data_4HIB # _model_server_result.job_id dGWUBe6fv2u9Ut0BPQ56BQ _model_server_result.datetime_utc '2024-10-14 08:19:48' _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 4hib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 4HIB # _exptl.entry_id 4HIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 339.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-hydroxycytidine 5'-(dihydrogen 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 112.08 _cell.angle_gamma 90 _cell.entry_id 4HIB _cell.length_a 69.78 _cell.length_b 61.64 _cell.length_c 71.37 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HIB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 4 F N N ? 4 G N N # _chem_comp.formula 'C9 H14 N3 O9 P' _chem_comp.formula_weight 339.196 _chem_comp.id 16B _chem_comp.mon_nstd_flag n _chem_comp.name "N-hydroxycytidine 5'-(dihydrogen 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 OAC N4 16B sing 1 n n N4 C4 16B sing 2 n n C4 C5 16B sing 3 n n C4 N3 16B doub 4 n n C5 C6 16B doub 5 n n N3 C2 16B sing 6 n n C6 N1 16B sing 7 n n C2 N1 16B sing 8 n n C2 O2 16B doub 9 n n N1 C1' 16B sing 10 n n O2' C2' 16B sing 11 n n C2' C1' 16B sing 12 n n C2' C3' 16B sing 13 n n C1' O4' 16B sing 14 n n O4' C4' 16B sing 15 n n OP1 P 16B doub 16 n n C3' C4' 16B sing 17 n n C3' O3' 16B sing 18 n n C5' C4' 16B sing 19 n n C5' O5' 16B sing 20 n n O5' P 16B sing 21 n n P OP3 16B sing 22 n n P OP2 16B sing 23 n n OP3 HOP3 16B sing 24 n n OP2 HOP2 16B sing 25 n n C5' H5' 16B sing 26 n n C5' "H5''" 16B sing 27 n n C4' H4' 16B sing 28 n n C3' H3' 16B sing 29 n n O3' HO3' 16B sing 30 n n C2' H2' 16B sing 31 n n O2' HO2' 16B sing 32 n n C1' H1' 16B sing 33 n n C6 H6 16B sing 34 n n C5 H5 16B sing 35 n n N4 H41 16B sing 36 n n OAC H14 16B sing 37 n n # _atom_sites.entry_id 4HIB _atom_sites.fract_transf_matrix[1][1] 0.014331 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005813 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016223 _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] 0.01512 _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 GOL A 1 301 1 GOL GOL . D 3 CL A 1 302 1 CL CL . E 3 CL A 1 303 1 CL CL . F 4 16B A 1 304 1 16B 16B . G 4 16B B 1 301 1 16B 16B . H 5 HOH A 1 401 3 HOH HOH . H 5 HOH A 2 402 4 HOH HOH . H 5 HOH A 3 403 9 HOH HOH . H 5 HOH A 4 404 15 HOH HOH . H 5 HOH A 5 405 16 HOH HOH . H 5 HOH A 6 406 18 HOH HOH . H 5 HOH A 7 407 20 HOH HOH . H 5 HOH A 8 408 23 HOH HOH . H 5 HOH A 9 409 26 HOH HOH . H 5 HOH A 10 410 28 HOH HOH . H 5 HOH A 11 411 29 HOH HOH . H 5 HOH A 12 412 31 HOH HOH . H 5 HOH A 13 413 34 HOH HOH . H 5 HOH A 14 414 37 HOH HOH . H 5 HOH A 15 415 38 HOH HOH . H 5 HOH A 16 416 39 HOH HOH . H 5 HOH A 17 417 42 HOH HOH . H 5 HOH A 18 418 43 HOH HOH . H 5 HOH A 19 419 44 HOH HOH . H 5 HOH A 20 420 45 HOH HOH . H 5 HOH A 21 421 46 HOH HOH . H 5 HOH A 22 422 47 HOH HOH . H 5 HOH A 23 423 48 HOH HOH . H 5 HOH A 24 424 50 HOH HOH . H 5 HOH A 25 425 51 HOH HOH . H 5 HOH A 26 426 54 HOH HOH . H 5 HOH A 27 427 57 HOH HOH . H 5 HOH A 28 428 60 HOH HOH . H 5 HOH A 29 429 63 HOH HOH . H 5 HOH A 30 430 65 HOH HOH . H 5 HOH A 31 431 67 HOH HOH . H 5 HOH A 32 432 73 HOH HOH . H 5 HOH A 33 433 75 HOH HOH . H 5 HOH A 34 434 76 HOH HOH . H 5 HOH A 35 435 78 HOH HOH . H 5 HOH A 36 436 79 HOH HOH . H 5 HOH A 37 437 81 HOH HOH . H 5 HOH A 38 438 83 HOH HOH . H 5 HOH A 39 439 91 HOH HOH . H 5 HOH A 40 440 92 HOH HOH . H 5 HOH A 41 441 96 HOH HOH . H 5 HOH A 42 442 97 HOH HOH . H 5 HOH A 43 443 98 HOH HOH . H 5 HOH A 44 444 99 HOH HOH . H 5 HOH A 45 445 103 HOH HOH . H 5 HOH A 46 446 104 HOH HOH . H 5 HOH A 47 447 114 HOH HOH . H 5 HOH A 48 448 115 HOH HOH . H 5 HOH A 49 449 117 HOH HOH . H 5 HOH A 50 450 123 HOH HOH . H 5 HOH A 51 451 126 HOH HOH . H 5 HOH A 52 452 138 HOH HOH . H 5 HOH A 53 453 139 HOH HOH . H 5 HOH A 54 454 140 HOH HOH . H 5 HOH A 55 455 144 HOH HOH . H 5 HOH A 56 456 145 HOH HOH . H 5 HOH A 57 457 146 HOH HOH . H 5 HOH A 58 458 158 HOH HOH . H 5 HOH A 59 459 161 HOH HOH . H 5 HOH A 60 460 173 HOH HOH . H 5 HOH A 61 461 174 HOH HOH . H 5 HOH A 62 462 181 HOH HOH . H 5 HOH A 63 463 182 HOH HOH . H 5 HOH A 64 464 185 HOH HOH . H 5 HOH A 65 465 186 HOH HOH . H 5 HOH A 66 466 187 HOH HOH . I 5 HOH B 1 401 2 HOH HOH . I 5 HOH B 2 402 5 HOH HOH . I 5 HOH B 3 403 7 HOH HOH . I 5 HOH B 4 404 8 HOH HOH . I 5 HOH B 5 405 10 HOH HOH . I 5 HOH B 6 406 11 HOH HOH . I 5 HOH B 7 407 13 HOH HOH . I 5 HOH B 8 408 14 HOH HOH . I 5 HOH B 9 409 17 HOH HOH . I 5 HOH B 10 410 19 HOH HOH . I 5 HOH B 11 411 21 HOH HOH . I 5 HOH B 12 412 22 HOH HOH . I 5 HOH B 13 413 24 HOH HOH . I 5 HOH B 14 414 25 HOH HOH . I 5 HOH B 15 415 27 HOH HOH . I 5 HOH B 16 416 32 HOH HOH . I 5 HOH B 17 417 33 HOH HOH . I 5 HOH B 18 418 35 HOH HOH . I 5 HOH B 19 419 36 HOH HOH . I 5 HOH B 20 420 41 HOH HOH . I 5 HOH B 21 421 52 HOH HOH . I 5 HOH B 22 422 55 HOH HOH . I 5 HOH B 23 423 58 HOH HOH . I 5 HOH B 24 424 59 HOH HOH . I 5 HOH B 25 425 61 HOH HOH . I 5 HOH B 26 426 62 HOH HOH . I 5 HOH B 27 427 64 HOH HOH . I 5 HOH B 28 428 68 HOH HOH . I 5 HOH B 29 429 69 HOH HOH . I 5 HOH B 30 430 70 HOH HOH . I 5 HOH B 31 431 72 HOH HOH . I 5 HOH B 32 432 77 HOH HOH . I 5 HOH B 33 433 80 HOH HOH . I 5 HOH B 34 434 82 HOH HOH . I 5 HOH B 35 435 85 HOH HOH . I 5 HOH B 36 436 89 HOH HOH . I 5 HOH B 37 437 93 HOH HOH . I 5 HOH B 38 438 113 HOH HOH . I 5 HOH B 39 439 124 HOH HOH . I 5 HOH B 40 440 150 HOH HOH . I 5 HOH B 41 441 151 HOH HOH . I 5 HOH B 42 442 153 HOH HOH . I 5 HOH B 43 443 159 HOH HOH . I 5 HOH B 44 444 163 HOH HOH . I 5 HOH B 45 445 176 HOH HOH . I 5 HOH B 46 446 179 HOH HOH . I 5 HOH B 47 447 188 HOH HOH . I 5 HOH B 48 448 189 HOH HOH . I 5 HOH B 49 449 190 HOH HOH . I 5 HOH B 50 450 191 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 OP1 16B . A . G 4 27.059 -7.862 13.414 0.5 24.81 ? OP1 16B 301 B 1 HETATM 2 O OP1 16B . B . G 4 27.062 -7.897 13.415 0.5 23.45 ? OP1 16B 301 B 1 HETATM 3 P P 16B . A . G 4 26.177 -8.559 14.451 0.5 22.84 ? P 16B 301 B 1 HETATM 4 P P 16B . B . G 4 26.17 -8.55 14.461 0.5 21.67 ? P 16B 301 B 1 HETATM 5 O OP3 16B . A . G 4 24.776 -8.837 13.925 0.5 22.18 ? OP3 16B 301 B 1 HETATM 6 O OP3 16B . B . G 4 24.788 -8.845 13.92 0.5 20.96 ? OP3 16B 301 B 1 HETATM 7 O OP2 16B . A . G 4 26.741 -9.203 15.679 0.5 24.37 ? OP2 16B 301 B 1 HETATM 8 O OP2 16B . B . G 4 26.736 -9.196 15.683 0.5 23.55 ? OP2 16B 301 B 1 HETATM 9 O O5' 16B . A . G 4 25.751 -7.151 15.217 0.5 26.78 ? O5' 16B 301 B 1 HETATM 10 O O5' 16B . B . G 4 25.752 -7.128 15.205 0.5 25.55 ? O5' 16B 301 B 1 HETATM 11 C C5' 16B . A . G 4 25.288 -5.949 14.619 0.5 25.39 ? C5' 16B 301 B 1 HETATM 12 C C5' 16B . B . G 4 25.195 -5.969 14.606 0.5 23.66 ? C5' 16B 301 B 1 HETATM 13 C C4' 16B . A . G 4 25.285 -4.776 15.676 0.5 24.11 ? C4' 16B 301 B 1 HETATM 14 C C4' 16B . B . G 4 25.194 -4.767 15.632 0.5 21.93 ? C4' 16B 301 B 1 HETATM 15 O O4' 16B . A . G 4 24.597 -3.736 14.945 0.5 26.53 ? O4' 16B 301 B 1 HETATM 16 O O4' 16B . B . G 4 24.449 -3.762 14.907 0.5 24.1 ? O4' 16B 301 B 1 HETATM 17 C C3' 16B . A . G 4 24.444 -5.025 16.95 0.5 22.59 ? C3' 16B 301 B 1 HETATM 18 C C3' 16B . B . G 4 24.399 -5.045 16.927 0.5 20.14 ? C3' 16B 301 B 1 HETATM 19 O O3' 16B . A . G 4 24.986 -4.377 18.116 0.5 24.4 ? O3' 16B 301 B 1 HETATM 20 O O3' 16B . B . G 4 24.925 -4.358 18.075 0.5 22.11 ? O3' 16B 301 B 1 HETATM 21 C C2' 16B . A . G 4 23.074 -4.41 16.617 0.5 25.05 ? C2' 16B 301 B 1 HETATM 22 C C2' 16B . B . G 4 22.961 -4.559 16.624 0.5 22.35 ? C2' 16B 301 B 1 HETATM 23 O O2' 16B . A . G 4 22.406 -4.003 17.86 0.5 23.04 ? O2' 16B 301 B 1 HETATM 24 O O2' 16B . B . G 4 22.358 -4.072 17.872 0.5 20.52 ? O2' 16B 301 B 1 HETATM 25 C C1' 16B . A . G 4 23.518 -3.238 15.743 0.5 24.9 ? C1' 16B 301 B 1 HETATM 26 C C1' 16B . B . G 4 23.238 -3.438 15.625 0.5 22.54 ? C1' 16B 301 B 1 HETATM 27 N N1 16B . A . G 4 22.486 -2.819 14.746 0.5 26.44 ? N1 16B 301 B 1 HETATM 28 N N1 16B . B . G 4 22.167 -3.106 14.622 0.5 21.56 ? N1 16B 301 B 1 HETATM 29 C C2 16B . A . G 4 21.898 -3.741 13.899 0.5 27.8 ? C2 16B 301 B 1 HETATM 30 C C2 16B . B . G 4 21.655 -3.989 13.656 0.5 25.72 ? C2 16B 301 B 1 HETATM 31 O O2 16B . A . G 4 22.225 -4.925 13.941 0.5 31.25 ? O2 16B 301 B 1 HETATM 32 O O2 16B . B . G 4 22.115 -5.132 13.59 0.5 26.38 ? O2 16B 301 B 1 HETATM 33 N N3 16B . A . G 4 20.971 -3.342 13.01 0.5 30.31 ? N3 16B 301 B 1 HETATM 34 N N3 16B . B . G 4 20.676 -3.584 12.788 0.5 26.21 ? N3 16B 301 B 1 HETATM 35 C C6 16B . A . G 4 22.15 -1.446 14.665 0.5 25.59 ? C6 16B 301 B 1 HETATM 36 C C6 16B . B . G 4 21.667 -1.8 14.684 0.5 26.96 ? C6 16B 301 B 1 HETATM 37 C C5 16B . A . G 4 21.152 -1.051 13.763 0.5 29.93 ? C5 16B 301 B 1 HETATM 38 C C5 16B . B . G 4 20.647 -1.405 13.814 0.5 26.61 ? C5 16B 301 B 1 HETATM 39 C C4 16B . A . G 4 20.599 -2.048 12.947 0.5 29.59 ? C4 16B 301 B 1 HETATM 40 C C4 16B . B . G 4 20.19 -2.317 12.878 0.5 29.21 ? C4 16B 301 B 1 HETATM 41 N N4 16B . A . G 4 19.703 -1.781 12.02 0.5 32.27 ? N4 16B 301 B 1 HETATM 42 N N4 16B . B . G 4 19.25 -1.853 12.056 0.5 32.3 ? N4 16B 301 B 1 HETATM 43 O OAC 16B . A . G 4 19.409 -2.828 11.205 0.5 31.08 ? OAC 16B 301 B 1 HETATM 44 O OAC 16B . B . G 4 19.104 -0.485 12 0.5 33.84 ? OAC 16B 301 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 522 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #