data_5KT3 # _model_server_result.job_id 05h0CRJ5gPGmXDmvbIMBXw _model_server_result.datetime_utc '2024-10-12 10:21:00' _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 5kt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5KT3 # _exptl.entry_id 5KT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.172 _entity.id 4 _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 5KT3 _cell.length_a 97.829 _cell.length_b 97.829 _cell.length_c 202.887 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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,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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 B OP1 DC 6 P DC 872 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc2 B O3' DC 7 P DC 873 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc3 C OD2 ASP 34 A ASP 59 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc4 C OD1 ASP 34 A ASP 59 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc5 C O LEU 35 A LEU 60 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc6 C OD2 ASP 126 A ASP 151 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc7 C OD1 ASP 126 A ASP 151 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc8 C OE2 GLU 127 A GLU 152 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc9 C O LYS 237 A LYS 262 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc10 C O ILE 242 A ILE 267 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc11 D O1G 0KX . A 0KX 501 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc12 D O2B 0KX . A 0KX 501 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc13 D O2A 0KX . A 0KX 501 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc14 D O2A 0KX . A 0KX 501 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? hydrog WATSON-CRICK hydrog1 A N1 DG 4 T DG 841 1_555 B N3 DC 7 P DC 873 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 4 T DG 841 1_555 B O2 DC 7 P DC 873 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 4 T DG 841 1_555 B N4 DC 7 P DC 873 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 5 T DG 842 1_555 B N3 DC 6 P DC 872 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 5 T DG 842 1_555 B O2 DC 6 P DC 872 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 5 T DG 842 1_555 B N4 DC 6 P DC 872 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 6 T DG 843 1_555 B N3 DC 5 P DC 871 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 6 T DG 843 1_555 B O2 DC 5 P DC 871 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 6 T DG 843 1_555 B N4 DC 5 P DC 871 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DT 7 T DT 844 1_555 B N1 DA 4 P DA 870 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O4 DT 7 T DT 844 1_555 B N6 DA 4 P DA 870 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 8 T DC 845 1_555 B N1 DG 3 P DG 869 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 8 T DC 845 1_555 B O6 DG 3 P DG 869 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 8 T DC 845 1_555 B N2 DG 3 P DG 869 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 9 T DC 846 1_555 B N1 DG 2 P DG 868 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 9 T DC 846 1_555 B O6 DG 2 P DG 868 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 9 T DC 846 1_555 B N2 DG 2 P DG 868 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DT 10 T DT 847 1_555 B N1 DA 1 P DA 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O4 DT 10 T DT 847 1_555 B N6 DA 1 P DA 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5KT3 _atom_sites.fract_transf_matrix[1][1] 0.010222 _atom_sites.fract_transf_matrix[1][2] 0.005902 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011803 _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] 0.004929 _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 0KX A 1 501 501 0KX 0KX . E 5 MN A 1 502 502 MN MN . F 5 MN A 1 503 503 MN MN . G 5 MN A 1 504 504 MN MN . H 6 HOH T 1 901 655 HOH HOH . H 6 HOH T 2 902 656 HOH HOH . H 6 HOH T 3 903 605 HOH HOH . H 6 HOH T 4 904 632 HOH HOH . H 6 HOH T 5 905 654 HOH HOH . H 6 HOH T 6 906 659 HOH HOH . H 6 HOH T 7 907 650 HOH HOH . I 6 HOH P 1 901 611 HOH HOH . J 6 HOH A 1 601 620 HOH HOH . J 6 HOH A 2 602 663 HOH HOH . J 6 HOH A 3 603 608 HOH HOH . J 6 HOH A 4 604 614 HOH HOH . J 6 HOH A 5 605 619 HOH HOH . J 6 HOH A 6 606 640 HOH HOH . J 6 HOH A 7 607 642 HOH HOH . J 6 HOH A 8 608 601 HOH HOH . J 6 HOH A 9 609 604 HOH HOH . J 6 HOH A 10 610 609 HOH HOH . J 6 HOH A 11 611 603 HOH HOH . J 6 HOH A 12 612 628 HOH HOH . J 6 HOH A 13 613 610 HOH HOH . J 6 HOH A 14 614 602 HOH HOH . J 6 HOH A 15 615 648 HOH HOH . J 6 HOH A 16 616 623 HOH HOH . J 6 HOH A 17 617 624 HOH HOH . J 6 HOH A 18 618 665 HOH HOH . J 6 HOH A 19 619 630 HOH HOH . J 6 HOH A 20 620 645 HOH HOH . J 6 HOH A 21 621 612 HOH HOH . J 6 HOH A 22 622 606 HOH HOH . J 6 HOH A 23 623 621 HOH HOH . J 6 HOH A 24 624 615 HOH HOH . J 6 HOH A 25 625 636 HOH HOH . J 6 HOH A 26 626 635 HOH HOH . J 6 HOH A 27 627 622 HOH HOH . J 6 HOH A 28 628 660 HOH HOH . J 6 HOH A 29 629 662 HOH HOH . J 6 HOH A 30 630 637 HOH HOH . J 6 HOH A 31 631 629 HOH HOH . J 6 HOH A 32 632 644 HOH HOH . J 6 HOH A 33 633 627 HOH HOH . J 6 HOH A 34 634 618 HOH HOH . J 6 HOH A 35 635 639 HOH HOH . J 6 HOH A 36 636 647 HOH HOH . J 6 HOH A 37 637 625 HOH HOH . J 6 HOH A 38 638 633 HOH HOH . J 6 HOH A 39 639 638 HOH HOH . J 6 HOH A 40 640 657 HOH HOH . J 6 HOH A 41 641 616 HOH HOH . J 6 HOH A 42 642 649 HOH HOH . J 6 HOH A 43 643 658 HOH HOH . J 6 HOH A 44 644 651 HOH HOH . J 6 HOH A 45 645 607 HOH HOH . J 6 HOH A 46 646 617 HOH HOH . J 6 HOH A 47 647 643 HOH HOH . J 6 HOH A 48 648 664 HOH HOH . J 6 HOH A 49 649 626 HOH HOH . J 6 HOH A 50 650 631 HOH HOH . J 6 HOH A 51 651 652 HOH HOH . J 6 HOH A 52 652 661 HOH HOH . J 6 HOH A 53 653 646 HOH HOH . J 6 HOH A 54 654 634 HOH HOH . J 6 HOH A 55 655 641 HOH HOH . J 6 HOH A 56 656 613 HOH HOH . J 6 HOH A 57 657 653 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 P PG 0KX . . . D 4 1.85 17.86 14.044 1 34.47 ? PG 0KX 501 A 1 HETATM 2 O O1G 0KX . . . D 4 3.051 18.741 13.74 1 32.05 ? O1G 0KX 501 A 1 HETATM 3 O O2G 0KX . . . D 4 0.681 18.114 13.105 1 36.5 ? O2G 0KX 501 A 1 HETATM 4 O O3G 0KX . . . D 4 2.186 16.407 14.263 1 38.34 ? O3G 0KX 501 A 1 HETATM 5 P PB 0KX . . . D 4 1.998 19.384 16.451 1 29.9 ? PB 0KX 501 A 1 HETATM 6 O O1B 0KX . . . D 4 1.397 19.224 17.813 1 35.41 ? O1B 0KX 501 A 1 HETATM 7 O O2B 0KX . . . D 4 3.5 19.269 16.377 1 30.45 ? O2B 0KX 501 A 1 HETATM 8 O O3B 0KX . . . D 4 1.336 18.246 15.525 1 35 ? O3B 0KX 501 A 1 HETATM 9 P PA 0KX . . . D 4 2.552 22.045 15.372 1 26.78 ? PA 0KX 501 A 1 HETATM 10 O O1A 0KX . . . D 4 1.822 23.118 14.6 1 25.15 ? O1A 0KX 501 A 1 HETATM 11 O O2A 0KX . . . D 4 3.671 21.295 14.72 1 29.32 ? O2A 0KX 501 A 1 HETATM 12 N N3A 0KX . . . D 4 1.341 20.87 15.833 1 27.57 ? N3A 0KX 501 A 1 HETATM 13 O O5' 0KX . . . D 4 3.048 22.799 16.715 1 34.63 ? O5' 0KX 501 A 1 HETATM 14 C C5' 0KX . . . D 4 3.974 22.221 17.623 1 33.8 ? C5' 0KX 501 A 1 HETATM 15 C C4' 0KX . . . D 4 3.522 22.406 19.076 1 36.04 ? C4' 0KX 501 A 1 HETATM 16 O O4' 0KX . . . D 4 3.444 23.793 19.39 1 36.83 ? O4' 0KX 501 A 1 HETATM 17 C C3' 0KX . . . D 4 2.145 21.838 19.387 1 35.98 ? C3' 0KX 501 A 1 HETATM 18 O O3' 0KX . . . D 4 2.213 20.48 19.845 1 31.2 ? O3' 0KX 501 A 1 HETATM 19 C C2' 0KX . . . D 4 1.597 22.753 20.465 1 27.94 ? C2' 0KX 501 A 1 HETATM 20 C C1' 0KX . . . D 4 2.342 24.064 20.251 1 30.02 ? C1' 0KX 501 A 1 HETATM 21 N N1 0KX . . . D 4 1.514 25.062 19.573 1 34.34 ? N1 0KX 501 A 1 HETATM 22 C C2 0KX . . . D 4 0.806 25.99 20.346 1 32.01 ? C2 0KX 501 A 1 HETATM 23 N N3 0KX . . . D 4 0.045 26.931 19.764 1 30.85 ? N3 0KX 501 A 1 HETATM 24 C C4 0KX . . . D 4 -0.043 27.002 18.422 1 32.25 ? C4 0KX 501 A 1 HETATM 25 C C5 0KX . . . D 4 0.652 26.094 17.629 1 25.91 ? C5 0KX 501 A 1 HETATM 26 C C6 0KX . . . D 4 1.436 25.118 18.235 1 30.26 ? C6 0KX 501 A 1 HETATM 27 O O2 0KX . . . D 4 0.887 25.95 21.588 1 40.05 ? O2 0KX 501 A 1 HETATM 28 N N4 0KX . . . D 4 -0.823 27.966 17.87 1 33.1 ? N4 0KX 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #