data_4PDA # _model_server_result.job_id 2hE4HavRzBxLbDmx5OL3LA _model_server_result.datetime_utc '2024-11-01 19:36:24' _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 4pda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PDA # _exptl.entry_id 4PDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 2 _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 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 4PDA _cell.length_a 120.017 _cell.length_b 120.017 _cell.length_c 82.465 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.0085 -103.937771 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 120.017 0 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 O ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? # _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 4PDA _atom_sites.fract_transf_matrix[1][1] 0.008332 _atom_sites.fract_transf_matrix[1][2] 0.004811 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009621 _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] 0.012126 _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 CTN A 1 501 1 CTN Cr . C 3 NA A 1 502 1 NA NA . D 4 DMU A 1 503 503 DMU DMU . E 5 HOH A 1 601 37 HOH HOH . E 5 HOH A 2 602 17 HOH HOH . E 5 HOH A 3 603 1 HOH HOH . E 5 HOH A 4 604 2 HOH HOH . E 5 HOH A 5 605 3 HOH HOH . E 5 HOH A 6 606 4 HOH HOH . E 5 HOH A 7 607 6 HOH HOH . E 5 HOH A 8 608 7 HOH HOH . E 5 HOH A 9 609 8 HOH HOH . E 5 HOH A 10 610 14 HOH HOH . E 5 HOH A 11 611 19 HOH HOH . E 5 HOH A 12 612 25 HOH HOH . E 5 HOH A 13 613 27 HOH HOH . E 5 HOH A 14 614 28 HOH HOH . E 5 HOH A 15 615 29 HOH HOH . E 5 HOH A 16 616 32 HOH HOH . E 5 HOH A 17 617 33 HOH HOH . E 5 HOH A 18 618 38 HOH HOH . E 5 HOH A 19 619 40 HOH HOH . E 5 HOH A 20 620 41 HOH HOH . E 5 HOH A 21 621 42 HOH HOH . E 5 HOH A 22 622 47 HOH HOH . E 5 HOH A 23 623 53 HOH HOH . E 5 HOH A 24 624 58 HOH HOH . E 5 HOH A 25 625 1 HOH HOH . E 5 HOH A 26 626 1 HOH HOH . E 5 HOH A 27 627 1 HOH HOH . E 5 HOH A 28 628 1 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 . . . B 2 52.029 -19.173 -4.02 1 46.11 ? O5' CTN 501 A 1 HETATM 2 C C5' CTN . . . B 2 53.246 -18.611 -4.488 1 46.11 ? C5' CTN 501 A 1 HETATM 3 C C4' CTN . . . B 2 53.211 -18.375 -5.977 1 46.11 ? C4' CTN 501 A 1 HETATM 4 O O4' CTN . . . B 2 53.131 -19.644 -6.675 1 46.11 ? O4' CTN 501 A 1 HETATM 5 C C1' CTN . . . B 2 52.365 -19.499 -7.853 1 46.11 ? C1' CTN 501 A 1 HETATM 6 N N1 CTN . . . B 2 51.206 -20.419 -7.785 1 46.11 ? N1 CTN 501 A 1 HETATM 7 C C6 CTN . . . B 2 50.799 -20.953 -6.593 1 46.11 ? C6 CTN 501 A 1 HETATM 8 C C5 CTN . . . B 2 49.753 -21.788 -6.528 1 46.11 ? C5 CTN 501 A 1 HETATM 9 C C4 CTN . . . B 2 49.086 -22.099 -7.749 1 46.11 ? C4 CTN 501 A 1 HETATM 10 N N3 CTN . . . B 2 49.475 -21.587 -8.917 1 46.11 ? N3 CTN 501 A 1 HETATM 11 C C2 CTN . . . B 2 50.533 -20.745 -8.968 1 46.11 ? C2 CTN 501 A 1 HETATM 12 O O2 CTN . . . B 2 50.92 -20.252 -10.039 1 46.11 ? O2 CTN 501 A 1 HETATM 13 N N4 CTN . . . B 2 48.037 -22.925 -7.749 1 46.11 ? N4 CTN 501 A 1 HETATM 14 C C2' CTN . . . B 2 51.94 -18.032 -7.955 1 46.11 ? C2' CTN 501 A 1 HETATM 15 O O2' CTN . . . B 2 52.901 -17.34 -8.739 1 46.11 ? O2' CTN 501 A 1 HETATM 16 C C3' CTN . . . B 2 52.018 -17.592 -6.5 1 46.11 ? C3' CTN 501 A 1 HETATM 17 O O3' CTN . . . B 2 52.166 -16.192 -6.342 1 46.11 ? O3' CTN 501 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 17 #