data_4DL5 # _model_server_result.job_id 9hsq4XXhulX1P3nIee8gsA _model_server_result.datetime_utc '2024-10-18 17:24:43' _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 4dl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 4DL5 # _exptl.entry_id 4DL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.172 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine" _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 120 _cell.entry_id 4DL5 _cell.length_a 99.414 _cell.length_b 99.414 _cell.length_c 82.085 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DL5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.175 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.154 ? metalc ? metalc7 D MG MG . A MG 501 1_555 F O2B 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.139 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O2G 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.206 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O1A 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.28 ? metalc ? metalc10 E MG MG . A MG 502 1_555 F O1A 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.259 ? metalc ? metalc11 E MG MG . A MG 502 1_555 C O3' DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.542 ? metalc ? metalc12 B N7 DG 4 T DG 4 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.061 ? metalc ? metalc13 B N7 DG 4 T DG 4 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.101 ? metalc ? metalc14 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.102 ? metalc ? metalc15 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.112 ? hydrog WATSON-CRICK hydrog1 B N1 DG 5 T DG 5 1_555 C N3 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 5 T DG 5 1_555 C O2 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 5 T DG 5 1_555 C N4 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 6 1_555 C N1 DA 8 P DA 8 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 6 1_555 C N6 DA 8 P DA 8 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 7 T DC 7 1_555 C N1 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 7 T DC 7 1_555 C O6 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 7 T DC 7 1_555 C N2 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 8 T DA 8 1_555 C N3 DT 6 P DT 6 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 8 T DA 8 1_555 C O4 DT 6 P DT 6 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 9 T DC 9 1_555 C N1 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 9 T DC 9 1_555 C O6 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 9 T DC 9 1_555 C N2 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 T DA 10 1_555 C N3 DT 4 P DT 4 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 T DA 10 1_555 C O4 DT 4 P DT 4 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 2 P DA 2 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 2 P DA 2 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H17 N4 O12 P3' _chem_comp.formula_weight 466.172 _chem_comp.id 0KX _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine" _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 O4' C4' 0KX sing 1 n n O4' C1' 0KX sing 2 n n C4' C5' 0KX sing 3 n n C4' C3' 0KX sing 4 n n C5' O5' 0KX sing 5 n n C1' N1 0KX sing 6 n n C1' C2' 0KX sing 7 n n O5' PA 0KX sing 8 n n O1A PA 0KX doub 9 n n O2 C2 0KX doub 10 n n N1 C2 0KX sing 11 n n N1 C6 0KX sing 12 n n C3' C2' 0KX sing 13 n n C3' O3' 0KX sing 14 n n C2 N3 0KX sing 15 n n C6 C5 0KX doub 16 n n O2B PB 0KX doub 17 n n PA O2A 0KX sing 18 n n PA N3A 0KX sing 19 n n N3 C4 0KX doub 20 n n C5 C4 0KX sing 21 n n C4 N4 0KX sing 22 n n O2G PG 0KX doub 23 n n PB N3A 0KX sing 24 n n PB O1B 0KX sing 25 n n PB O3B 0KX sing 26 n n PG O3B 0KX sing 27 n n PG O3G 0KX sing 28 n n PG O1G 0KX sing 29 n n O1G H1 0KX sing 30 n n O3G H2 0KX sing 31 n n O1B H3 0KX sing 32 n n O2A H4 0KX sing 33 n n N3A H5 0KX sing 34 n n C5' H6 0KX sing 35 n n C5' H7 0KX sing 36 n n C4' H8 0KX sing 37 n n C3' H9 0KX sing 38 n n O3' H10 0KX sing 39 n n C2' H11 0KX sing 40 n n C2' H12 0KX sing 41 n n C1' H13 0KX sing 42 n n C5 H14 0KX sing 43 n n C6 H15 0KX sing 44 n n N4 H16 0KX sing 45 n n N4 H17 0KX sing 46 n n # _atom_sites.entry_id 4DL5 _atom_sites.fract_transf_matrix[1][1] 0.010059 _atom_sites.fract_transf_matrix[1][2] 0.005808 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011615 _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] 0.012182 _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 D 4 MG A 1 501 433 MG MG2 . E 4 MG A 1 502 434 MG MG2 . F 5 0KX A 1 503 10 0KX DC4 . G 6 CPT T 1 101 13 CPT CPT . # 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 PG 0KX . A . F 5 55.836 2.722 6.799 0.5 63.44 ? PG 0KX 503 A 1 HETATM 2 O O1G 0KX . A . F 5 57.139 3.268 7.032 0.5 67.63 ? O1G 0KX 503 A 1 HETATM 3 O O2G 0KX . A . F 5 55.661 2.059 5.571 0.5 68.56 ? O2G 0KX 503 A 1 HETATM 4 O O3G 0KX . A . F 5 55.53 1.845 7.848 0.5 64.38 ? O3G 0KX 503 A 1 HETATM 5 P PB 0KX . A . F 5 53.741 4.243 5.777 0.5 67.51 ? PB 0KX 503 A 1 HETATM 6 O O1B 0KX . A . F 5 53.146 5.312 6.151 0.5 71.58 ? O1B 0KX 503 A 1 HETATM 7 O O2B 0KX . A . F 5 54.284 4.439 4.504 0.5 69.83 ? O2B 0KX 503 A 1 HETATM 8 O O3B 0KX . A . F 5 54.826 3.899 6.912 0.5 72.99 ? O3B 0KX 503 A 1 HETATM 9 P PA 0KX . A . F 5 52.192 2.107 4.389 0.5 82.4 ? PA 0KX 503 A 1 HETATM 10 O O1A 0KX . A . F 5 53.253 1.853 3.614 0.5 78.31 ? O1A 0KX 503 A 1 HETATM 11 O O2A 0KX . A . F 5 51.42 1.004 4.919 0.5 77.53 ? O2A 0KX 503 A 1 HETATM 12 N N3A 0KX . A . F 5 52.634 3.023 5.615 0.5 74.85 ? N3A 0KX 503 A 1 HETATM 13 O O5' 0KX . A . F 5 51.2 2.934 3.588 0.5 79.32 ? O5' 0KX 503 A 1 HETATM 14 C C5' 0KX . A . F 5 51.554 4.128 2.828 0.5 76.87 ? C5' 0KX 503 A 1 HETATM 15 C C4' 0KX . A . F 5 50.519 5.287 2.798 0.5 73.85 ? C4' 0KX 503 A 1 HETATM 16 O O4' 0KX . A . F 5 49.219 4.94 2.405 0.5 79.77 ? O4' 0KX 503 A 1 HETATM 17 C C3' 0KX . A . F 5 50.525 6.004 4.167 0.5 74.67 ? C3' 0KX 503 A 1 HETATM 18 O O3' 0KX . A . F 5 51.53 6.878 4.423 0.5 74.6 ? O3' 0KX 503 A 1 HETATM 19 C C2' 0KX . A . F 5 49.063 6.434 4.171 0.5 78.37 ? C2' 0KX 503 A 1 HETATM 20 C C1' 0KX . A . F 5 48.288 5.482 3.214 0.5 77.44 ? C1' 0KX 503 A 1 HETATM 21 N N1 0KX . A . F 5 47.545 4.307 3.999 0.5 82.17 ? N1 0KX 503 A 1 HETATM 22 C C2 0KX . A . F 5 46.262 4.649 4.228 0.5 81.64 ? C2 0KX 503 A 1 HETATM 23 N N3 0KX . A . F 5 45.457 3.868 4.956 0.5 81 ? N3 0KX 503 A 1 HETATM 24 C C4 0KX . A . F 5 45.909 2.713 5.489 0.5 81.81 ? C4 0KX 503 A 1 HETATM 25 C C5 0KX . A . F 5 47.233 2.348 5.267 0.5 81.81 ? C5 0KX 503 A 1 HETATM 26 C C6 0KX . A . F 5 48.055 3.171 4.505 0.5 81.41 ? C6 0KX 503 A 1 HETATM 27 O O2 0KX . A . F 5 45.846 5.633 3.776 0.5 80.06 ? O2 0KX 503 A 1 HETATM 28 N N4 0KX . A . F 5 45.071 1.913 6.248 0.5 83.67 ? N4 0KX 503 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #