data_5ARL # _model_server_result.job_id JACBVqi8GtlMMAd6OKrfVQ _model_server_result.datetime_utc '2024-10-28 02:28:04' _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 5arl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1120}' # _entry.id 5ARL # _exptl.entry_id 5ARL _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 89.78 _cell.angle_beta 79.21 _cell.angle_gamma 78.9 _cell.entry_id 5ARL _cell.length_a 30.962 _cell.length_b 62.515 _cell.length_c 70.216 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ARL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E 1 1 B,F 2 1 C,G 3 1 D,H 4 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 disulf ? disulf1 A SG CYS 40 A CYS 25 1_555 A SG CYS 96 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 54 A CYS 39 1_555 A SG CYS 107 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf3 A SG CYS 72 A CYS 57 1_555 A SG CYS 122 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 79 A CYS 64 1_555 A SG CYS 86 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 B SG CYS 40 B CYS 25 1_555 B SG CYS 96 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? disulf ? disulf6 B SG CYS 54 B CYS 39 1_555 B SG CYS 107 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf7 B SG CYS 72 B CYS 57 1_555 B SG CYS 122 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 B SG CYS 79 B CYS 64 1_555 B SG CYS 86 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf9 C SG CYS 40 C CYS 25 1_555 C SG CYS 96 C CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf10 C SG CYS 54 C CYS 39 1_555 C SG CYS 107 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf11 C SG CYS 72 C CYS 57 1_555 C SG CYS 122 C CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 C SG CYS 79 C CYS 64 1_555 C SG CYS 86 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf13 D SG CYS 40 D CYS 25 1_555 D SG CYS 96 D CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf14 D SG CYS 54 D CYS 39 1_555 D SG CYS 107 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf15 D SG CYS 72 D CYS 57 1_555 D SG CYS 122 D CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf16 D SG CYS 79 D CYS 64 1_555 D SG CYS 86 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? # _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 5ARL _atom_sites.fract_transf_matrix[1][1] 0.032298 _atom_sites.fract_transf_matrix[1][2] -0.006337 _atom_sites.fract_transf_matrix[1][3] -0.006371 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016301 _atom_sites.fract_transf_matrix[2][3] 0.000545 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014506 _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 DCM A 1 1120 1120 DCM DCM . F 2 DCM B 1 1120 1120 DCM DCM . G 2 DCM C 1 1120 1120 DCM DCM . H 2 DCM D 1 1120 1120 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 . . . F 2 -25.182 -30.836 -12.002 0.6 39.75 ? N1 DCM 1120 B 1 HETATM 2 C C2 DCM . . . F 2 -26.242 -30.327 -11.203 0.6 37.32 ? C2 DCM 1120 B 1 HETATM 3 N N3 DCM . . . F 2 -26.194 -29.031 -10.787 0.6 39.85 ? N3 DCM 1120 B 1 HETATM 4 C C4 DCM . . . F 2 -25.151 -28.215 -11.144 0.6 44.21 ? C4 DCM 1120 B 1 HETATM 5 C C5 DCM . . . F 2 -24.127 -28.71 -11.939 0.6 43.55 ? C5 DCM 1120 B 1 HETATM 6 C C6 DCM . . . F 2 -24.174 -30.032 -12.361 0.6 42.63 ? C6 DCM 1120 B 1 HETATM 7 O O2 DCM . . . F 2 -27.203 -31.052 -10.868 0.6 29.84 ? O2 DCM 1120 B 1 HETATM 8 N N4 DCM . . . F 2 -25.073 -26.914 -10.748 0.6 46.25 ? N4 DCM 1120 B 1 HETATM 9 C C1' DCM . . . F 2 -25.181 -32.21 -12.502 0.6 40.38 ? C1' DCM 1120 B 1 HETATM 10 C C2' DCM . . . F 2 -26.015 -32.131 -13.761 0.6 39.69 ? C2' DCM 1120 B 1 HETATM 11 C C3' DCM . . . F 2 -25.107 -32.407 -14.913 0.6 40.52 ? C3' DCM 1120 B 1 HETATM 12 C C4' DCM . . . F 2 -23.83 -32.958 -14.293 0.6 43.9 ? C4' DCM 1120 B 1 HETATM 13 O O4' DCM . . . F 2 -23.877 -32.674 -12.877 0.6 41.28 ? O4' DCM 1120 B 1 HETATM 14 O O3' DCM . . . F 2 -25.731 -33.397 -15.727 0.6 38.01 ? O3' DCM 1120 B 1 HETATM 15 C C5' DCM . . . F 2 -22.591 -32.428 -15.027 0.6 47.05 ? C5' DCM 1120 B 1 HETATM 16 O O5' DCM . . . F 2 -22.358 -33.278 -16.161 0.6 51.73 ? O5' DCM 1120 B 1 HETATM 17 P P DCM . . . F 2 -21.695 -32.845 -17.591 0.6 60.76 ? P DCM 1120 B 1 HETATM 18 O O1P DCM . . . F 2 -22.387 -33.719 -18.627 0.6 53.5 ? O1P DCM 1120 B 1 HETATM 19 O O2P DCM . . . F 2 -21.978 -31.358 -17.74 0.6 53.71 ? O2P DCM 1120 B 1 HETATM 20 O O3P DCM . . . F 2 -20.225 -33.224 -17.435 0.6 59.41 ? O3P DCM 1120 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #