data_3G2R # _model_server_result.job_id qbBF7unJ3iNxLEu4F6cjXw _model_server_result.datetime_utc '2024-12-11 10:32:59' _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 3g2r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 3G2R # _exptl.entry_id 3G2R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 3G2R _cell.length_a 17.878 _cell.length_b 30.97 _cell.length_c 43.405 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G2R _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 30.97 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 O6 DG 2 A DG 2 1_555 C MN MN . A MN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 A N1 DG 4 A DG 4 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 A O6 DG 4 A DG 4 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 A N2 DG 4 A DG 4 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog4 A N2 DG 2 A DG 2 1_555 A O2 DT 3 A DT 3 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DG MISPAIR' hydrog5 A N3 DT 3 A DT 3 1_555 A O6 DG 2 A DG 2 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DG 4 A DG 4 1_555 A N3 DC 1 A DC 1 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 4 A DG 4 1_555 A O2 DC 1 A DC 1 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 4 A DG 4 1_555 A N4 DC 1 A DC 1 4_565 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 36 n n N1 C6 DCM sing 37 n n N1 C1' DCM sing 38 n n C2 N3 DCM sing 39 n n C2 O2 DCM doub 40 n n N3 C4 DCM doub 41 n n C4 C5 DCM sing 42 n n C4 N4 DCM sing 43 n n C5 C6 DCM doub 44 n n C5 H5 DCM sing 45 n n C6 H6 DCM sing 46 n n N4 HN41 DCM sing 47 n n N4 HN42 DCM sing 48 n n C1' C2' DCM sing 49 n n C1' O4' DCM sing 50 n n C1' H1' DCM sing 51 n n C2' C3' DCM sing 52 n n C2' "H2'1" DCM sing 53 n n C2' "H2'2" DCM sing 54 n n C3' C4' DCM sing 55 n n C3' O3' DCM sing 56 n n C3' H3' DCM sing 57 n n C4' O4' DCM sing 58 n n C4' C5' DCM sing 59 n n C4' H4' DCM sing 60 n n O3' HO3' DCM sing 61 n n C5' O5' DCM sing 62 n n C5' "H5'1" DCM sing 63 n n C5' "H5'2" DCM sing 64 n n O5' P DCM sing 65 n n P O1P DCM doub 66 n n P O2P DCM sing 67 n n P O3P DCM sing 68 n n O2P HOP2 DCM sing 69 n n O3P HOP3 DCM sing 70 n n # _atom_sites.entry_id 3G2R _atom_sites.fract_transf_matrix[1][1] 0.055935 _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] 0.032289 _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] 0.023039 _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 B 2 DCM A 1 7 7 DCM C . C 3 MN A 1 8 1 MN MN . D 4 HOH A 1 9 1 HOH HOH . D 4 HOH A 2 10 2 HOH HOH . D 4 HOH A 3 11 3 HOH HOH . D 4 HOH A 4 12 4 HOH HOH . D 4 HOH A 5 13 5 HOH HOH . D 4 HOH A 6 14 7 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 P P DCM . . . B 2 -8.177 19.24 14.839 0.5 35.91 ? P DCM 7 A 1 HETATM 2 O O1P DCM . . . B 2 -8.184 18.246 15.94 0.5 28.82 ? O1P DCM 7 A 1 HETATM 3 O O2P DCM . . . B 2 -7.67 20.623 14.946 0.5 30.82 ? O2P DCM 7 A 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 3 #