C4' 6SZ sing 24 n n C4' O4' 6SZ sing 25 n n N2 H1 6SZ sing 26 n n N2 H2 6SZ sing 27 n n C6 H3 6SZ sing 28 n n C8 H4 6SZ sing 29 n n C1' H5 6SZ sing 30 n n C2' H6 6SZ sing 31 n n O2' H7 6SZ sing 32 n n C3' H8 6SZ sing 33 n n O1A H9 6SZ sing 34 n n C4' H10 6SZ sing 35 n n C5' H11 6SZ sing 36 n n C5' H12 6SZ sing 37 n n # _atom_sites.entry_id 5KHK _atom_sites.fract_transf_matrix[1][1] 0.01037 _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] 0.01037 _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] 0.021541 _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 6SZ A 1 701 1 6SZ NCP . C 3 HOH A 1 801 18 HOH HOH . C 3 HOH A 2 802 31 HOH HOH . C 3 HOH A 3 803 43 HOH HOH . C 3 HOH A 4 804 68 HOH HOH . C 3 HOH A 5 805 28 HOH HOH . C 3 HOH A 6 806 77 HOH HOH . C 3 HOH A 7 807 74 HOH HOH . C 3 HOH A 8 808 19 HOH HOH . C 3 HOH A 9 809 45 HOH HOH . C 3 HOH A 10 810 38 HOH HOH . C 3 HOH A 11 811 52 HOH HOH . C 3 HOH A 12 812 47 HOH HOH . C 3 HOH A 13 813 5 HOH HOH . C 3 HOH A 14 814 24 HOH HOH . C 3 HOH A 15 815 37 HOH HOH . C 3 HOH A 16 816 1 HOH HOH . C 3 HOH A 17 817 3 HOH HOH . C 3 HOH A 18 818 13 HOH HOH . C 3 HOH A 19 819 9 HOH HOH . C 3 HOH A 20 820 33 HOH HOH . C 3 HOH A 21 821 22 HOH HOH . C 3 HOH A 22 822 6 HOH HOH . C 3 HOH A 23 823 14 HOH HOH . C 3 HOH A 24 824 12 HOH HOH . C 3 HOH A 25 825 15 HOH HOH . C 3 HOH A 26 826 76 HOH HOH . C 3 HOH A 27 827 58 HOH HOH . C 3 HOH A 28 828 67 HOH HOH . C 3 HOH A 29 829 40 HOH HOH . C 3 HOH A 30 830 26 HOH HOH . C 3 HOH A 31 831 75 HOH HOH . C 3 HOH A 32 832 10 HOH HOH . C 3 HOH A 33 833 27 HOH HOH . C 3 HOH A 34 834 41 HOH HOH . C 3 HOH A 35 835 17 HOH HOH . C 3 HOH A 36 836 11 HOH HOH . C 3 HOH A 37 837 30 HOH HOH . C 3 HOH A 38 838 29 HOH HOH . C 3 HOH A 39 839 35 HOH HOH . C 3 HOH A 40 840 4 HOH HOH . C 3 HOH A 41 841 25 HOH HOH . C 3 HOH A 42 842 57 HOH HOH . C 3 HOH A 43 843 16 HOH HOH . C 3 HOH A 44 844 49 HOH HOH . C 3 HOH A 45 845 69 HOH HOH . C 3 HOH A 46 846 21 HOH HOH . C 3 HOH A 47 847 2 HOH HOH . C 3 HOH A 48 848 59 HOH HOH . C 3 HOH A 49 849 7 HOH HOH . C 3 HOH A 50 850 8 HOH HOH . C 3 HOH A 51 851 66 HOH HOH . C 3 HOH A 52 852 73 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 6SZ . . . B 2 12.042 2.575 54.378 1 59.2 ? N1 6SZ 701 A 1 HETATM 2 N N2 6SZ . . . B 2 12.352 1.384 56.382 1 60.56 ? N2 6SZ 701 A 1 HETATM 3 C C6 6SZ . . . B 2 12.533 3.413 53.272 1 58.11 ? C6 6SZ 701 A 1 HETATM 4 C C2 6SZ . . . B 2 12.844 2.158 55.393 1 62.52 ? C2 6SZ 701 A 1 HETATM 5 N N3 6SZ . . . B 2 14.147 2.463 55.493 1 56.71 ? N3 6SZ 701 A 1 HETATM 6 C C4 6SZ . . . B 2 14.703 3.209 54.551 1 53.91 ? C4 6SZ 701 A 1 HETATM 7 C C5 6SZ . . . B 2 13.944 3.714 53.43 1 56 ? C5 6SZ 701 A 1 HETATM 8 N N7 6SZ . . . B 2 14.774 4.454 52.681 1 59.47 ? N7 6SZ 701 A 1 HETATM 9 C C8 6SZ . . . B 2 15.99 4.398 53.287 1 57.51 ? C8 6SZ 701 A 1 HETATM 10 N N9 6SZ . . . B 2 15.906 3.64 54.388 1 56.37 ? N9 6SZ 701 A 1 HETATM 11 C C1' 6SZ . . . B 2 16.908 3.312 55.381 1 48.98 ? C1' 6SZ 701 A 1 HETATM 12 O O4' 6SZ . . . B 2 17.493 4.53 55.773 1 47.58 ? O4' 6SZ 701 A 1 HETATM 13 C C2' 6SZ . . . B 2 17.937 2.464 54.721 1 46.13 ? C2' 6SZ 701 A 1 HETATM 14 O O2' 6SZ . . . B 2 18.405 1.556 55.702 1 43.82 ? O2' 6SZ 701 A 1 HETATM 15 C C3' 6SZ . . . B 2 18.955 3.474 54.354 1 40.49 ? C3' 6SZ 701 A 1 HETATM 16 O O3' 6SZ . . . B 2 20.238 2.981 54.251 1 41.53 ? O3' 6SZ 701 A 1 HETATM 17 P PA 6SZ . . . B 2 21.209 4.264 54.063 1 42.95 ? PA 6SZ 701 A 1 HETATM 18 O O2A 6SZ . . . B 2 20.571 4.949 52.9 1 49.63 ? O2A 6SZ 701 A 1 HETATM 19 O O1A 6SZ . . . B 2 22.627 3.853 54.092 1 41.4 ? O1A 6SZ 701 A 1 HETATM 20 C C4' 6SZ . . . B 2 18.875 4.361 55.562 1 42.94 ? C4' 6SZ 701 A 1 HETATM 21 C C5' 6SZ . . . B 2 19.638 5.636 55.481 1 41.72 ? C5' 6SZ 701 A 1 HETATM 22 O O5' 6SZ . . . B 2 20.966 5.173 55.342 1 43.02 ? O5' 6SZ 701 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 22 #