data_5KHG # _model_server_result.job_id e-oG59qNIrDsLXJvsNMtyA _model_server_result.datetime_utc '2024-10-12 16:35:34' _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 5khg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5KHG # _exptl.entry_id 5KHG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 305.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one _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 5KHG _cell.length_a 96.204 _cell.length_b 96.204 _cell.length_c 46.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KHG _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 96.204 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 48.102 -48.102 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 48.102 48.102 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C CSX 69 A CSX 508 1_555 A N ARG 70 A ARG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? # _chem_comp.formula 'C9 H12 N3 O7 P' _chem_comp.formula_weight 305.181 _chem_comp.id CC7 _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one _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 O2 C2 CC7 doub 70 n n C2 N3 CC7 sing 71 n n C2 N1 CC7 sing 72 n n N3 C4 CC7 doub 73 n n C4 N4 CC7 sing 74 n n C4 C5 CC7 sing 75 n n C5 C6 CC7 doub 76 n n C6 N1 CC7 sing 77 n n N1 C1' CC7 sing 78 n n C1' O4' CC7 sing 79 n n C1' C2' CC7 sing 80 n n O4' C4' CC7 sing 81 n n C4' C5' CC7 sing 82 n n C4' C3' CC7 sing 83 n n C5' O5' CC7 sing 84 n n O5' P CC7 sing 85 n n P O2P CC7 sing 86 n n P O1P CC7 doub 87 n n P O3' CC7 sing 88 n n O3' C3' CC7 sing 89 n n C3' C2' CC7 sing 90 n n C2' O2' CC7 sing 91 n n N4 HN4 CC7 sing 92 n n N4 HN4A CC7 sing 93 n n C5 H5 CC7 sing 94 n n C6 H6 CC7 sing 95 n n C1' H1' CC7 sing 96 n n C4' H4' CC7 sing 97 n n C5' H5' CC7 sing 98 n n C5' "H5'A" CC7 sing 99 n n O2P HO2P CC7 sing 100 n n C3' H3' CC7 sing 101 n n C2' H2' CC7 sing 102 n n O2' HO2' CC7 sing 103 n n # _atom_sites.entry_id 5KHG _atom_sites.fract_transf_matrix[1][1] 0.010395 _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] 0.010395 _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] 0.021422 _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 CC7 A 1 701 1 CC7 CC7 . C 3 HOH A 1 801 10 HOH HOH . C 3 HOH A 2 802 18 HOH HOH . C 3 HOH A 3 803 17 HOH HOH . C 3 HOH A 4 804 21 HOH HOH . C 3 HOH A 5 805 9 HOH HOH . C 3 HOH A 6 806 33 HOH HOH . C 3 HOH A 7 807 1 HOH HOH . C 3 HOH A 8 808 11 HOH HOH . C 3 HOH A 9 809 5 HOH HOH . C 3 HOH A 10 810 15 HOH HOH . C 3 HOH A 11 811 30 HOH HOH . C 3 HOH A 12 812 14 HOH HOH . C 3 HOH A 13 813 8 HOH HOH . C 3 HOH A 14 814 13 HOH HOH . C 3 HOH A 15 815 3 HOH HOH . C 3 HOH A 16 816 37 HOH HOH . C 3 HOH A 17 817 24 HOH HOH . C 3 HOH A 18 818 16 HOH HOH . C 3 HOH A 19 819 23 HOH HOH . C 3 HOH A 20 820 29 HOH HOH . C 3 HOH A 21 821 4 HOH HOH . C 3 HOH A 22 822 6 HOH HOH . C 3 HOH A 23 823 7 HOH HOH . C 3 HOH A 24 824 12 HOH HOH . C 3 HOH A 25 825 36 HOH HOH . C 3 HOH A 26 826 35 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 O2 CC7 . . . B 2 14.647 2.144 56.608 1 75.73 ? O2 CC7 701 A 1 HETATM 2 C C2 CC7 . . . B 2 14.542 2.676 55.55 1 74.15 ? C2 CC7 701 A 1 HETATM 3 N N3 CC7 . . . B 2 13.243 2.702 54.848 1 80.6 ? N3 CC7 701 A 1 HETATM 4 C C4 CC7 . . . B 2 13.134 3.356 53.567 1 81.79 ? C4 CC7 701 A 1 HETATM 5 N N4 CC7 . . . B 2 11.837 3.357 52.912 1 87.51 ? N4 CC7 701 A 1 HETATM 6 C C5 CC7 . . . B 2 14.311 4.01 52.936 1 72.92 ? C5 CC7 701 A 1 HETATM 7 C C6 CC7 . . . B 2 15.619 3.99 53.642 1 70.42 ? C6 CC7 701 A 1 HETATM 8 N N1 CC7 . . . B 2 15.707 3.342 54.936 1 69.48 ? N1 CC7 701 A 1 HETATM 9 C C1' CC7 . . . B 2 16.975 3.256 55.676 1 65.7 ? C1' CC7 701 A 1 HETATM 10 O O4' CC7 . . . B 2 17.514 4.542 55.897 1 64.23 ? O4' CC7 701 A 1 HETATM 11 C C4' CC7 . . . B 2 18.938 4.425 55.776 1 62.94 ? C4' CC7 701 A 1 HETATM 12 C C5' CC7 . . . B 2 19.636 5.751 55.713 1 63.89 ? C5' CC7 701 A 1 HETATM 13 O O5' CC7 . . . B 2 20.987 5.533 55.352 1 67.73 ? O5' CC7 701 A 1 HETATM 14 P P CC7 . . . B 2 21.344 4.405 54.286 1 62.18 ? P CC7 701 A 1 HETATM 15 O O2P CC7 . . . B 2 22.699 3.955 54.555 1 64.08 ? O2P CC7 701 A 1 HETATM 16 O O1P CC7 . . . B 2 20.998 5.131 52.859 1 69.04 ? O1P CC7 701 A 1 HETATM 17 O O3' CC7 . . . B 2 20.377 3.061 54.368 1 60.07 ? O3' CC7 701 A 1 HETATM 18 C C3' CC7 . . . B 2 19.064 3.524 54.577 1 59.83 ? C3' CC7 701 A 1 HETATM 19 C C2' CC7 . . . B 2 18.023 2.447 54.894 1 65.8 ? C2' CC7 701 A 1 HETATM 20 O O2' CC7 . . . B 2 18.539 1.459 55.771 1 59.5 ? O2' CC7 701 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #