data_2JAT # _model_server_result.job_id -W-trxXdcqUHRTV5wWQyig _model_server_result.datetime_utc '2024-11-12 20:43:36' _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 2jat # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1205}' # _entry.id 2JAT # _exptl.entry_id 2JAT _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 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 120 _cell.entry_id 2JAT _cell.length_a 83.931 _cell.length_b 83.931 _cell.length_c 53.31 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JAT _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 E N N ? 4 H 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 C MG MG . A MG 1203 1_555 D O2 POP . A POP 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc2 C MG MG . A MG 1203 1_555 E O1P DCM . A DCM 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc3 F MG MG . B MG 1202 1_555 G O5 POP . B POP 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc4 F MG MG . B MG 1202 1_555 H O1P DCM . B DCM 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? # _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 70 n n N1 C6 DCM sing 71 n n N1 C1' DCM sing 72 n n C2 N3 DCM sing 73 n n C2 O2 DCM doub 74 n n N3 C4 DCM doub 75 n n C4 C5 DCM sing 76 n n C4 N4 DCM sing 77 n n C5 C6 DCM doub 78 n n C5 H5 DCM sing 79 n n C6 H6 DCM sing 80 n n N4 HN41 DCM sing 81 n n N4 HN42 DCM sing 82 n n C1' C2' DCM sing 83 n n C1' O4' DCM sing 84 n n C1' H1' DCM sing 85 n n C2' C3' DCM sing 86 n n C2' "H2'1" DCM sing 87 n n C2' "H2'2" DCM sing 88 n n C3' C4' DCM sing 89 n n C3' O3' DCM sing 90 n n C3' H3' DCM sing 91 n n C4' O4' DCM sing 92 n n C4' C5' DCM sing 93 n n C4' H4' DCM sing 94 n n O3' HO3' DCM sing 95 n n C5' O5' DCM sing 96 n n C5' "H5'1" DCM sing 97 n n C5' "H5'2" DCM sing 98 n n O5' P DCM sing 99 n n P O1P DCM doub 100 n n P O2P DCM sing 101 n n P O3P DCM sing 102 n n O2P HOP2 DCM sing 103 n n O3P HOP3 DCM sing 104 n n # _atom_sites.entry_id 2JAT _atom_sites.fract_transf_matrix[1][1] 0.011915 _atom_sites.fract_transf_matrix[1][2] 0.006879 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013758 _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] 0.018758 _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 1203 1203 MG MG . D 3 POP A 1 1204 1204 POP POP . E 4 DCM A 1 1205 1205 DCM DCM . F 2 MG B 1 1202 1202 MG MG . G 3 POP B 1 1203 1203 POP POP . H 4 DCM B 1 1204 1204 DCM DCM . I 5 HOH A 1 2001 2001 HOH HOH . I 5 HOH A 2 2002 2002 HOH HOH . I 5 HOH A 3 2003 2003 HOH HOH . I 5 HOH A 4 2004 2004 HOH HOH . J 5 HOH B 1 2001 2001 HOH HOH . J 5 HOH B 2 2002 2002 HOH HOH . J 5 HOH B 3 2003 2003 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 . . . E 4 6.301 25.014 13.719 1 56 ? N1 DCM 1205 A 1 HETATM 2 C C2 DCM . . . E 4 5.799 25.321 12.426 1 56.98 ? C2 DCM 1205 A 1 HETATM 3 N N3 DCM . . . E 4 5.984 24.401 11.383 1 57.13 ? N3 DCM 1205 A 1 HETATM 4 C C4 DCM . . . E 4 6.663 23.203 11.61 1 56.31 ? C4 DCM 1205 A 1 HETATM 5 C C5 DCM . . . E 4 7.167 22.897 12.876 1 56.49 ? C5 DCM 1205 A 1 HETATM 6 C C6 DCM . . . E 4 6.989 23.792 13.93 1 55.65 ? C6 DCM 1205 A 1 HETATM 7 O O2 DCM . . . E 4 5.198 26.37 12.186 1 56.89 ? O2 DCM 1205 A 1 HETATM 8 N N4 DCM . . . E 4 6.82 22.37 10.596 1 56.31 ? N4 DCM 1205 A 1 HETATM 9 C C1' DCM . . . E 4 6.116 25.961 14.843 1 54.99 ? C1' DCM 1205 A 1 HETATM 10 C C2' DCM . . . E 4 4.746 25.621 15.408 1 54.17 ? C2' DCM 1205 A 1 HETATM 11 C C3' DCM . . . E 4 4.927 25.688 16.911 1 54.18 ? C3' DCM 1205 A 1 HETATM 12 C C4' DCM . . . E 4 6.433 25.848 17.131 1 53.82 ? C4' DCM 1205 A 1 HETATM 13 O O4' DCM . . . E 4 7.062 25.618 15.855 1 53.26 ? O4' DCM 1205 A 1 HETATM 14 O O3' DCM . . . E 4 4.263 26.852 17.41 1 55.15 ? O3' DCM 1205 A 1 HETATM 15 C C5' DCM . . . E 4 6.996 24.869 18.202 1 53.03 ? C5' DCM 1205 A 1 HETATM 16 O O5' DCM . . . E 4 6.432 23.555 18.108 1 52.81 ? O5' DCM 1205 A 1 HETATM 17 P P DCM . . . E 4 5.888 22.723 19.396 1 51.89 ? P DCM 1205 A 1 HETATM 18 O O1P DCM . . . E 4 7.103 21.895 20.039 1 49.99 ? O1P DCM 1205 A 1 HETATM 19 O O2P DCM . . . E 4 5.508 23.824 20.559 1 51.54 ? O2P DCM 1205 A 1 HETATM 20 O O3P DCM . . . E 4 4.778 21.828 19.021 1 50.28 ? O3P DCM 1205 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #