data_2QRN # _model_server_result.job_id osOwuNPYMB6kOO85F96BBQ _model_server_result.datetime_utc '2024-10-18 15:25:42' _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 2qrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":403}' # _entry.id 2QRN # _exptl.entry_id 2QRN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-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 90 _cell.angle_gamma 90 _cell.entry_id 2QRN _cell.length_a 94.565 _cell.length_b 94.565 _cell.length_c 335.334 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QRN _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # 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,I,J 1 1 C,D,K,L,M,N,O,P 2 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 G N N ? 4 J N N ? 4 M N N ? 4 P 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 OG SER 55 A SER 35 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A OE1 GLU 147 A GLU 127 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 B OG SER 55 B SER 35 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc4 C OG SER 55 C SER 35 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc5 K MG MG . C MG 401 1_555 L O1B UDP . C UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc6 D OG SER 55 D SER 35 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _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 2QRN _atom_sites.fract_transf_matrix[1][1] 0.010575 _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] 0.010575 _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] 0.002982 _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 MG A 1 401 401 MG MG . F 3 UDP A 1 402 402 UDP UDP . G 4 DCM A 1 403 403 DCM DCM . H 2 MG B 1 401 401 MG MG . I 3 UDP B 1 402 402 UDP UDP . J 4 DCM B 1 403 403 DCM DCM . K 2 MG C 1 401 401 MG MG . L 3 UDP C 1 402 402 UDP UDP . M 4 DCM C 1 403 403 DCM DCM . N 2 MG D 1 401 401 MG MG . O 3 UDP D 1 402 402 UDP UDP . P 4 DCM D 1 403 403 DCM DCM . # 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 . . . J 4 35.537 79 10.778 1 84.86 ? N1 DCM 403 B 1 HETATM 2 C C2 DCM . . . J 4 36.532 79.486 9.931 1 86.13 ? C2 DCM 403 B 1 HETATM 3 N N3 DCM . . . J 4 37.317 78.652 9.239 1 88.4 ? N3 DCM 403 B 1 HETATM 4 C C4 DCM . . . J 4 37.168 77.326 9.344 1 89.42 ? C4 DCM 403 B 1 HETATM 5 C C5 DCM . . . J 4 36.148 76.789 10.207 1 87.3 ? C5 DCM 403 B 1 HETATM 6 C C6 DCM . . . J 4 35.346 77.657 10.914 1 86.13 ? C6 DCM 403 B 1 HETATM 7 O O2 DCM . . . J 4 36.698 80.696 9.824 1 83.94 ? O2 DCM 403 B 1 HETATM 8 N N4 DCM . . . J 4 37.983 76.486 8.64 1 89.62 ? N4 DCM 403 B 1 HETATM 9 C C1' DCM . . . J 4 34.703 79.964 11.584 1 82.42 ? C1' DCM 403 B 1 HETATM 10 C C2' DCM . . . J 4 33.868 80.835 10.675 1 81.66 ? C2' DCM 403 B 1 HETATM 11 C C3' DCM . . . J 4 32.476 80.883 11.332 1 79.66 ? C3' DCM 403 B 1 HETATM 12 C C4' DCM . . . J 4 32.395 79.561 12.112 1 77.58 ? C4' DCM 403 B 1 HETATM 13 O O4' DCM . . . J 4 33.811 79.244 12.497 1 80.06 ? O4' DCM 403 B 1 HETATM 14 O O3' DCM . . . J 4 32.361 82.002 12.213 1 77.74 ? O3' DCM 403 B 1 HETATM 15 C C5' DCM . . . J 4 31.8 78.478 11.268 1 72.7 ? C5' DCM 403 B 1 HETATM 16 O O5' DCM . . . J 4 31.685 77.314 12.023 1 64.97 ? O5' DCM 403 B 1 HETATM 17 P P DCM . . . J 4 30.919 76.249 11.113 1 58.73 ? P DCM 403 B 1 HETATM 18 O O1P DCM . . . J 4 29.518 76.804 10.79 1 51.11 ? O1P DCM 403 B 1 HETATM 19 O O2P DCM . . . J 4 31.695 76.034 9.894 1 57.8 ? O2P DCM 403 B 1 HETATM 20 O O3P DCM . . . J 4 30.763 74.855 11.971 1 52.7 ? O3P DCM 403 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #