data_6SQY # _model_server_result.job_id bfmcYm_i-e-9IkzqkgNs-w _model_server_result.datetime_utc '2024-11-09 23:24:57' _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 6sqy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 6SQY # _exptl.entry_id 6SQY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _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 6SQY _cell.length_a 59.277 _cell.length_b 59.277 _cell.length_c 140.537 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SQY _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 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 metalc ? metalc1 A OE1 GLU 63 A GLU 63 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A OE2 GLU 66 A GLU 66 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc3 A OE1 GLU 95 A GLU 95 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc4 A OD2 ASP 98 A ASP 98 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 C MG MG . A MG 201 1_555 G O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc7 B OE1 GLU 63 D GLU 63 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc8 B OE2 GLU 66 D GLU 66 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc9 B OE1 GLU 95 D GLU 95 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc10 B OD2 ASP 98 D ASP 98 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc11 E MG MG . D MG 201 1_555 H O HOH . D HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc12 E MG MG . D MG 201 1_555 H O HOH . D HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DCM _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-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 N1 C2 DCM sing 83 n n N1 C6 DCM sing 84 n n N1 C1' DCM sing 85 n n C2 N3 DCM sing 86 n n C2 O2 DCM doub 87 n n N3 C4 DCM doub 88 n n C4 C5 DCM sing 89 n n C4 N4 DCM sing 90 n n C5 C6 DCM doub 91 n n C5 H5 DCM sing 92 n n C6 H6 DCM sing 93 n n N4 HN41 DCM sing 94 n n N4 HN42 DCM sing 95 n n C1' C2' DCM sing 96 n n C1' O4' DCM sing 97 n n C1' H1' DCM sing 98 n n C2' C3' DCM sing 99 n n C2' "H2'1" DCM sing 100 n n C2' "H2'2" DCM sing 101 n n C3' C4' DCM sing 102 n n C3' O3' DCM sing 103 n n C3' H3' DCM sing 104 n n C4' O4' DCM sing 105 n n C4' C5' DCM sing 106 n n C4' H4' DCM sing 107 n n O3' HO3' DCM sing 108 n n C5' O5' DCM sing 109 n n C5' "H5'1" DCM sing 110 n n C5' "H5'2" DCM sing 111 n n O5' P DCM sing 112 n n P O1P DCM doub 113 n n P O2P DCM sing 114 n n P O3P DCM sing 115 n n O2P HOP2 DCM sing 116 n n O3P HOP3 DCM sing 117 n n # _atom_sites.entry_id 6SQY _atom_sites.fract_transf_matrix[1][1] 0.01687 _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] 0.01687 _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] 0.007116 _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 MG A 1 201 140 MG MG . D 3 DCM A 1 202 150 DCM DCM . E 2 MG D 1 201 140 MG MG . F 3 DCM D 1 202 150 DCM DCM . G 4 HOH A 1 301 95 HOH HOH . G 4 HOH A 2 302 172 HOH HOH . G 4 HOH A 3 303 148 HOH HOH . G 4 HOH A 4 304 83 HOH HOH . G 4 HOH A 5 305 136 HOH HOH . G 4 HOH A 6 306 72 HOH HOH . G 4 HOH A 7 307 56 HOH HOH . G 4 HOH A 8 308 65 HOH HOH . G 4 HOH A 9 309 142 HOH HOH . G 4 HOH A 10 310 106 HOH HOH . G 4 HOH A 11 311 74 HOH HOH . G 4 HOH A 12 312 64 HOH HOH . G 4 HOH A 13 313 58 HOH HOH . G 4 HOH A 14 314 48 HOH HOH . G 4 HOH A 15 315 101 HOH HOH . G 4 HOH A 16 316 1 HOH HOH . G 4 HOH A 17 317 2 HOH HOH . G 4 HOH A 18 318 16 HOH HOH . G 4 HOH A 19 319 54 HOH HOH . G 4 HOH A 20 320 139 HOH HOH . G 4 HOH A 21 321 25 HOH HOH . G 4 HOH A 22 322 26 HOH HOH . G 4 HOH A 23 323 31 HOH HOH . G 4 HOH A 24 324 50 HOH HOH . G 4 HOH A 25 325 6 HOH HOH . G 4 HOH A 26 326 42 HOH HOH . G 4 HOH A 27 327 158 HOH HOH . G 4 HOH A 28 328 144 HOH HOH . G 4 HOH A 29 329 153 HOH HOH . G 4 HOH A 30 330 82 HOH HOH . G 4 HOH A 31 331 51 HOH HOH . G 4 HOH A 32 332 32 HOH HOH . G 4 HOH A 33 333 141 HOH HOH . G 4 HOH A 34 334 150 HOH HOH . G 4 HOH A 35 335 102 HOH HOH . G 4 HOH A 36 336 151 HOH HOH . G 4 HOH A 37 337 90 HOH HOH . G 4 HOH A 38 338 78 HOH HOH . G 4 HOH A 39 339 24 HOH HOH . G 4 HOH A 40 340 79 HOH HOH . G 4 HOH A 41 341 57 HOH HOH . G 4 HOH A 42 342 37 HOH HOH . G 4 HOH A 43 343 140 HOH HOH . G 4 HOH A 44 344 96 HOH HOH . G 4 HOH A 45 345 12 HOH HOH . G 4 HOH A 46 346 75 HOH HOH . G 4 HOH A 47 347 40 HOH HOH . G 4 HOH A 48 348 73 HOH HOH . G 4 HOH A 49 349 23 HOH HOH . G 4 HOH A 50 350 52 HOH HOH . G 4 HOH A 51 351 29 HOH HOH . G 4 HOH A 52 352 81 HOH HOH . G 4 HOH A 53 353 170 HOH HOH . G 4 HOH A 54 354 91 HOH HOH . G 4 HOH A 55 355 176 HOH HOH . G 4 HOH A 56 356 55 HOH HOH . G 4 HOH A 57 357 70 HOH HOH . G 4 HOH A 58 358 117 HOH HOH . G 4 HOH A 59 359 15 HOH HOH . G 4 HOH A 60 360 110 HOH HOH . G 4 HOH A 61 361 77 HOH HOH . G 4 HOH A 62 362 115 HOH HOH . G 4 HOH A 63 363 38 HOH HOH . G 4 HOH A 64 364 116 HOH HOH . G 4 HOH A 65 365 163 HOH HOH . G 4 HOH A 66 366 13 HOH HOH . G 4 HOH A 67 367 99 HOH HOH . G 4 HOH A 68 368 80 HOH HOH . G 4 HOH A 69 369 146 HOH HOH . G 4 HOH A 70 370 100 HOH HOH . G 4 HOH A 71 371 152 HOH HOH . G 4 HOH A 72 372 114 HOH HOH . G 4 HOH A 73 373 160 HOH HOH . G 4 HOH A 74 374 162 HOH HOH . G 4 HOH A 75 375 76 HOH HOH . G 4 HOH A 76 376 147 HOH HOH . G 4 HOH A 77 377 171 HOH HOH . G 4 HOH A 78 378 137 HOH HOH . G 4 HOH A 79 379 61 HOH HOH . G 4 HOH A 80 380 161 HOH HOH . G 4 HOH A 81 381 134 HOH HOH . G 4 HOH A 82 382 154 HOH HOH . G 4 HOH A 83 383 63 HOH HOH . G 4 HOH A 84 384 149 HOH HOH . G 4 HOH A 85 385 112 HOH HOH . G 4 HOH A 86 386 62 HOH HOH . H 4 HOH D 1 301 111 HOH HOH . H 4 HOH D 2 302 71 HOH HOH . H 4 HOH D 3 303 123 HOH HOH . H 4 HOH D 4 304 174 HOH HOH . H 4 HOH D 5 305 156 HOH HOH . H 4 HOH D 6 306 135 HOH HOH . H 4 HOH D 7 307 166 HOH HOH . H 4 HOH D 8 308 36 HOH HOH . H 4 HOH D 9 309 4 HOH HOH . H 4 HOH D 10 310 45 HOH HOH . H 4 HOH D 11 311 10 HOH HOH . H 4 HOH D 12 312 113 HOH HOH . H 4 HOH D 13 313 11 HOH HOH . H 4 HOH D 14 314 46 HOH HOH . H 4 HOH D 15 315 28 HOH HOH . H 4 HOH D 16 316 9 HOH HOH . H 4 HOH D 17 317 39 HOH HOH . H 4 HOH D 18 318 41 HOH HOH . H 4 HOH D 19 319 43 HOH HOH . H 4 HOH D 20 320 138 HOH HOH . H 4 HOH D 21 321 14 HOH HOH . H 4 HOH D 22 322 86 HOH HOH . H 4 HOH D 23 323 132 HOH HOH . H 4 HOH D 24 324 107 HOH HOH . H 4 HOH D 25 325 34 HOH HOH . H 4 HOH D 26 326 89 HOH HOH . H 4 HOH D 27 327 118 HOH HOH . H 4 HOH D 28 328 5 HOH HOH . H 4 HOH D 29 329 21 HOH HOH . H 4 HOH D 30 330 3 HOH HOH . H 4 HOH D 31 331 33 HOH HOH . H 4 HOH D 32 332 119 HOH HOH . H 4 HOH D 33 333 8 HOH HOH . H 4 HOH D 34 334 53 HOH HOH . H 4 HOH D 35 335 47 HOH HOH . H 4 HOH D 36 336 85 HOH HOH . H 4 HOH D 37 337 59 HOH HOH . H 4 HOH D 38 338 22 HOH HOH . H 4 HOH D 39 339 145 HOH HOH . H 4 HOH D 40 340 133 HOH HOH . H 4 HOH D 41 341 129 HOH HOH . H 4 HOH D 42 342 44 HOH HOH . H 4 HOH D 43 343 104 HOH HOH . H 4 HOH D 44 344 169 HOH HOH . H 4 HOH D 45 345 164 HOH HOH . H 4 HOH D 46 346 30 HOH HOH . H 4 HOH D 47 347 173 HOH HOH . H 4 HOH D 48 348 109 HOH HOH . H 4 HOH D 49 349 93 HOH HOH . H 4 HOH D 50 350 68 HOH HOH . H 4 HOH D 51 351 35 HOH HOH . H 4 HOH D 52 352 27 HOH HOH . H 4 HOH D 53 353 143 HOH HOH . H 4 HOH D 54 354 167 HOH HOH . H 4 HOH D 55 355 128 HOH HOH . H 4 HOH D 56 356 18 HOH HOH . H 4 HOH D 57 357 131 HOH HOH . H 4 HOH D 58 358 103 HOH HOH . H 4 HOH D 59 359 20 HOH HOH . H 4 HOH D 60 360 84 HOH HOH . H 4 HOH D 61 361 94 HOH HOH . H 4 HOH D 62 362 178 HOH HOH . H 4 HOH D 63 363 69 HOH HOH . H 4 HOH D 64 364 19 HOH HOH . H 4 HOH D 65 365 105 HOH HOH . H 4 HOH D 66 366 97 HOH HOH . H 4 HOH D 67 367 7 HOH HOH . H 4 HOH D 68 368 60 HOH HOH . H 4 HOH D 69 369 49 HOH HOH . H 4 HOH D 70 370 17 HOH HOH . H 4 HOH D 71 371 168 HOH HOH . H 4 HOH D 72 372 124 HOH HOH . H 4 HOH D 73 373 127 HOH HOH . H 4 HOH D 74 374 177 HOH HOH . H 4 HOH D 75 375 92 HOH HOH . H 4 HOH D 76 376 157 HOH HOH . H 4 HOH D 77 377 125 HOH HOH . H 4 HOH D 78 378 130 HOH HOH . H 4 HOH D 79 379 126 HOH HOH . H 4 HOH D 80 380 122 HOH HOH . H 4 HOH D 81 381 66 HOH HOH . H 4 HOH D 82 382 98 HOH HOH . H 4 HOH D 83 383 159 HOH HOH . H 4 HOH D 84 384 155 HOH HOH . H 4 HOH D 85 385 108 HOH HOH . H 4 HOH D 86 386 87 HOH HOH . H 4 HOH D 87 387 120 HOH HOH . H 4 HOH D 88 388 175 HOH HOH . H 4 HOH D 89 389 88 HOH HOH . H 4 HOH D 90 390 165 HOH HOH . H 4 HOH D 91 391 67 HOH HOH . H 4 HOH D 92 392 121 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 N N1 DCM . . . D 3 -15.392 0.414 -9.592 1 37.04 ? N1 DCM 202 A 1 HETATM 2 C C2 DCM . . . D 3 -14.838 -0.519 -10.528 1 36.59 ? C2 DCM 202 A 1 HETATM 3 N N3 DCM . . . D 3 -14.226 -0.067 -11.673 1 36.42 ? N3 DCM 202 A 1 HETATM 4 C C4 DCM . . . D 3 -14.156 1.274 -11.938 1 36.84 ? C4 DCM 202 A 1 HETATM 5 C C5 DCM . . . D 3 -14.714 2.205 -11.042 1 36.51 ? C5 DCM 202 A 1 HETATM 6 C C6 DCM . . . D 3 -15.319 1.747 -9.868 1 36.8 ? C6 DCM 202 A 1 HETATM 7 O O2 DCM . . . D 3 -14.876 -1.755 -10.274 1 36.17 ? O2 DCM 202 A 1 HETATM 8 N N4 DCM . . . D 3 -13.558 1.726 -13.061 1 37.59 ? N4 DCM 202 A 1 HETATM 9 C C1' DCM . . . D 3 -16.037 -0.06 -8.34 1 37.97 ? C1' DCM 202 A 1 HETATM 10 C C2' DCM . . . D 3 -15.159 -0.921 -7.408 1 37.37 ? C2' DCM 202 A 1 HETATM 11 C C3' DCM . . . D 3 -15.092 -0.207 -6.038 1 37.05 ? C3' DCM 202 A 1 HETATM 12 C C4' DCM . . . D 3 -15.713 1.159 -6.285 1 39.02 ? C4' DCM 202 A 1 HETATM 13 O O4' DCM . . . D 3 -16.438 1.082 -7.543 1 39.56 ? O4' DCM 202 A 1 HETATM 14 O O3' DCM . . . D 3 -15.815 -0.866 -4.98 1 33.1 ? O3' DCM 202 A 1 HETATM 15 C C5' DCM . . . D 3 -14.687 2.292 -6.323 1 39.36 ? C5' DCM 202 A 1 HETATM 16 O O5' DCM . . . D 3 -15.372 3.473 -6.737 1 39.18 ? O5' DCM 202 A 1 HETATM 17 P P DCM . . . D 3 -14.694 4.946 -6.646 1 43.27 ? P DCM 202 A 1 HETATM 18 O O1P DCM . . . D 3 -15.644 5.754 -7.506 1 42.31 ? O1P DCM 202 A 1 HETATM 19 O O2P DCM . . . D 3 -14.81 5.277 -5.175 1 40.35 ? O2P DCM 202 A 1 HETATM 20 O O3P DCM . . . D 3 -13.235 4.76 -7.2 1 37.47 ? O3P DCM 202 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 50 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #