data_6SQW # _model_server_result.job_id SZyuXDEW_KtnYtvs26nVaA _model_server_result.datetime_utc '2024-11-12 20:22:08' _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 6sqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 6SQW # _exptl.entry_id 6SQW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 321.224 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-METHYL-2'-DEOXY-CYTIDINE-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 6SQW _cell.length_a 58.516 _cell.length_b 58.516 _cell.length_c 140.905 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SQW _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 70.4525 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc2 A OE2 GLU 66 A GLU 66 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc3 A OE1 GLU 95 A GLU 95 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 A OD2 ASP 98 A ASP 98 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc6 C MG MG . A MG 201 1_555 G O HOH . A HOH 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc7 B OE1 GLU 63 D GLU 63 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc8 B OE2 GLU 66 D GLU 66 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc9 B OE1 GLU 95 D GLU 95 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc10 B OD2 ASP 98 D ASP 98 1_555 E MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc11 E MG MG . D MG 201 1_555 H O HOH . D HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc12 E MG MG . D MG 201 1_555 H O HOH . D HOH 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? # _chem_comp.formula 'C10 H16 N3 O7 P' _chem_comp.formula_weight 321.224 _chem_comp.id 5CM _chem_comp.mon_nstd_flag n _chem_comp.name "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna 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 N1 C2 5CM sing 1 n n N1 C6 5CM sing 2 n n N1 C1' 5CM sing 3 n n C2 N3 5CM sing 4 n n C2 O2 5CM doub 5 n n N3 C4 5CM doub 6 n n C4 C5 5CM sing 7 n n C4 N4 5CM sing 8 n n C5 C5A 5CM sing 9 n n C5 C6 5CM doub 10 n n C5A H5A1 5CM sing 11 n n C5A H5A2 5CM sing 12 n n C5A H5A3 5CM sing 13 n n C6 H6 5CM sing 14 n n N4 HN41 5CM sing 15 n n N4 HN42 5CM sing 16 n n C1' C2' 5CM sing 17 n n C1' O4' 5CM sing 18 n n C1' H1' 5CM sing 19 n n C2' C3' 5CM sing 20 n n C2' H2' 5CM sing 21 n n C2' "H2''" 5CM sing 22 n n C3' C4' 5CM sing 23 n n C3' O3' 5CM sing 24 n n C3' H3' 5CM sing 25 n n C4' O4' 5CM sing 26 n n C4' C5' 5CM sing 27 n n C4' H4' 5CM sing 28 n n O3' HO3' 5CM sing 29 n n C5' O5' 5CM sing 30 n n C5' H5' 5CM sing 31 n n C5' "H5''" 5CM sing 32 n n O5' P 5CM sing 33 n n P OP1 5CM doub 34 n n P OP2 5CM sing 35 n n P OP3 5CM sing 36 n n OP2 HOP2 5CM sing 37 n n OP3 HOP3 5CM sing 38 n n # _atom_sites.entry_id 6SQW _atom_sites.fract_transf_matrix[1][1] 0.017089 _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] 0.017089 _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] 0.007097 _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 5CM A 1 202 150 5CM 5CM . E 2 MG D 1 201 140 MG MG . F 3 5CM D 1 202 150 5CM 5CM . G 4 HOH A 1 301 40 HOH HOH . G 4 HOH A 2 302 149 HOH HOH . G 4 HOH A 3 303 72 HOH HOH . G 4 HOH A 4 304 55 HOH HOH . G 4 HOH A 5 305 150 HOH HOH . G 4 HOH A 6 306 141 HOH HOH . G 4 HOH A 7 307 155 HOH HOH . G 4 HOH A 8 308 136 HOH HOH . G 4 HOH A 9 309 63 HOH HOH . G 4 HOH A 10 310 165 HOH HOH . G 4 HOH A 11 311 153 HOH HOH . G 4 HOH A 12 312 151 HOH HOH . G 4 HOH A 13 313 88 HOH HOH . G 4 HOH A 14 314 87 HOH HOH . G 4 HOH A 15 315 33 HOH HOH . G 4 HOH A 16 316 21 HOH HOH . G 4 HOH A 17 317 23 HOH HOH . G 4 HOH A 18 318 177 HOH HOH . G 4 HOH A 19 319 34 HOH HOH . G 4 HOH A 20 320 152 HOH HOH . G 4 HOH A 21 321 157 HOH HOH . G 4 HOH A 22 322 26 HOH HOH . G 4 HOH A 23 323 73 HOH HOH . G 4 HOH A 24 324 61 HOH HOH . G 4 HOH A 25 325 39 HOH HOH . G 4 HOH A 26 326 103 HOH HOH . G 4 HOH A 27 327 58 HOH HOH . G 4 HOH A 28 328 129 HOH HOH . G 4 HOH A 29 329 154 HOH HOH . G 4 HOH A 30 330 49 HOH HOH . G 4 HOH A 31 331 35 HOH HOH . G 4 HOH A 32 332 5 HOH HOH . G 4 HOH A 33 333 135 HOH HOH . G 4 HOH A 34 334 32 HOH HOH . G 4 HOH A 35 335 56 HOH HOH . G 4 HOH A 36 336 19 HOH HOH . G 4 HOH A 37 337 146 HOH HOH . G 4 HOH A 38 338 98 HOH HOH . G 4 HOH A 39 339 52 HOH HOH . G 4 HOH A 40 340 16 HOH HOH . G 4 HOH A 41 341 105 HOH HOH . G 4 HOH A 42 342 166 HOH HOH . G 4 HOH A 43 343 31 HOH HOH . G 4 HOH A 44 344 145 HOH HOH . G 4 HOH A 45 345 38 HOH HOH . G 4 HOH A 46 346 122 HOH HOH . G 4 HOH A 47 347 53 HOH HOH . G 4 HOH A 48 348 25 HOH HOH . G 4 HOH A 49 349 3 HOH HOH . G 4 HOH A 50 350 20 HOH HOH . G 4 HOH A 51 351 104 HOH HOH . G 4 HOH A 52 352 22 HOH HOH . G 4 HOH A 53 353 36 HOH HOH . G 4 HOH A 54 354 60 HOH HOH . G 4 HOH A 55 355 78 HOH HOH . G 4 HOH A 56 356 37 HOH HOH . G 4 HOH A 57 357 75 HOH HOH . G 4 HOH A 58 358 125 HOH HOH . G 4 HOH A 59 359 119 HOH HOH . G 4 HOH A 60 360 161 HOH HOH . G 4 HOH A 61 361 107 HOH HOH . G 4 HOH A 62 362 66 HOH HOH . G 4 HOH A 63 363 163 HOH HOH . G 4 HOH A 64 364 7 HOH HOH . G 4 HOH A 65 365 4 HOH HOH . G 4 HOH A 66 366 51 HOH HOH . G 4 HOH A 67 367 167 HOH HOH . G 4 HOH A 68 368 2 HOH HOH . G 4 HOH A 69 369 127 HOH HOH . G 4 HOH A 70 370 77 HOH HOH . G 4 HOH A 71 371 57 HOH HOH . G 4 HOH A 72 372 143 HOH HOH . G 4 HOH A 73 373 148 HOH HOH . G 4 HOH A 74 374 168 HOH HOH . G 4 HOH A 75 375 96 HOH HOH . G 4 HOH A 76 376 113 HOH HOH . G 4 HOH A 77 377 92 HOH HOH . G 4 HOH A 78 378 142 HOH HOH . G 4 HOH A 79 379 8 HOH HOH . G 4 HOH A 80 380 137 HOH HOH . G 4 HOH A 81 381 160 HOH HOH . G 4 HOH A 82 382 117 HOH HOH . G 4 HOH A 83 383 70 HOH HOH . G 4 HOH A 84 384 162 HOH HOH . G 4 HOH A 85 385 95 HOH HOH . G 4 HOH A 86 386 24 HOH HOH . G 4 HOH A 87 387 59 HOH HOH . G 4 HOH A 88 388 82 HOH HOH . G 4 HOH A 89 389 156 HOH HOH . G 4 HOH A 90 390 139 HOH HOH . G 4 HOH A 91 391 140 HOH HOH . G 4 HOH A 92 392 84 HOH HOH . G 4 HOH A 93 393 138 HOH HOH . G 4 HOH A 94 394 170 HOH HOH . G 4 HOH A 95 395 62 HOH HOH . G 4 HOH A 96 396 86 HOH HOH . G 4 HOH A 97 397 1 HOH HOH . G 4 HOH A 98 398 114 HOH HOH . G 4 HOH A 99 399 144 HOH HOH . G 4 HOH A 100 400 67 HOH HOH . H 4 HOH D 1 301 111 HOH HOH . H 4 HOH D 2 302 124 HOH HOH . H 4 HOH D 3 303 128 HOH HOH . H 4 HOH D 4 304 97 HOH HOH . H 4 HOH D 5 305 79 HOH HOH . H 4 HOH D 6 306 116 HOH HOH . H 4 HOH D 7 307 69 HOH HOH . H 4 HOH D 8 308 64 HOH HOH . H 4 HOH D 9 309 121 HOH HOH . H 4 HOH D 10 310 99 HOH HOH . H 4 HOH D 11 311 29 HOH HOH . H 4 HOH D 12 312 15 HOH HOH . H 4 HOH D 13 313 50 HOH HOH . H 4 HOH D 14 314 46 HOH HOH . H 4 HOH D 15 315 10 HOH HOH . H 4 HOH D 16 316 159 HOH HOH . H 4 HOH D 17 317 131 HOH HOH . H 4 HOH D 18 318 28 HOH HOH . H 4 HOH D 19 319 9 HOH HOH . H 4 HOH D 20 320 17 HOH HOH . H 4 HOH D 21 321 109 HOH HOH . H 4 HOH D 22 322 130 HOH HOH . H 4 HOH D 23 323 85 HOH HOH . H 4 HOH D 24 324 43 HOH HOH . H 4 HOH D 25 325 14 HOH HOH . H 4 HOH D 26 326 27 HOH HOH . H 4 HOH D 27 327 171 HOH HOH . H 4 HOH D 28 328 164 HOH HOH . H 4 HOH D 29 329 6 HOH HOH . H 4 HOH D 30 330 13 HOH HOH . H 4 HOH D 31 331 41 HOH HOH . H 4 HOH D 32 332 68 HOH HOH . H 4 HOH D 33 333 91 HOH HOH . H 4 HOH D 34 334 74 HOH HOH . H 4 HOH D 35 335 12 HOH HOH . H 4 HOH D 36 336 48 HOH HOH . H 4 HOH D 37 337 42 HOH HOH . H 4 HOH D 38 338 54 HOH HOH . H 4 HOH D 39 339 30 HOH HOH . H 4 HOH D 40 340 100 HOH HOH . H 4 HOH D 41 341 101 HOH HOH . H 4 HOH D 42 342 147 HOH HOH . H 4 HOH D 43 343 134 HOH HOH . H 4 HOH D 44 344 45 HOH HOH . H 4 HOH D 45 345 81 HOH HOH . H 4 HOH D 46 346 118 HOH HOH . H 4 HOH D 47 347 44 HOH HOH . H 4 HOH D 48 348 108 HOH HOH . H 4 HOH D 49 349 47 HOH HOH . H 4 HOH D 50 350 94 HOH HOH . H 4 HOH D 51 351 90 HOH HOH . H 4 HOH D 52 352 169 HOH HOH . H 4 HOH D 53 353 65 HOH HOH . H 4 HOH D 54 354 80 HOH HOH . H 4 HOH D 55 355 173 HOH HOH . H 4 HOH D 56 356 11 HOH HOH . H 4 HOH D 57 357 76 HOH HOH . H 4 HOH D 58 358 71 HOH HOH . H 4 HOH D 59 359 112 HOH HOH . H 4 HOH D 60 360 106 HOH HOH . H 4 HOH D 61 361 172 HOH HOH . H 4 HOH D 62 362 176 HOH HOH . H 4 HOH D 63 363 93 HOH HOH . H 4 HOH D 64 364 123 HOH HOH . H 4 HOH D 65 365 158 HOH HOH . H 4 HOH D 66 366 175 HOH HOH . H 4 HOH D 67 367 132 HOH HOH . H 4 HOH D 68 368 18 HOH HOH . H 4 HOH D 69 369 178 HOH HOH . H 4 HOH D 70 370 115 HOH HOH . H 4 HOH D 71 371 110 HOH HOH . H 4 HOH D 72 372 89 HOH HOH . H 4 HOH D 73 373 102 HOH HOH . H 4 HOH D 74 374 133 HOH HOH . H 4 HOH D 75 375 126 HOH HOH . H 4 HOH D 76 376 174 HOH HOH . H 4 HOH D 77 377 120 HOH HOH . H 4 HOH D 78 378 83 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 5CM . . . F 3 16.943 0.258 43.111 1 30.81 ? N1 5CM 202 D 1 HETATM 2 C C2 5CM . . . F 3 16.523 -0.54 44.206 1 30.31 ? C2 5CM 202 D 1 HETATM 3 N N3 5CM . . . F 3 16.06 0.087 45.319 1 30.57 ? N3 5CM 202 D 1 HETATM 4 C C4 5CM . . . F 3 16.047 1.435 45.42 1 30.34 ? C4 5CM 202 D 1 HETATM 5 C C5 5CM . . . F 3 16.514 2.244 44.292 1 30.13 ? C5 5CM 202 D 1 HETATM 6 C C5A 5CM . . . F 3 16.515 3.747 44.331 1 30.84 ? C5A 5CM 202 D 1 HETATM 7 C C6 5CM . . . F 3 16.947 1.6 43.183 1 30.43 ? C6 5CM 202 D 1 HETATM 8 O O2 5CM . . . F 3 16.567 -1.819 44.181 1 29.97 ? O2 5CM 202 D 1 HETATM 9 N N4 5CM . . . F 3 15.612 1.992 46.552 1 30.86 ? N4 5CM 202 D 1 HETATM 10 C C1' 5CM . . . F 3 17.465 -0.4 41.917 1 31.93 ? C1' 5CM 202 D 1 HETATM 11 C C2' 5CM . . . F 3 16.429 -1.3 41.212 1 30.92 ? C2' 5CM 202 D 1 HETATM 12 C C3' 5CM . . . F 3 16.337 -0.805 39.799 1 30.95 ? C3' 5CM 202 D 1 HETATM 13 C C4' 5CM . . . F 3 17.104 0.52 39.784 1 32.47 ? C4' 5CM 202 D 1 HETATM 14 O O4' 5CM . . . F 3 17.93 0.552 40.969 1 33.04 ? O4' 5CM 202 D 1 HETATM 15 O O3' 5CM . . . F 3 16.947 -1.663 38.822 1 31.05 ? O3' 5CM 202 D 1 HETATM 16 C C5' 5CM . . . F 3 16.089 1.656 39.726 1 31.99 ? C5' 5CM 202 D 1 HETATM 17 O O5' 5CM . . . F 3 16.633 2.904 40.163 1 33.55 ? O5' 5CM 202 D 1 HETATM 18 P P 5CM . . . F 3 16.008 4.366 39.783 1 33.18 ? P 5CM 202 D 1 HETATM 19 O OP1 5CM . . . F 3 14.659 4.266 40.503 1 32.45 ? OP1 5CM 202 D 1 HETATM 20 O OP2 5CM . . . F 3 16.998 5.363 40.435 1 35.06 ? OP2 5CM 202 D 1 HETATM 21 O OP3 5CM . . . F 3 15.975 4.399 38.28 1 33.5 ? OP3 5CM 202 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #