data_1RB8 # _model_server_result.job_id 60kCqHCoFJPJ-y4YNY8j7A _model_server_result.datetime_utc '2024-11-13 12:19:32' _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 1rb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":5}' # _entry.id 1RB8 # _exptl.entry_id 1RB8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 120 _cell.entry_id 1RB8 _cell.length_a 295.143 _cell.length_b 295.143 _cell.length_c 678.235 _cell.Z_PDB 180 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RB8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 240-MERIC 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 ? 80-meric 80 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 (1-60) A,B,C,D,E,F,G,H,I,J 2 1 A,B,C,D,E,F,G,H,I,J 3 (1-5) A,B,C,D,E,F,G,H,I,J 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J 5 P A,B,C,D,E,F,G,H,I,J 6 (X0)(1-20) # 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] X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 P 'transform to point frame' ? ? -0.52467 -0.625662 0.577295 0.804033 -0.141359 0.577536 -0.279736 0.76718 0.57722 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.332601 -0.681926 0.651424 0.829571 0.540091 0.141822 -0.44854 0.493232 0.745341 0 0 0 3 'point symmetry operation' ? ? -0.747272 -0.273809 0.605485 0.660348 -0.204057 0.722704 -0.074329 0.939888 0.333295 0 0 0 4 'point symmetry operation' ? ? -0.747272 0.660348 -0.07433 -0.273809 -0.204057 0.939888 0.605486 0.722704 0.333295 0 0 0 5 'point symmetry operation' ? ? 0.332601 0.829571 -0.44854 -0.681926 0.540091 0.493232 0.651424 0.141822 0.745341 0 0 0 6 'point symmetry operation' ? ? -0.843495 -0.429216 -0.322939 -0.429216 0.17713 0.885663 -0.322939 0.885663 -0.333635 0 0 0 7 'point symmetry operation' ? ? -0.491762 0.184102 -0.851044 -0.393071 0.825197 0.405641 0.776959 0.534 -0.333435 0 0 0 8 'point symmetry operation' ? ? 0.370893 0.015015 -0.928554 0.371878 0.913802 0.163316 0.850967 -0.405881 0.333339 0 0 0 9 'point symmetry operation' ? ? 0.552309 -0.702805 -0.448352 0.808498 0.320496 0.493573 -0.20319 -0.635097 0.745229 0 0 0 10 'point symmetry operation' ? ? -0.198224 -0.977355 -0.074061 0.313394 -0.134793 0.940008 -0.928704 0.163122 0.333016 0 0 0 11 'point symmetry operation' ? ? 0.292939 -0.227315 0.928717 -0.227315 -0.960035 -0.16328 0.928717 -0.16328 -0.332904 0 0 0 12 'point symmetry operation' ? ? -0.507709 0.135539 0.8508 -0.798785 -0.444029 -0.405932 0.322761 -0.885701 0.333704 0 0 0 13 'point symmetry operation' ? ? -0.438043 0.839066 0.322625 -0.451954 0.104678 -0.885878 -0.777081 -0.533865 0.333366 0 0 0 14 'point symmetry operation' ? ? 0.40566 0.911014 0.074112 0.333869 -0.072209 -0.93985 -0.850865 0.406003 -0.333452 0 0 0 15 'point symmetry operation' ? ? 0.857432 0.251955 0.448697 0.472703 -0.730237 -0.49326 0.203376 0.635037 -0.745229 0 0 0 16 'point symmetry operation' ? ? -0.449444 0.656531 -0.605778 0.656531 -0.217095 -0.722382 -0.605778 -0.722382 -0.333461 0 0 0 17 'point symmetry operation' ? ? 0.66687 0.362285 -0.651179 0.362285 -0.921259 -0.14153 -0.651179 -0.14153 -0.74561 0 0 0 18 'point symmetry operation' ? ? 0.814423 -0.580271 0.000444 -0.580272 -0.814423 -0.000142 0.000443 -0.000142 -1 0 0 0 19 'point symmetry operation' ? ? -0.210697 -0.868557 0.44857 -0.868557 -0.04423 -0.493611 0.44857 -0.493611 -0.745073 0 0 0 20 'point symmetry operation' ? ? -0.99181 -0.104171 0.073904 -0.104171 0.324939 -0.93998 0.073904 -0.93998 -0.333129 0 0 0 21 'point symmetry operation' ? ? -0.5 -0.866025 -0.000243 0.866025 -0.5 0.000324 -0.000402 -0.000049 1 0 0 0 22 'point symmetry operation' ? ? -0.884621 -0.12689 -0.448714 -0.12689 -0.860451 0.49348 -0.448714 0.49348 0.745073 0 0 0 23 'point symmetry operation' ? ? -0.198224 0.313394 -0.928704 -0.977355 -0.134793 0.163122 -0.074061 0.940008 0.333017 0 0 0 24 'point symmetry operation' ? ? 0.610614 -0.153631 -0.776883 -0.510056 0.67414 -0.534207 0.605799 0.722449 0.333279 0 0 0 25 'point symmetry operation' ? ? 0.424106 -0.882553 -0.203063 0.629215 0.44843 -0.634822 0.651323 0.141462 0.745498 0 0 0 26 'point symmetry operation' ? ? 0.793538 0.060993 -0.605456 -0.515985 -0.45999 -0.722612 -0.322579 0.885827 -0.333548 0 0 0 27 'point symmetry operation' ? ? 0.586102 -0.806823 0.074308 -0.229091 -0.252989 -0.939954 0.777176 0.533885 -0.333113 0 0 0 28 'point symmetry operation' ? ? -0.507709 -0.798785 0.32276 0.135539 -0.444029 -0.885701 0.8508 -0.405932 0.333704 0 0 0 29 'point symmetry operation' ? ? -0.976285 0.073999 -0.203452 0.073999 -0.7691 -0.63483 -0.203452 -0.63483 0.745385 0 0 0 30 'point symmetry operation' ? ? -0.17207 0.605372 -0.777121 -0.328665 -0.778965 -0.534035 -0.92864 0.163521 0.333 0 0 0 31 'point symmetry operation' ? ? 0.050165 0.945112 -0.322872 0.367651 0.283104 0.885825 0.92861 -0.163142 -0.333269 0 0 0 32 'point symmetry operation' ? ? 0.945544 0.316987 -0.073934 -0.040192 0.339108 0.939888 0.323004 -0.885734 0.333382 0 0 0 33 'point symmetry operation' ? ? 0.610614 -0.510056 0.605799 -0.153631 0.67414 0.722449 -0.776883 -0.534207 0.333279 0 0 0 34 'point symmetry operation' ? ? -0.491762 -0.393071 0.776959 0.184102 0.825197 0.534 -0.851044 0.405641 -0.333435 0 0 0 35 'point symmetry operation' ? ? -0.838138 0.506272 0.203008 0.506272 0.583524 0.634971 0.203008 0.634971 -0.745385 0 0 0 36 'point symmetry operation' ? ? -0.343704 -0.14008 0.928572 -0.717691 0.676886 -0.163536 -0.605629 -0.722636 -0.333183 0 0 0 37 'point symmetry operation' ? ? -0.647024 0.616726 0.44834 0.396173 0.774332 -0.493414 -0.651465 -0.141631 -0.745342 0 0 0 38 'point symmetry operation' ? ? 0.095318 0.995447 0.000144 0.995447 -0.095318 0.000131 0.000144 0.000131 -1 0 0 0 39 'point symmetry operation' ? ? 0.857432 0.472703 0.203376 0.251955 -0.730237 0.635037 0.448697 -0.49326 -0.745229 0 0 0 40 'point symmetry operation' ? ? 0.586102 -0.229091 0.777176 -0.806823 -0.252989 0.533885 0.074308 -0.939954 -0.333113 0 0 0 41 'point symmetry operation' ? ? -0.5 0.866025 -0.000402 -0.866025 -0.5 -0.000049 -0.000243 0.000324 1 0 0 0 42 'point symmetry operation' ? ? 0.552309 0.808497 -0.20319 -0.702805 0.320496 -0.635097 -0.448352 0.493573 0.745229 0 0 0 43 'point symmetry operation' ? ? 0.945544 -0.040192 0.323004 0.316987 0.339108 -0.885734 -0.073934 0.939888 0.333382 0 0 0 44 'point symmetry operation' ? ? 0.136267 -0.507183 0.850998 0.784032 -0.469885 -0.405589 0.605579 0.722478 0.333618 0 0 0 45 'point symmetry operation' ? ? -0.757128 0.05289 0.651122 0.05289 -0.988482 0.141795 0.651122 0.141795 0.74561 0 0 0 46 'point symmetry operation' ? ? 0.050165 0.367651 0.92861 0.945112 0.283104 -0.163142 -0.322872 0.885824 -0.333269 0 0 0 47 'point symmetry operation' ? ? -0.094841 0.622376 0.776951 0.622376 -0.572062 0.534222 0.776951 0.534222 -0.333097 0 0 0 48 'point symmetry operation' ? ? 0.136267 0.784032 0.605579 -0.507183 -0.469885 0.722478 0.850998 -0.405589 0.333618 0 0 0 49 'point symmetry operation' ? ? 0.424106 0.629215 0.651323 -0.882553 0.44843 0.141462 -0.203063 -0.634822 0.745498 0 0 0 50 'point symmetry operation' ? ? 0.370893 0.371878 0.850967 0.015015 0.913802 -0.405881 -0.928554 0.163316 0.333339 0 0 0 51 'point symmetry operation' ? ? -0.343704 -0.717691 -0.605629 -0.14008 0.676886 -0.722636 0.928572 -0.163536 -0.333183 0 0 0 52 'point symmetry operation' ? ? -0.438043 -0.451954 -0.777081 0.839066 0.104678 -0.533865 0.322625 -0.885878 0.333366 0 0 0 53 'point symmetry operation' ? ? -0.17207 -0.328665 -0.92864 0.605372 -0.778965 0.163521 -0.777121 -0.534035 0.333 0 0 0 54 'point symmetry operation' ? ? 0.086651 -0.518205 -0.850856 -0.518205 -0.752877 0.405758 -0.850856 0.405758 -0.333774 0 0 0 55 'point symmetry operation' ? ? -0.019425 -0.758637 -0.651224 -0.97892 0.146888 -0.141917 0.203321 0.634739 -0.745498 0 0 0 56 'point symmetry operation' ? ? 0.793538 -0.515985 -0.322578 0.060994 -0.45999 0.885827 -0.605456 -0.722612 -0.333548 0 0 0 57 'point symmetry operation' ? ? -0.019425 -0.978919 0.203321 -0.758637 0.146888 0.634739 -0.651224 -0.141917 -0.745498 0 0 0 58 'point symmetry operation' ? ? -0.909741 -0.415175 0.000057 -0.415175 0.909741 -0.000264 0.000057 -0.000264 -1 0 0 0 59 'point symmetry operation' ? ? -0.647024 0.396173 -0.651465 0.616726 0.774332 -0.141631 0.44834 -0.493414 -0.745341 0 0 0 60 'point symmetry operation' ? ? 0.40566 0.333869 -0.850865 0.911014 -0.072209 0.406003 0.074112 -0.93985 -0.333451 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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DC _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYCYTIDINE-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 OP3 P DC sing 121 n n OP3 HOP3 DC sing 122 n n P OP1 DC doub 123 n n P OP2 DC sing 124 n n P O5' DC sing 125 n n OP2 HOP2 DC sing 126 n n O5' C5' DC sing 127 n n C5' C4' DC sing 128 n n C5' H5' DC sing 129 n n C5' "H5''" DC sing 130 n n C4' O4' DC sing 131 n n C4' C3' DC sing 132 n n C4' H4' DC sing 133 n n O4' C1' DC sing 134 n n C3' O3' DC sing 135 n n C3' C2' DC sing 136 n n C3' H3' DC sing 137 n n O3' HO3' DC sing 138 n n C2' C1' DC sing 139 n n C2' H2' DC sing 140 n n C2' "H2''" DC sing 141 n n C1' N1 DC sing 142 n n C1' H1' DC sing 143 n n N1 C2 DC sing 144 n n N1 C6 DC sing 145 n n C2 O2 DC doub 146 n n C2 N3 DC sing 147 n n N3 C4 DC doub 148 n n C4 N4 DC sing 149 n n C4 C5 DC sing 150 n n N4 H41 DC sing 151 n n N4 H42 DC sing 152 n n C5 C6 DC doub 153 n n C5 H5 DC sing 154 n n C6 H6 DC sing 155 n n # _atom_sites.entry_id 1RB8 _atom_sites.fract_transf_matrix[1][1] 0.003388 _atom_sites.fract_transf_matrix[1][2] 0.001956 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003912 _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] 0.001474 _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 5 DC X 1 5 5 DC DC . F 5 DC X 1 6 6 DC DC . G 5 DC X 1 7 7 DC DC . H 5 DC X 1 8 8 DC DC . I 5 DC X 1 9 9 DC DC . J 5 DC X 1 10 10 DC DC . # 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 DC . . . E 5 -37.291 59.085 72.23 1 1 ? P DC 5 X 1 HETATM 2 O OP1 DC . . . E 5 -36.703 59.374 73.556 1 1 ? OP1 DC 5 X 1 HETATM 3 O OP2 DC . . . E 5 -38.319 59.755 71.401 1 1 ? OP2 DC 5 X 1 HETATM 4 O O5' DC . . . E 5 -38.095 57.534 72.802 1 1 ? O5' DC 5 X 1 HETATM 5 C C5' DC . . . E 5 -39.489 57.371 73.074 1 1 ? C5' DC 5 X 1 HETATM 6 C C4' DC . . . E 5 -39.713 56.244 74.06 1 1 ? C4' DC 5 X 1 HETATM 7 O O4' DC . . . E 5 -38.523 55.447 74.084 1 1 ? O4' DC 5 X 1 HETATM 8 C C3' DC . . . E 5 -39.864 56.809 75.493 1 1 ? C3' DC 5 X 1 HETATM 9 O O3' DC . . . E 5 -40.86 56.003 76.106 1 1 ? O3' DC 5 X 1 HETATM 10 C C2' DC . . . E 5 -38.531 56.559 76.155 1 1 ? C2' DC 5 X 1 HETATM 11 C C1' DC . . . E 5 -38.017 55.348 75.44 1 1 ? C1' DC 5 X 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 11 #