data_1KDR # _model_server_result.job_id 6oUUjFtwovzO4ZXZ9i6JSw _model_server_result.datetime_utc '2025-01-03 06:46:47' _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 1kdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":5407}' # _entry.id 1KDR # _exptl.entry_id 1KDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTOSINE ARABINOSE-5'-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 90 _cell.angle_gamma 90 _cell.entry_id 1KDR _cell.length_a 73.585 _cell.length_b 73.772 _cell.length_c 77.644 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KDR _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,H 1 1 B,E,F,G,I 2 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 ? 3 D N N ? 3 G N N # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id CAR _chem_comp.mon_nstd_flag n _chem_comp.name "CYTOSINE ARABINOSE-5'-PHOSPHATE" _chem_comp.type 'rna linking' _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 P OP1 CAR doub 70 n n P OP2 CAR sing 71 n n P OP3 CAR sing 72 n n P O5' CAR sing 73 n n OP2 HOP2 CAR sing 74 n n OP3 HOP3 CAR sing 75 n n O5' C5' CAR sing 76 n n C5' C4' CAR sing 77 n n C5' H5' CAR sing 78 n n C5' "H5''" CAR sing 79 n n C4' O4' CAR sing 80 n n C4' C3' CAR sing 81 n n C4' H4' CAR sing 82 n n O4' C1' CAR sing 83 n n C3' O3' CAR sing 84 n n C3' C2' CAR sing 85 n n C3' H3' CAR sing 86 n n O3' HO3' CAR sing 87 n n C2' O2' CAR sing 88 n n C2' C1' CAR sing 89 n n C2' H2' CAR sing 90 n n O2' HO2' CAR sing 91 n n C1' N1 CAR sing 92 n n C1' H1' CAR sing 93 n n N1 C2 CAR sing 94 n n N1 C6 CAR sing 95 n n C2 O2 CAR doub 96 n n C2 N3 CAR sing 97 n n N3 C4 CAR doub 98 n n C4 N4 CAR sing 99 n n C4 C5 CAR sing 100 n n N4 HN41 CAR sing 101 n n N4 HN42 CAR sing 102 n n C5 C6 CAR doub 103 n n C5 H5 CAR sing 104 n n C6 H6 CAR sing 105 n n # _atom_sites.entry_id 1KDR _atom_sites.fract_transf_matrix[1][1] 0.01359 _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] 0.013555 _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] 0.012879 _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 SO4 A 1 501 501 SO4 SO4 . D 3 CAR A 1 5407 5407 CAR CAR . E 2 SO4 B 1 601 601 SO4 SO4 . F 2 SO4 B 1 602 602 SO4 SO4 . G 3 CAR B 1 6407 6407 CAR CAR . H 4 HOH A 1 5408 1 HOH HOH . H 4 HOH A 2 5409 2 HOH HOH . H 4 HOH A 3 5410 3 HOH HOH . H 4 HOH A 4 5411 4 HOH HOH . H 4 HOH A 5 5412 5 HOH HOH . H 4 HOH A 6 5413 7 HOH HOH . H 4 HOH A 7 5414 8 HOH HOH . H 4 HOH A 8 5415 9 HOH HOH . H 4 HOH A 9 5416 10 HOH HOH . H 4 HOH A 10 5417 11 HOH HOH . H 4 HOH A 11 5418 19 HOH HOH . H 4 HOH A 12 5419 21 HOH HOH . H 4 HOH A 13 5420 26 HOH HOH . H 4 HOH A 14 5421 27 HOH HOH . H 4 HOH A 15 5422 28 HOH HOH . H 4 HOH A 16 5423 29 HOH HOH . H 4 HOH A 17 5424 31 HOH HOH . H 4 HOH A 18 5425 33 HOH HOH . H 4 HOH A 19 5426 34 HOH HOH . H 4 HOH A 20 5427 40 HOH HOH . H 4 HOH A 21 5428 42 HOH HOH . H 4 HOH A 22 5429 43 HOH HOH . H 4 HOH A 23 5430 46 HOH HOH . H 4 HOH A 24 5431 47 HOH HOH . H 4 HOH A 25 5432 50 HOH HOH . H 4 HOH A 26 5433 51 HOH HOH . H 4 HOH A 27 5434 57 HOH HOH . H 4 HOH A 28 5435 58 HOH HOH . H 4 HOH A 29 5436 59 HOH HOH . H 4 HOH A 30 5437 64 HOH HOH . H 4 HOH A 31 5438 67 HOH HOH . H 4 HOH A 32 5439 70 HOH HOH . H 4 HOH A 33 5440 71 HOH HOH . H 4 HOH A 34 5441 75 HOH HOH . H 4 HOH A 35 5442 76 HOH HOH . H 4 HOH A 36 5443 79 HOH HOH . I 4 HOH B 1 6408 6 HOH HOH . I 4 HOH B 2 6409 12 HOH HOH . I 4 HOH B 3 6410 13 HOH HOH . I 4 HOH B 4 6411 14 HOH HOH . I 4 HOH B 5 6412 15 HOH HOH . I 4 HOH B 6 6413 16 HOH HOH . I 4 HOH B 7 6414 17 HOH HOH . I 4 HOH B 8 6415 18 HOH HOH . I 4 HOH B 9 6416 20 HOH HOH . I 4 HOH B 10 6417 22 HOH HOH . I 4 HOH B 11 6418 23 HOH HOH . I 4 HOH B 12 6419 24 HOH HOH . I 4 HOH B 13 6420 25 HOH HOH . I 4 HOH B 14 6421 30 HOH HOH . I 4 HOH B 15 6422 32 HOH HOH . I 4 HOH B 16 6423 35 HOH HOH . I 4 HOH B 17 6424 36 HOH HOH . I 4 HOH B 18 6425 37 HOH HOH . I 4 HOH B 19 6426 38 HOH HOH . I 4 HOH B 20 6427 39 HOH HOH . I 4 HOH B 21 6428 41 HOH HOH . I 4 HOH B 22 6429 44 HOH HOH . I 4 HOH B 23 6430 45 HOH HOH . I 4 HOH B 24 6431 48 HOH HOH . I 4 HOH B 25 6432 49 HOH HOH . I 4 HOH B 26 6433 52 HOH HOH . I 4 HOH B 27 6434 53 HOH HOH . I 4 HOH B 28 6435 54 HOH HOH . I 4 HOH B 29 6436 55 HOH HOH . I 4 HOH B 30 6437 56 HOH HOH . I 4 HOH B 31 6438 60 HOH HOH . I 4 HOH B 32 6439 61 HOH HOH . I 4 HOH B 33 6440 62 HOH HOH . I 4 HOH B 34 6441 63 HOH HOH . I 4 HOH B 35 6442 65 HOH HOH . I 4 HOH B 36 6443 66 HOH HOH . I 4 HOH B 37 6444 68 HOH HOH . I 4 HOH B 38 6445 69 HOH HOH . I 4 HOH B 39 6446 72 HOH HOH . I 4 HOH B 40 6447 73 HOH HOH . I 4 HOH B 41 6448 74 HOH HOH . I 4 HOH B 42 6449 77 HOH HOH . I 4 HOH B 43 6450 78 HOH HOH . I 4 HOH B 44 6451 80 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 P CAR . . . D 3 2.953 17.902 32.799 1 34.51 ? P CAR 5407 A 1 HETATM 2 O OP1 CAR . . . D 3 4.089 17.687 31.867 1 41.75 ? OP1 CAR 5407 A 1 HETATM 3 O OP2 CAR . . . D 3 2.621 19.281 33.234 1 56.4 ? OP2 CAR 5407 A 1 HETATM 4 O OP3 CAR . . . D 3 3.25 17.045 34.106 1 13.53 ? OP3 CAR 5407 A 1 HETATM 5 O O5' CAR . . . D 3 1.655 17.279 32.114 1 33.3 ? O5' CAR 5407 A 1 HETATM 6 C C5' CAR . . . D 3 0.762 16.436 32.84 1 27.54 ? C5' CAR 5407 A 1 HETATM 7 C C4' CAR . . . D 3 0.068 15.474 31.9 1 24.14 ? C4' CAR 5407 A 1 HETATM 8 O O4' CAR . . . D 3 -0.54 16.214 30.816 1 33.55 ? O4' CAR 5407 A 1 HETATM 9 C C3' CAR . . . D 3 0.953 14.424 31.235 1 14.42 ? C3' CAR 5407 A 1 HETATM 10 O O3' CAR . . . D 3 0.832 13.249 32.035 1 23.33 ? O3' CAR 5407 A 1 HETATM 11 C C2' CAR . . . D 3 0.237 14.134 29.914 1 25.03 ? C2' CAR 5407 A 1 HETATM 12 O O2' CAR . . . D 3 1.084 13.811 28.832 1 20.48 ? O2' CAR 5407 A 1 HETATM 13 C C1' CAR . . . D 3 -0.472 15.455 29.624 1 24.4 ? C1' CAR 5407 A 1 HETATM 14 N N1 CAR . . . D 3 0.086 16.29 28.544 1 25.5 ? N1 CAR 5407 A 1 HETATM 15 C C2 CAR . . . D 3 -0.281 16.022 27.213 1 24.73 ? C2 CAR 5407 A 1 HETATM 16 O O2 CAR . . . D 3 -1.056 15.083 26.973 1 22.93 ? O2 CAR 5407 A 1 HETATM 17 N N3 CAR . . . D 3 0.226 16.792 26.225 1 22.52 ? N3 CAR 5407 A 1 HETATM 18 C C4 CAR . . . D 3 1.07 17.78 26.515 1 22.06 ? C4 CAR 5407 A 1 HETATM 19 N N4 CAR . . . D 3 1.542 18.513 25.503 1 21.99 ? N4 CAR 5407 A 1 HETATM 20 C C5 CAR . . . D 3 1.464 18.075 27.855 1 22.17 ? C5 CAR 5407 A 1 HETATM 21 C C6 CAR . . . D 3 0.953 17.313 28.829 1 24.4 ? C6 CAR 5407 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 21 #