data_5W1C # _model_server_result.job_id p2xiYtsX310Qrj8YR8Rtng _model_server_result.datetime_utc '2024-11-22 15:18:02' _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 5w1c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2002}' # _entry.id 5W1C # _exptl.entry_id 5W1C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _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 90.27 _cell.angle_gamma 90 _cell.entry_id 5W1C _cell.length_a 125.456 _cell.length_b 39.824 _cell.length_c 155.304 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W1C _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 ? 5 F N N ? 5 I 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 O THR 367 B THR 367 1_555 G CA CA . B CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc2 A O ASN 368 B ASN 368 1_555 G CA CA . B CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc3 A ND1 HIS 424 B HIS 1056 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc4 A SG CYS 455 B CYS 1087 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc5 A SG CYS 458 B CYS 1090 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc6 E ZN ZN . B ZN 2001 1_555 K O HOH . B HOH 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc7 D O THR 367 A THR 367 1_555 J CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc8 D O ASN 368 A ASN 368 1_555 J CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc9 D OD1 ASP 413 A ASP 1045 1_555 J CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc10 D ND1 HIS 424 A HIS 1056 1_555 H ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc11 D SG CYS 455 A CYS 1087 1_555 H ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc12 H ZN ZN . A ZN 2001 1_555 L O HOH . A HOH 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 D DG 1 1_555 C N3 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 D DG 1 1_555 C O2 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 D DG 1 1_555 C N4 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 2 D DT 2 1_555 C N1 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 2 D DT 2 1_555 C N6 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 3 D DT 3 1_555 C N1 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 3 D DT 3 1_555 C N6 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 4 D DC 4 1_555 C N1 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 4 D DC 4 1_555 C O6 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 4 D DC 4 1_555 C N2 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 5 D DA 5 1_555 C N3 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 DA 5 D DA 5 1_555 C O4 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DA 6 D DA 6 1_555 C N3 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 6 D DA 6 1_555 C O4 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DG 7 D DG 7 1_555 C N3 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N2 DG 7 D DG 7 1_555 C O2 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O6 DG 7 D DG 7 1_555 C N4 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DG 8 D DG 8 1_555 C N3 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N2 DG 8 D DG 8 1_555 C O2 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O6 DG 8 D DG 8 1_555 C N4 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 9 D DC 9 1_555 C N1 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 9 D DC 9 1_555 C O6 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 9 D DC 9 1_555 C N2 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DC 10 D DC 10 1_555 C N1 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N4 DC 10 D DC 10 1_555 C O6 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O2 DC 10 D DC 10 1_555 C N2 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N1 DA 11 D DA 11 1_555 C N3 DT 2 G DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N6 DA 11 D DA 11 1_555 C O4 DT 2 G DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N1 DG 12 D DG 12 1_555 C N3 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N2 DG 12 D DG 12 1_555 C O2 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O6 DG 12 D DG 12 1_555 C N4 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id CTN _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTIDINE # 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 O5' C5' CTN sing 70 n n O5' H5' CTN sing 71 n n C5' C4' CTN sing 72 n n C5' "H5'1" CTN sing 73 n n C5' "H5'2" CTN sing 74 n n C4' O4' CTN sing 75 n n C4' C3' CTN sing 76 n n C4' H4' CTN sing 77 n n O4' C1' CTN sing 78 n n C1' N1 CTN sing 79 n n C1' C2' CTN sing 80 n n C1' H1' CTN sing 81 n n N1 C6 CTN sing 82 n y N1 C2 CTN sing 83 n y C6 C5 CTN doub 84 n y C6 H6 CTN sing 85 n n C5 C4 CTN sing 86 n y C5 H5 CTN sing 87 n n C4 N3 CTN doub 88 n y C4 N4 CTN sing 89 n n N3 C2 CTN sing 90 n y C2 O2 CTN doub 91 n n N4 HN41 CTN sing 92 n n N4 HN42 CTN sing 93 n n C2' O2' CTN sing 94 n n C2' C3' CTN sing 95 n n C2' H2' CTN sing 96 n n O2' H1 CTN sing 97 n n C3' O3' CTN sing 98 n n C3' H3' CTN sing 99 n n O3' H2 CTN sing 100 n n # _atom_sites.entry_id 5W1C _atom_sites.fract_transf_matrix[1][1] 0.007971 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000037 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02511 _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] 0.006439 _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 4 ZN B 1 2001 2001 ZN ZN . F 5 CTN B 1 2002 4001 CTN CTN . G 6 CA B 1 2003 5001 CA CA . H 4 ZN A 1 2001 2001 ZN ZN . I 5 CTN A 1 2002 4001 CTN CTN . J 6 CA A 1 2003 5001 CA CA . K 7 HOH B 1 3001 3001 HOH HOH . L 7 HOH A 1 3001 3001 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 O O5' CTN . . . F 5 232.851 -3.616 1291.185 1 149.61 ? O5' CTN 2002 B 1 HETATM 2 C C5' CTN . . . F 5 233.755 -3.38 1290.099 1 126.85 ? C5' CTN 2002 B 1 HETATM 3 C C4' CTN . . . F 5 233.373 -4.266 1288.92 1 154.23 ? C4' CTN 2002 B 1 HETATM 4 O O4' CTN . . . F 5 233.271 -3.472 1287.734 1 148.24 ? O4' CTN 2002 B 1 HETATM 5 C C1' CTN . . . F 5 234.159 -3.93 1286.707 1 134.53 ? C1' CTN 2002 B 1 HETATM 6 N N1 CTN . . . F 5 235.107 -2.881 1286.307 1 141.61 ? N1 CTN 2002 B 1 HETATM 7 C C6 CTN . . . F 5 234.956 -1.617 1286.722 1 128.54 ? C6 CTN 2002 B 1 HETATM 8 C C5 CTN . . . F 5 235.865 -0.644 1286.329 1 112.07 ? C5 CTN 2002 B 1 HETATM 9 C C4 CTN . . . F 5 236.929 -0.987 1285.504 1 94.43 ? C4 CTN 2002 B 1 HETATM 10 N N3 CTN . . . F 5 237.076 -2.263 1285.088 1 101.21 ? N3 CTN 2002 B 1 HETATM 11 C C2 CTN . . . F 5 236.193 -3.212 1285.469 1 139.46 ? C2 CTN 2002 B 1 HETATM 12 O O2 CTN . . . F 5 236.341 -4.389 1285.076 1 152.69 ? O2 CTN 2002 B 1 HETATM 13 N N4 CTN . . . F 5 237.82 -0.042 1285.118 1 106.36 ? N4 CTN 2002 B 1 HETATM 14 C C2' CTN . . . F 5 234.923 -5.124 1287.259 1 137.14 ? C2' CTN 2002 B 1 HETATM 15 O O2' CTN . . . F 5 234.659 -6.284 1286.465 1 134.52 ? O2' CTN 2002 B 1 HETATM 16 C C3' CTN . . . F 5 234.422 -5.338 1288.673 1 134.2 ? C3' CTN 2002 B 1 HETATM 17 O O3' CTN . . . F 5 233.834 -6.636 1288.794 1 169.17 ? O3' CTN 2002 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #