data_6IJA # _model_server_result.job_id 0rPRsWmjlq7SkFCrr3bz_Q _model_server_result.datetime_utc '2024-12-23 17:04:04' _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 6ija # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":900}' # _entry.id 6IJA # _exptl.entry_id 6IJA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 550.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate' _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 89.92 _cell.angle_gamma 90 _cell.entry_id 6IJA _cell.length_a 90.671 _cell.length_b 84.983 _cell.length_c 125.472 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IJA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,G 1 1 B,F,H 2 1 C,I 3 1 D,J 4 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F 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 disulf ? disulf1 A SG CYS 75 A CYS 75 1_555 D SG CYS 75 D CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 B SG CYS 75 B CYS 75 1_555 C SG CYS 75 C CYS 75 2_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? # _chem_comp.formula 'C15 H24 N2 O16 P2' _chem_comp.formula_weight 550.302 _chem_comp.id AWU _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate' _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 O3' C3' AWU sing 70 n n O4' C4' AWU sing 71 n n C3' C4' AWU sing 72 n n C3' C2' AWU sing 73 n n C4' C5' AWU sing 74 n n O3C C3C AWU sing 75 n n C2' O2' AWU sing 76 n n C2' C1' AWU sing 77 n n C4C C5C AWU sing 78 n n C4C O4C AWU sing 79 n n C4C C3C AWU sing 80 n n O1B PB AWU doub 81 n n C5C O5C AWU sing 82 n n C5' C6' AWU sing 83 n n C5' O5' AWU sing 84 n n O4C C1C AWU sing 85 n n C1' O5' AWU sing 86 n n C1' O3B AWU sing 87 n n O5C PA AWU sing 88 n n C3C C2C AWU sing 89 n n O3A PB AWU sing 90 n n O3A PA AWU sing 91 n n C1C C2C AWU sing 92 n n C1C N1 AWU sing 93 n n O3B PB AWU sing 94 n n PB O2B AWU sing 95 n n O2 C2 AWU doub 96 n n O1A PA AWU doub 97 n n PA O2A AWU sing 98 n n C2C O2C AWU sing 99 n n N1 C2 AWU sing 100 n n N1 C6 AWU sing 101 n n C2 N3 AWU sing 102 n n C6 C5 AWU doub 103 n n N3 C4 AWU sing 104 n n C5 C4 AWU sing 105 n n C4 O4 AWU doub 106 n n O2A H1 AWU sing 107 n n O2B H2 AWU sing 108 n n C5' H3 AWU sing 109 n n C4' H4 AWU sing 110 n n O4' H5 AWU sing 111 n n C3' H6 AWU sing 112 n n O3' H7 AWU sing 113 n n C2' H8 AWU sing 114 n n C1' H9 AWU sing 115 n n N3 H10 AWU sing 116 n n C5 H11 AWU sing 117 n n C6 H12 AWU sing 118 n n C1C H13 AWU sing 119 n n C2C H14 AWU sing 120 n n C3C H15 AWU sing 121 n n C4C H16 AWU sing 122 n n C5C H17 AWU sing 123 n n C5C H18 AWU sing 124 n n C6' H19 AWU sing 125 n n C6' H20 AWU sing 126 n n C6' H21 AWU sing 127 n n O2' H22 AWU sing 128 n n O2C H23 AWU sing 129 n n O3C H24 AWU sing 130 n n # _atom_sites.entry_id 6IJA _atom_sites.fract_transf_matrix[1][1] 0.011029 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000016 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011767 _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] 0.00797 _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 E 2 AWU A 1 900 900 AWU UPR . F 2 AWU B 1 900 900 AWU UPR . G 3 HOH A 1 1001 1 HOH HOH . G 3 HOH A 2 1002 19 HOH HOH . G 3 HOH A 3 1003 5 HOH HOH . G 3 HOH A 4 1004 18 HOH HOH . G 3 HOH A 5 1005 27 HOH HOH . G 3 HOH A 6 1006 10 HOH HOH . G 3 HOH A 7 1007 25 HOH HOH . G 3 HOH A 8 1008 4 HOH HOH . G 3 HOH A 9 1009 16 HOH HOH . G 3 HOH A 10 1010 9 HOH HOH . G 3 HOH A 11 1011 6 HOH HOH . G 3 HOH A 12 1012 23 HOH HOH . G 3 HOH A 13 1013 22 HOH HOH . H 3 HOH B 1 1001 26 HOH HOH . H 3 HOH B 2 1002 14 HOH HOH . H 3 HOH B 3 1003 12 HOH HOH . H 3 HOH B 4 1004 2 HOH HOH . H 3 HOH B 5 1005 11 HOH HOH . H 3 HOH B 6 1006 21 HOH HOH . H 3 HOH B 7 1007 3 HOH HOH . H 3 HOH B 8 1008 8 HOH HOH . H 3 HOH B 9 1009 17 HOH HOH . I 3 HOH C 1 501 28 HOH HOH . I 3 HOH C 2 502 7 HOH HOH . I 3 HOH C 3 503 20 HOH HOH . J 3 HOH D 1 501 13 HOH HOH . J 3 HOH D 2 502 15 HOH HOH . J 3 HOH D 3 503 24 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 PA AWU . . . F 2 -29.116 -23.932 14.526 1 38.51 ? PA AWU 900 B 1 HETATM 2 O O1A AWU . . . F 2 -27.771 -24.436 14.046 1 35.46 ? O1A AWU 900 B 1 HETATM 3 O O2A AWU . . . F 2 -29.011 -23.506 15.993 1 28.12 ? O2A AWU 900 B 1 HETATM 4 O O3A AWU . . . F 2 -30.355 -24.99 14.23 1 46.47 ? O3A AWU 900 B 1 HETATM 5 P PB AWU . . . F 2 -30.095 -26.602 13.961 1 31.89 ? PB AWU 900 B 1 HETATM 6 O O1B AWU . . . F 2 -30.416 -26.829 12.488 1 38.19 ? O1B AWU 900 B 1 HETATM 7 O O2B AWU . . . F 2 -30.999 -27.417 14.893 1 42.23 ? O2B AWU 900 B 1 HETATM 8 O O3B AWU . . . F 2 -28.556 -27.068 14.456 1 62.83 ? O3B AWU 900 B 1 HETATM 9 C C5' AWU . . . F 2 -25.764 -26.807 12.208 1 78.01 ? C5' AWU 900 B 1 HETATM 10 O O5' AWU . . . F 2 -26.538 -26.504 13.365 1 80.72 ? O5' AWU 900 B 1 HETATM 11 C C4' AWU . . . F 2 -25.063 -28.128 12.488 1 76.07 ? C4' AWU 900 B 1 HETATM 12 O O4' AWU . . . F 2 -24.163 -28.434 11.432 1 78.87 ? O4' AWU 900 B 1 HETATM 13 C C3' AWU . . . F 2 -26.1 -29.23 12.619 1 73.09 ? C3' AWU 900 B 1 HETATM 14 O O3' AWU . . . F 2 -25.46 -30.456 12.932 1 72.11 ? O3' AWU 900 B 1 HETATM 15 C C2' AWU . . . F 2 -27.087 -28.869 13.721 1 72.22 ? C2' AWU 900 B 1 HETATM 16 C C1' AWU . . . F 2 -27.601 -27.439 13.545 1 78.96 ? C1' AWU 900 B 1 HETATM 17 N N1 AWU . . . F 2 -34.428 -20.067 14.669 1 38.31 ? N1 AWU 900 B 1 HETATM 18 C C2 AWU . . . F 2 -35.186 -19.019 14.901 1 37.01 ? C2 AWU 900 B 1 HETATM 19 O O2 AWU . . . F 2 -34.795 -17.95 14.597 1 38.24 ? O2 AWU 900 B 1 HETATM 20 N N3 AWU . . . F 2 -36.364 -19.116 15.459 1 37.96 ? N3 AWU 900 B 1 HETATM 21 C C4 AWU . . . F 2 -36.847 -20.292 15.801 1 33.88 ? C4 AWU 900 B 1 HETATM 22 O O4 AWU . . . F 2 -38.103 -20.411 16.389 1 33.49 ? O4 AWU 900 B 1 HETATM 23 C C5 AWU . . . F 2 -36.079 -21.422 15.56 1 34.45 ? C5 AWU 900 B 1 HETATM 24 C C6 AWU . . . F 2 -34.856 -21.28 14.965 1 37.11 ? C6 AWU 900 B 1 HETATM 25 C C1C AWU . . . F 2 -33.108 -19.956 13.958 1 40.86 ? C1C AWU 900 B 1 HETATM 26 C C2C AWU . . . F 2 -31.978 -19.578 14.547 1 42.38 ? C2C AWU 900 B 1 HETATM 27 C C3C AWU . . . F 2 -30.927 -20.34 13.781 1 41.54 ? C3C AWU 900 B 1 HETATM 28 C C4C AWU . . . F 2 -31.363 -21.239 12.866 1 44.41 ? C4C AWU 900 B 1 HETATM 29 C C5C AWU . . . F 2 -30.749 -22.67 12.838 1 30.92 ? C5C AWU 900 B 1 HETATM 30 C C6' AWU . . . F 2 -24.723 -25.709 12.004 1 76.49 ? C6' AWU 900 B 1 HETATM 31 O O2' AWU . . . F 2 -26.452 -28.995 14.99 1 61.47 ? O2' AWU 900 B 1 HETATM 32 O O2C AWU . . . F 2 -31.787 -18.144 14.499 1 43.61 ? O2C AWU 900 B 1 HETATM 33 O O3C AWU . . . F 2 -30.426 -19.531 12.716 1 34.45 ? O3C AWU 900 B 1 HETATM 34 O O4C AWU . . . F 2 -32.856 -21.375 13.417 1 39.97 ? O4C AWU 900 B 1 HETATM 35 O O5C AWU . . . F 2 -29.531 -22.612 13.565 1 37.15 ? O5C AWU 900 B 1 # _model_server_stats.io_time_ms 113 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #