data_4DIE # _model_server_result.job_id -ZWfQv0QL3Vw0BUD06RKSw _model_server_result.datetime_utc '2025-07-30 21:43:59' _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 4die # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":301}' # _entry.id 4DIE # _exptl.entry_id 4DIE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.22 _cell.angle_gamma 90 _cell.entry_id 4DIE _cell.length_a 70.76 _cell.length_b 96.52 _cell.length_c 78.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DIE _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 PISA monomeric 1 software_defined_assembly 4 PISA monomeric 1 software_defined_assembly 5 PISA monomeric 1 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 1 A,E,F,M 3 1 B,G,H,N 4 1 C,I,J,O 5 1 D,K,L,P 6 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 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE" _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 O3P P C5P sing 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 4DIE _atom_sites.fract_transf_matrix[1][1] 0.014132 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001789 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010361 _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] 0.012793 _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 C5P A 1 301 231 C5P C5P . F 3 PO4 A 1 302 3 PO4 PO4 . G 2 C5P B 1 301 231 C5P C5P . H 3 PO4 B 1 302 2 PO4 PO4 . I 2 C5P C 1 301 231 C5P C5P . J 3 PO4 C 1 302 4 PO4 PO4 . K 2 C5P D 1 301 231 C5P C5P . L 3 PO4 D 1 302 1 PO4 PO4 . M 4 HOH A 1 401 1 HOH HOH . M 4 HOH A 2 402 2 HOH HOH . M 4 HOH A 3 403 3 HOH HOH . M 4 HOH A 4 404 4 HOH HOH . M 4 HOH A 5 405 5 HOH HOH . M 4 HOH A 6 406 6 HOH HOH . M 4 HOH A 7 407 7 HOH HOH . M 4 HOH A 8 408 8 HOH HOH . M 4 HOH A 9 409 9 HOH HOH . M 4 HOH A 10 410 10 HOH HOH . M 4 HOH A 11 411 11 HOH HOH . M 4 HOH A 12 412 14 HOH HOH . M 4 HOH A 13 413 15 HOH HOH . M 4 HOH A 14 414 16 HOH HOH . M 4 HOH A 15 415 17 HOH HOH . M 4 HOH A 16 416 18 HOH HOH . M 4 HOH A 17 417 19 HOH HOH . M 4 HOH A 18 418 20 HOH HOH . M 4 HOH A 19 419 21 HOH HOH . M 4 HOH A 20 420 22 HOH HOH . M 4 HOH A 21 421 23 HOH HOH . M 4 HOH A 22 422 25 HOH HOH . M 4 HOH A 23 423 26 HOH HOH . M 4 HOH A 24 424 27 HOH HOH . M 4 HOH A 25 425 51 HOH HOH . M 4 HOH A 26 426 52 HOH HOH . M 4 HOH A 27 427 127 HOH HOH . M 4 HOH A 28 428 128 HOH HOH . M 4 HOH A 29 429 129 HOH HOH . M 4 HOH A 30 430 131 HOH HOH . M 4 HOH A 31 431 132 HOH HOH . M 4 HOH A 32 432 133 HOH HOH . N 4 HOH B 1 401 12 HOH HOH . N 4 HOH B 2 402 13 HOH HOH . N 4 HOH B 3 403 29 HOH HOH . N 4 HOH B 4 404 30 HOH HOH . N 4 HOH B 5 405 32 HOH HOH . N 4 HOH B 6 406 33 HOH HOH . N 4 HOH B 7 407 34 HOH HOH . N 4 HOH B 8 408 35 HOH HOH . N 4 HOH B 9 409 36 HOH HOH . N 4 HOH B 10 410 37 HOH HOH . N 4 HOH B 11 411 38 HOH HOH . N 4 HOH B 12 412 39 HOH HOH . N 4 HOH B 13 413 40 HOH HOH . N 4 HOH B 14 414 42 HOH HOH . N 4 HOH B 15 415 43 HOH HOH . N 4 HOH B 16 416 44 HOH HOH . N 4 HOH B 17 417 45 HOH HOH . N 4 HOH B 18 418 46 HOH HOH . N 4 HOH B 19 419 48 HOH HOH . N 4 HOH B 20 420 49 HOH HOH . N 4 HOH B 21 421 50 HOH HOH . N 4 HOH B 22 422 53 HOH HOH . N 4 HOH B 23 423 54 HOH HOH . N 4 HOH B 24 424 55 HOH HOH . N 4 HOH B 25 425 124 HOH HOH . N 4 HOH B 26 426 130 HOH HOH . N 4 HOH B 27 427 135 HOH HOH . N 4 HOH B 28 428 136 HOH HOH . N 4 HOH B 29 429 137 HOH HOH . N 4 HOH B 30 430 138 HOH HOH . N 4 HOH B 31 431 139 HOH HOH . N 4 HOH B 32 432 140 HOH HOH . N 4 HOH B 33 433 152 HOH HOH . O 4 HOH C 1 401 56 HOH HOH . O 4 HOH C 2 402 57 HOH HOH . O 4 HOH C 3 403 58 HOH HOH . O 4 HOH C 4 404 59 HOH HOH . O 4 HOH C 5 405 60 HOH HOH . O 4 HOH C 6 406 62 HOH HOH . O 4 HOH C 7 407 64 HOH HOH . O 4 HOH C 8 408 66 HOH HOH . O 4 HOH C 9 409 68 HOH HOH . O 4 HOH C 10 410 69 HOH HOH . O 4 HOH C 11 411 71 HOH HOH . O 4 HOH C 12 412 72 HOH HOH . O 4 HOH C 13 413 75 HOH HOH . O 4 HOH C 14 414 76 HOH HOH . O 4 HOH C 15 415 77 HOH HOH . O 4 HOH C 16 416 78 HOH HOH . O 4 HOH C 17 417 79 HOH HOH . O 4 HOH C 18 418 80 HOH HOH . O 4 HOH C 19 419 81 HOH HOH . O 4 HOH C 20 420 82 HOH HOH . O 4 HOH C 21 421 83 HOH HOH . O 4 HOH C 22 422 84 HOH HOH . O 4 HOH C 23 423 85 HOH HOH . O 4 HOH C 24 424 86 HOH HOH . O 4 HOH C 25 425 90 HOH HOH . O 4 HOH C 26 426 91 HOH HOH . O 4 HOH C 27 427 92 HOH HOH . O 4 HOH C 28 428 93 HOH HOH . O 4 HOH C 29 429 94 HOH HOH . O 4 HOH C 30 430 95 HOH HOH . O 4 HOH C 31 431 96 HOH HOH . O 4 HOH C 32 432 97 HOH HOH . O 4 HOH C 33 433 123 HOH HOH . O 4 HOH C 34 434 141 HOH HOH . O 4 HOH C 35 435 142 HOH HOH . O 4 HOH C 36 436 147 HOH HOH . O 4 HOH C 37 437 148 HOH HOH . O 4 HOH C 38 438 149 HOH HOH . O 4 HOH C 39 439 150 HOH HOH . O 4 HOH C 40 440 151 HOH HOH . P 4 HOH D 1 401 61 HOH HOH . P 4 HOH D 2 402 63 HOH HOH . P 4 HOH D 3 403 65 HOH HOH . P 4 HOH D 4 404 67 HOH HOH . P 4 HOH D 5 405 70 HOH HOH . P 4 HOH D 6 406 73 HOH HOH . P 4 HOH D 7 407 74 HOH HOH . P 4 HOH D 8 408 87 HOH HOH . P 4 HOH D 9 409 88 HOH HOH . P 4 HOH D 10 410 98 HOH HOH . P 4 HOH D 11 411 99 HOH HOH . P 4 HOH D 12 412 100 HOH HOH . P 4 HOH D 13 413 101 HOH HOH . P 4 HOH D 14 414 102 HOH HOH . P 4 HOH D 15 415 103 HOH HOH . P 4 HOH D 16 416 104 HOH HOH . P 4 HOH D 17 417 105 HOH HOH . P 4 HOH D 18 418 106 HOH HOH . P 4 HOH D 19 419 107 HOH HOH . P 4 HOH D 20 420 108 HOH HOH . P 4 HOH D 21 421 109 HOH HOH . P 4 HOH D 22 422 110 HOH HOH . P 4 HOH D 23 423 111 HOH HOH . P 4 HOH D 24 424 112 HOH HOH . P 4 HOH D 25 425 113 HOH HOH . P 4 HOH D 26 426 114 HOH HOH . P 4 HOH D 27 427 115 HOH HOH . P 4 HOH D 28 428 116 HOH HOH . P 4 HOH D 29 429 117 HOH HOH . P 4 HOH D 30 430 118 HOH HOH . P 4 HOH D 31 431 119 HOH HOH . P 4 HOH D 32 432 120 HOH HOH . P 4 HOH D 33 433 121 HOH HOH . P 4 HOH D 34 434 122 HOH HOH . P 4 HOH D 35 435 125 HOH HOH . P 4 HOH D 36 436 143 HOH HOH . P 4 HOH D 37 437 144 HOH HOH . P 4 HOH D 38 438 145 HOH HOH . P 4 HOH D 39 439 146 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 O3P C5P . . . K 2 -6.407 -8.628 -34.827 1 32.34 ? O3P C5P 301 D 1 HETATM 2 P P C5P . . . K 2 -6.765 -7.184 -35.105 1 32.1 ? P C5P 301 D 1 HETATM 3 O O1P C5P . . . K 2 -5.58 -6.255 -35.074 1 33.98 ? O1P C5P 301 D 1 HETATM 4 O O2P C5P . . . K 2 -7.681 -7.025 -36.328 1 30.14 ? O2P C5P 301 D 1 HETATM 5 O O5' C5P . . . K 2 -7.614 -6.584 -33.877 1 29.13 ? O5' C5P 301 D 1 HETATM 6 C C5' C5P . . . K 2 -8.285 -5.353 -34.097 1 29.56 ? C5' C5P 301 D 1 HETATM 7 C C4' C5P . . . K 2 -8.7 -4.761 -32.766 1 31.02 ? C4' C5P 301 D 1 HETATM 8 O O4' C5P . . . K 2 -9.862 -5.432 -32.257 1 33.53 ? O4' C5P 301 D 1 HETATM 9 C C3' C5P . . . K 2 -7.665 -4.891 -31.667 1 31.27 ? C3' C5P 301 D 1 HETATM 10 O O3' C5P . . . K 2 -6.697 -3.864 -31.724 1 29.85 ? O3' C5P 301 D 1 HETATM 11 C C2' C5P . . . K 2 -8.521 -4.789 -30.426 1 32.62 ? C2' C5P 301 D 1 HETATM 12 O O2' C5P . . . K 2 -8.917 -3.44 -30.154 1 31.2 ? O2' C5P 301 D 1 HETATM 13 C C1' C5P . . . K 2 -9.774 -5.531 -30.832 1 32.28 ? C1' C5P 301 D 1 HETATM 14 N N1 C5P . . . K 2 -9.871 -6.933 -30.431 1 32.42 ? N1 C5P 301 D 1 HETATM 15 C C2 C5P . . . K 2 -10.401 -7.231 -29.15 1 33.07 ? C2 C5P 301 D 1 HETATM 16 N N3 C5P . . . K 2 -10.577 -8.507 -28.745 1 33.99 ? N3 C5P 301 D 1 HETATM 17 C C4 C5P . . . K 2 -10.272 -9.544 -29.564 1 33.38 ? C4 C5P 301 D 1 HETATM 18 C C5 C5P . . . K 2 -9.766 -9.278 -30.848 1 33.87 ? C5 C5P 301 D 1 HETATM 19 C C6 C5P . . . K 2 -9.569 -7.946 -31.26 1 33.08 ? C6 C5P 301 D 1 HETATM 20 O O2 C5P . . . K 2 -10.706 -6.329 -28.357 1 33.18 ? O2 C5P 301 D 1 HETATM 21 N N4 C5P . . . K 2 -10.462 -10.809 -29.112 1 32.3 ? N4 C5P 301 D 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #