data_1N1D # _model_server_result.job_id KFQfTEgtk1xNAEna18DQpw _model_server_result.datetime_utc '2024-11-23 21:21:20' _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 1n1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":130}' # _entry.id 1N1D # _exptl.entry_id 1N1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.255 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 88.99 _cell.angle_beta 75.03 _cell.angle_gamma 82.54 _cell.entry_id 1N1D _cell.length_a 37.795 _cell.length_b 55.929 _cell.length_c 63.701 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1N1D _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,L,M 1 1 C,D,I,J,K,N,O 2 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 ? 3 F N N ? 3 H N N ? 3 I N N ? 3 K N N # _chem_comp.formula 'C12 H21 N3 O13 P2' _chem_comp.formula_weight 477.255 _chem_comp.id C2G _chem_comp.mon_nstd_flag . _chem_comp.name "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "CYTIDINE 5'-DIPHOSPHOGLYCEROL" # 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 C2G sing 70 n y N1 C6 C2G sing 71 n y N1 C1' C2G sing 72 n n C2 N3 C2G sing 73 n y C2 O2 C2G doub 74 n n N3 C4 C2G doub 75 n y C4 C5 C2G sing 76 n y C4 N4 C2G sing 77 n n C5 C6 C2G doub 78 n y C5 HC5 C2G sing 79 n n C6 HC6 C2G sing 80 n n N4 HN41 C2G sing 81 n n N4 HN42 C2G sing 82 n n C1' C2' C2G sing 83 n n C1' O4' C2G sing 84 n n C1' HC1 C2G sing 85 n n C2' O2' C2G sing 86 n n C2' C3' C2G sing 87 n n C2' HC2 C2G sing 88 n n O2' HO2 C2G sing 89 n n C3' C4' C2G sing 90 n n C3' O3' C2G sing 91 n n C3' HC3 C2G sing 92 n n C4' O4' C2G sing 93 n n C4' C5' C2G sing 94 n n C4' HC4 C2G sing 95 n n O3' HO3 C2G sing 96 n n C5' O5' C2G sing 97 n n C5' HC51 C2G sing 98 n n C5' HC52 C2G sing 99 n n O5' PA C2G sing 100 n n PA O1A C2G doub 101 n n PA O2A C2G sing 102 n n PA O3A C2G sing 103 n n O2A H2A C2G sing 104 n n O3A PB C2G sing 105 n n PB O1B C2G doub 106 n n PB O2B C2G sing 107 n n PB O3B C2G sing 108 n n O2B H2B C2G sing 109 n n O3B C3G C2G sing 110 n n O1G C1G C2G sing 111 n n O1G H1G C2G sing 112 n n C1G C2G C2G sing 113 n n C1G H1G1 C2G sing 114 n n C1G H1G2 C2G sing 115 n n C2G O2G C2G sing 116 n n C2G C3G C2G sing 117 n n C2G H2G C2G sing 118 n n O2G HOG C2G sing 119 n n C3G H3G1 C2G sing 120 n n C3G H3G2 C2G sing 121 n n # _atom_sites.entry_id 1N1D _atom_sites.fract_transf_matrix[1][1] 0.026459 _atom_sites.fract_transf_matrix[1][2] -0.003465 _atom_sites.fract_transf_matrix[1][3] -0.007133 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018032 _atom_sites.fract_transf_matrix[2][3] 0.0003 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016252 _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 SO4 A 1 701 701 SO4 SO4 . F 3 C2G A 1 130 130 C2G C2G . G 2 SO4 B 1 705 705 SO4 SO4 . H 3 C2G B 1 230 130 C2G C2G . I 3 C2G C 1 330 130 C2G C2G . J 2 SO4 D 1 702 702 SO4 SO4 . K 3 C2G D 1 430 130 C2G C2G . L 4 HOH A 1 712 712 HOH WAT . L 4 HOH A 2 720 720 HOH WAT . L 4 HOH A 3 721 721 HOH WAT . L 4 HOH A 4 726 726 HOH WAT . L 4 HOH A 5 729 729 HOH WAT . L 4 HOH A 6 733 733 HOH WAT . L 4 HOH A 7 737 737 HOH WAT . L 4 HOH A 8 744 744 HOH WAT . L 4 HOH A 9 745 745 HOH WAT . L 4 HOH A 10 747 747 HOH WAT . L 4 HOH A 11 750 750 HOH WAT . L 4 HOH A 12 757 757 HOH WAT . L 4 HOH A 13 769 769 HOH WAT . L 4 HOH A 14 772 772 HOH WAT . L 4 HOH A 15 774 774 HOH WAT . L 4 HOH A 16 783 783 HOH WAT . L 4 HOH A 17 784 784 HOH WAT . L 4 HOH A 18 785 785 HOH WAT . L 4 HOH A 19 788 788 HOH WAT . L 4 HOH A 20 791 791 HOH WAT . L 4 HOH A 21 793 793 HOH WAT . L 4 HOH A 22 796 796 HOH WAT . L 4 HOH A 23 800 800 HOH WAT . L 4 HOH A 24 804 804 HOH WAT . L 4 HOH A 25 807 807 HOH WAT . L 4 HOH A 26 814 814 HOH WAT . L 4 HOH A 27 816 816 HOH WAT . L 4 HOH A 28 822 822 HOH WAT . L 4 HOH A 29 824 824 HOH WAT . L 4 HOH A 30 831 831 HOH WAT . L 4 HOH A 31 836 836 HOH WAT . L 4 HOH A 32 843 843 HOH WAT . L 4 HOH A 33 845 845 HOH WAT . L 4 HOH A 34 846 846 HOH WAT . L 4 HOH A 35 850 850 HOH WAT . L 4 HOH A 36 854 854 HOH WAT . L 4 HOH A 37 855 855 HOH WAT . L 4 HOH A 38 858 858 HOH WAT . L 4 HOH A 39 859 859 HOH WAT . L 4 HOH A 40 861 861 HOH WAT . L 4 HOH A 41 862 862 HOH WAT . L 4 HOH A 42 873 873 HOH WAT . L 4 HOH A 43 874 874 HOH WAT . L 4 HOH A 44 876 876 HOH WAT . L 4 HOH A 45 882 882 HOH WAT . L 4 HOH A 46 884 884 HOH WAT . L 4 HOH A 47 906 906 HOH WAT . L 4 HOH A 48 907 907 HOH WAT . L 4 HOH A 49 908 908 HOH WAT . L 4 HOH A 50 909 909 HOH WAT . L 4 HOH A 51 910 910 HOH WAT . L 4 HOH A 52 911 911 HOH WAT . M 4 HOH B 1 704 704 HOH WAT . M 4 HOH B 2 707 707 HOH WAT . M 4 HOH B 3 711 711 HOH WAT . M 4 HOH B 4 713 713 HOH WAT . M 4 HOH B 5 714 714 HOH WAT . M 4 HOH B 6 716 716 HOH WAT . M 4 HOH B 7 717 717 HOH WAT . M 4 HOH B 8 725 725 HOH WAT . M 4 HOH B 9 738 738 HOH WAT . M 4 HOH B 10 740 740 HOH WAT . M 4 HOH B 11 748 748 HOH WAT . M 4 HOH B 12 759 759 HOH WAT . M 4 HOH B 13 761 761 HOH WAT . M 4 HOH B 14 763 763 HOH WAT . M 4 HOH B 15 766 766 HOH WAT . M 4 HOH B 16 771 771 HOH WAT . M 4 HOH B 17 773 773 HOH WAT . M 4 HOH B 18 777 777 HOH WAT . M 4 HOH B 19 780 780 HOH WAT . M 4 HOH B 20 781 781 HOH WAT . M 4 HOH B 21 789 789 HOH WAT . M 4 HOH B 22 790 790 HOH WAT . M 4 HOH B 23 794 794 HOH WAT . M 4 HOH B 24 798 798 HOH WAT . M 4 HOH B 25 801 801 HOH WAT . M 4 HOH B 26 819 819 HOH WAT . M 4 HOH B 27 823 823 HOH WAT . M 4 HOH B 28 837 837 HOH WAT . M 4 HOH B 29 864 864 HOH WAT . M 4 HOH B 30 865 865 HOH WAT . M 4 HOH B 31 867 867 HOH WAT . M 4 HOH B 32 869 869 HOH WAT . M 4 HOH B 33 870 870 HOH WAT . M 4 HOH B 34 885 885 HOH WAT . M 4 HOH B 35 893 893 HOH WAT . M 4 HOH B 36 912 912 HOH WAT . M 4 HOH B 37 913 913 HOH WAT . M 4 HOH B 38 914 914 HOH WAT . M 4 HOH B 39 915 915 HOH WAT . M 4 HOH B 40 916 916 HOH WAT . M 4 HOH B 41 917 917 HOH WAT . N 4 HOH C 1 708 708 HOH WAT . N 4 HOH C 2 710 710 HOH WAT . N 4 HOH C 3 728 728 HOH WAT . N 4 HOH C 4 742 742 HOH WAT . N 4 HOH C 5 756 756 HOH WAT . N 4 HOH C 6 760 760 HOH WAT . N 4 HOH C 7 775 775 HOH WAT . N 4 HOH C 8 776 776 HOH WAT . N 4 HOH C 9 809 809 HOH WAT . N 4 HOH C 10 817 817 HOH WAT . N 4 HOH C 11 830 830 HOH WAT . N 4 HOH C 12 835 835 HOH WAT . N 4 HOH C 13 839 839 HOH WAT . N 4 HOH C 14 840 840 HOH WAT . N 4 HOH C 15 848 848 HOH WAT . N 4 HOH C 16 849 849 HOH WAT . N 4 HOH C 17 851 851 HOH WAT . N 4 HOH C 18 853 853 HOH WAT . N 4 HOH C 19 856 856 HOH WAT . N 4 HOH C 20 857 857 HOH WAT . N 4 HOH C 21 866 866 HOH WAT . N 4 HOH C 22 871 871 HOH WAT . N 4 HOH C 23 877 877 HOH WAT . N 4 HOH C 24 889 889 HOH WAT . N 4 HOH C 25 890 890 HOH WAT . O 4 HOH D 1 703 703 HOH WAT . O 4 HOH D 2 715 715 HOH WAT . O 4 HOH D 3 719 719 HOH WAT . O 4 HOH D 4 722 722 HOH WAT . O 4 HOH D 5 723 723 HOH WAT . O 4 HOH D 6 724 724 HOH WAT . O 4 HOH D 7 730 730 HOH WAT . O 4 HOH D 8 731 731 HOH WAT . O 4 HOH D 9 732 732 HOH WAT . O 4 HOH D 10 734 734 HOH WAT . O 4 HOH D 11 736 736 HOH WAT . O 4 HOH D 12 739 739 HOH WAT . O 4 HOH D 13 741 741 HOH WAT . O 4 HOH D 14 749 749 HOH WAT . O 4 HOH D 15 752 752 HOH WAT . O 4 HOH D 16 754 754 HOH WAT . O 4 HOH D 17 755 755 HOH WAT . O 4 HOH D 18 762 762 HOH WAT . O 4 HOH D 19 764 764 HOH WAT . O 4 HOH D 20 770 770 HOH WAT . O 4 HOH D 21 778 778 HOH WAT . O 4 HOH D 22 779 779 HOH WAT . O 4 HOH D 23 782 782 HOH WAT . O 4 HOH D 24 786 786 HOH WAT . O 4 HOH D 25 787 787 HOH WAT . O 4 HOH D 26 792 792 HOH WAT . O 4 HOH D 27 795 795 HOH WAT . O 4 HOH D 28 797 797 HOH WAT . O 4 HOH D 29 799 799 HOH WAT . O 4 HOH D 30 808 808 HOH WAT . O 4 HOH D 31 811 811 HOH WAT . O 4 HOH D 32 812 812 HOH WAT . O 4 HOH D 33 813 813 HOH WAT . O 4 HOH D 34 820 820 HOH WAT . O 4 HOH D 35 821 821 HOH WAT . O 4 HOH D 36 826 826 HOH WAT . O 4 HOH D 37 827 827 HOH WAT . O 4 HOH D 38 838 838 HOH WAT . O 4 HOH D 39 841 841 HOH WAT . O 4 HOH D 40 844 844 HOH WAT . O 4 HOH D 41 847 847 HOH WAT . O 4 HOH D 42 852 852 HOH WAT . O 4 HOH D 43 863 863 HOH WAT . O 4 HOH D 44 868 868 HOH WAT . O 4 HOH D 45 879 879 HOH WAT . O 4 HOH D 46 881 881 HOH WAT . O 4 HOH D 47 883 883 HOH WAT . O 4 HOH D 48 886 886 HOH WAT . O 4 HOH D 49 887 887 HOH WAT . O 4 HOH D 50 888 888 HOH WAT . O 4 HOH D 51 892 892 HOH WAT . # 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 C2G . . . F 3 21.014 61.175 27.797 1 3.2 ? N1 C2G 130 A 1 HETATM 2 C C2 C2G . . . F 3 20.007 61.83 28.489 1 4.23 ? C2 C2G 130 A 1 HETATM 3 N N3 C2G . . . F 3 20.206 62.999 29.146 1 2.23 ? N3 C2G 130 A 1 HETATM 4 C C4 C2G . . . F 3 21.434 63.566 29.137 1 3.71 ? C4 C2G 130 A 1 HETATM 5 C C5 C2G . . . F 3 22.492 62.967 28.457 1 2.71 ? C5 C2G 130 A 1 HETATM 6 C C6 C2G . . . F 3 22.213 61.775 27.809 1 4.59 ? C6 C2G 130 A 1 HETATM 7 O O2 C2G . . . F 3 18.848 61.384 28.549 1 2.59 ? O2 C2G 130 A 1 HETATM 8 N N4 C2G . . . F 3 21.587 64.706 29.798 1 1.16 ? N4 C2G 130 A 1 HETATM 9 C C1' C2G . . . F 3 20.782 59.853 27.15 1 6 ? C1' C2G 130 A 1 HETATM 10 C C2' C2G . . . F 3 20.825 59.936 25.666 1 6.88 ? C2' C2G 130 A 1 HETATM 11 O O2' C2G . . . F 3 19.623 60.52 25.204 1 9.82 ? O2' C2G 130 A 1 HETATM 12 C C3' C2G . . . F 3 21.037 58.503 25.27 1 7.04 ? C3' C2G 130 A 1 HETATM 13 C C4' C2G . . . F 3 21.801 57.909 26.461 1 8.85 ? C4' C2G 130 A 1 HETATM 14 O O4' C2G . . . F 3 21.863 58.988 27.405 1 6.67 ? O4' C2G 130 A 1 HETATM 15 O O3' C2G . . . F 3 19.854 57.734 25.132 1 8.5 ? O3' C2G 130 A 1 HETATM 16 C C5' C2G . . . F 3 23.117 57.6 25.781 1 10.05 ? C5' C2G 130 A 1 HETATM 17 O O5' C2G . . . F 3 24.178 58.492 26.087 1 9.51 ? O5' C2G 130 A 1 HETATM 18 P PA C2G . . . F 3 25.4 58.6 24.954 1 8.71 ? PA C2G 130 A 1 HETATM 19 O O1A C2G . . . F 3 26.688 58.248 25.767 1 9.24 ? O1A C2G 130 A 1 HETATM 20 O O2A C2G . . . F 3 25.465 60.07 24.426 1 10.01 ? O2A C2G 130 A 1 HETATM 21 O O3A C2G . . . F 3 25.223 57.448 23.798 1 8.44 ? O3A C2G 130 A 1 HETATM 22 P PB C2G . . . F 3 24.806 57.955 22.28 1 8.96 ? PB C2G 130 A 1 HETATM 23 O O1B C2G . . . F 3 26.077 58.574 21.6 1 9.35 ? O1B C2G 130 A 1 HETATM 24 O O2B C2G . . . F 3 23.605 58.968 22.352 1 9.11 ? O2B C2G 130 A 1 HETATM 25 O O3B C2G . . . F 3 24.444 56.563 21.462 1 11.53 ? O3B C2G 130 A 1 HETATM 26 O O1G C2G . . . F 3 22.696 53.684 18.386 1 6.16 ? O1G C2G 130 A 1 HETATM 27 C C1G C2G . . . F 3 22.668 54.92 19.109 1 9.28 ? C1G C2G 130 A 1 HETATM 28 C C2G C2G . . . F 3 24.108 55.221 19.372 1 10.14 ? C2G C2G 130 A 1 HETATM 29 O O2G C2G . . . F 3 24.721 54.194 20.176 1 9.84 ? O2G C2G 130 A 1 HETATM 30 C C3G C2G . . . F 3 24.328 56.56 20.041 1 11.27 ? C3G C2G 130 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 30 #