data_1VPA # _model_server_result.job_id pRpSoUmOXtccz7VmDbFtug _model_server_result.datetime_utc '2024-10-19 00:58:21' _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 1vpa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":500}' # _entry.id 1VPA # _exptl.entry_id 1VPA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _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 _cell.angle_gamma 120 _cell.entry_id 1VPA _cell.length_a 144.23 _cell.length_b 144.23 _cell.length_c 53.724 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VPA _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 D O2A CTP . A CTP 500 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc2 D O3G CTP . A CTP 500 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc3 D O1B CTP . A CTP 500 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc4 C MG MG . A MG 600 1_555 I O HOH . A HOH 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc5 G O2A CTP . B CTP 500 1_555 F MG MG . B MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc6 G O1B CTP . B CTP 500 1_555 F MG MG . B MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 G O3G CTP . B CTP 500 1_555 F MG MG . B MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-TRIPHOSPHATE" _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 N1 C2 CTP sing 77 n n N1 C6 CTP sing 78 n n N1 C1' CTP sing 79 n n C2 N3 CTP sing 80 n n C2 O2 CTP doub 81 n n N3 C4 CTP doub 82 n n C4 C5 CTP sing 83 n n C4 N4 CTP sing 84 n n C5 C6 CTP doub 85 n n C5 H5 CTP sing 86 n n C6 H6 CTP sing 87 n n N4 HN41 CTP sing 88 n n N4 HN42 CTP sing 89 n n C1' C2' CTP sing 90 n n C1' O4' CTP sing 91 n n C1' H1' CTP sing 92 n n C2' O2' CTP sing 93 n n C2' C3' CTP sing 94 n n C2' H2' CTP sing 95 n n O2' HO2' CTP sing 96 n n C3' C4' CTP sing 97 n n C3' O3' CTP sing 98 n n C3' H3' CTP sing 99 n n C4' O4' CTP sing 100 n n C4' C5' CTP sing 101 n n C4' H4' CTP sing 102 n n O3' HO3' CTP sing 103 n n C5' O5' CTP sing 104 n n C5' "H5'1" CTP sing 105 n n C5' "H5'2" CTP sing 106 n n O5' PA CTP sing 107 n n PA O1A CTP doub 108 n n PA O2A CTP sing 109 n n PA O3A CTP sing 110 n n O2A HOA2 CTP sing 111 n n O3A PB CTP sing 112 n n PB O1B CTP doub 113 n n PB O2B CTP sing 114 n n PB O3B CTP sing 115 n n O2B HOB2 CTP sing 116 n n O3B PG CTP sing 117 n n PG O1G CTP doub 118 n n PG O2G CTP sing 119 n n PG O3G CTP sing 120 n n O2G HOG2 CTP sing 121 n n O3G HOG3 CTP sing 122 n n # _atom_sites.entry_id 1VPA _atom_sites.fract_transf_matrix[1][1] 0.006933 _atom_sites.fract_transf_matrix[1][2] 0.004003 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008006 _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] 0.018614 _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 C 2 MG A 1 600 600 MG MG . D 3 CTP A 1 500 500 CTP CTP . E 4 ACY A 1 700 700 ACY ACY . F 2 MG B 1 600 600 MG MG . G 3 CTP B 1 500 500 CTP CTP . H 4 ACY B 1 700 700 ACY ACY . I 5 HOH A 1 701 1 HOH HOH . I 5 HOH A 2 702 2 HOH HOH . I 5 HOH A 3 703 5 HOH HOH . I 5 HOH A 4 704 6 HOH HOH . I 5 HOH A 5 705 7 HOH HOH . I 5 HOH A 6 706 15 HOH HOH . I 5 HOH A 7 707 17 HOH HOH . I 5 HOH A 8 708 18 HOH HOH . I 5 HOH A 9 709 19 HOH HOH . I 5 HOH A 10 710 21 HOH HOH . I 5 HOH A 11 711 22 HOH HOH . I 5 HOH A 12 712 23 HOH HOH . I 5 HOH A 13 713 24 HOH HOH . I 5 HOH A 14 714 25 HOH HOH . I 5 HOH A 15 715 26 HOH HOH . I 5 HOH A 16 716 27 HOH HOH . I 5 HOH A 17 717 28 HOH HOH . I 5 HOH A 18 718 30 HOH HOH . I 5 HOH A 19 719 31 HOH HOH . I 5 HOH A 20 720 32 HOH HOH . I 5 HOH A 21 721 33 HOH HOH . I 5 HOH A 22 722 37 HOH HOH . I 5 HOH A 23 723 39 HOH HOH . I 5 HOH A 24 724 40 HOH HOH . I 5 HOH A 25 725 41 HOH HOH . I 5 HOH A 26 726 42 HOH HOH . I 5 HOH A 27 727 43 HOH HOH . I 5 HOH A 28 728 47 HOH HOH . I 5 HOH A 29 729 49 HOH HOH . I 5 HOH A 30 730 51 HOH HOH . I 5 HOH A 31 731 54 HOH HOH . I 5 HOH A 32 732 55 HOH HOH . I 5 HOH A 33 733 56 HOH HOH . I 5 HOH A 34 734 57 HOH HOH . I 5 HOH A 35 735 58 HOH HOH . I 5 HOH A 36 736 61 HOH HOH . I 5 HOH A 37 737 63 HOH HOH . I 5 HOH A 38 738 64 HOH HOH . I 5 HOH A 39 739 67 HOH HOH . I 5 HOH A 40 740 68 HOH HOH . I 5 HOH A 41 741 71 HOH HOH . I 5 HOH A 42 742 72 HOH HOH . I 5 HOH A 43 743 74 HOH HOH . I 5 HOH A 44 744 76 HOH HOH . I 5 HOH A 45 745 78 HOH HOH . I 5 HOH A 46 746 79 HOH HOH . I 5 HOH A 47 747 81 HOH HOH . I 5 HOH A 48 748 82 HOH HOH . I 5 HOH A 49 749 83 HOH HOH . I 5 HOH A 50 750 86 HOH HOH . I 5 HOH A 51 751 87 HOH HOH . I 5 HOH A 52 752 88 HOH HOH . I 5 HOH A 53 753 90 HOH HOH . I 5 HOH A 54 754 93 HOH HOH . I 5 HOH A 55 755 94 HOH HOH . I 5 HOH A 56 756 95 HOH HOH . I 5 HOH A 57 757 99 HOH HOH . I 5 HOH A 58 758 100 HOH HOH . I 5 HOH A 59 759 101 HOH HOH . I 5 HOH A 60 760 102 HOH HOH . I 5 HOH A 61 761 104 HOH HOH . I 5 HOH A 62 762 106 HOH HOH . I 5 HOH A 63 763 108 HOH HOH . I 5 HOH A 64 764 110 HOH HOH . I 5 HOH A 65 765 111 HOH HOH . I 5 HOH A 66 766 112 HOH HOH . I 5 HOH A 67 767 113 HOH HOH . I 5 HOH A 68 768 114 HOH HOH . I 5 HOH A 69 769 115 HOH HOH . I 5 HOH A 70 770 116 HOH HOH . J 5 HOH B 1 701 3 HOH HOH . J 5 HOH B 2 702 4 HOH HOH . J 5 HOH B 3 703 8 HOH HOH . J 5 HOH B 4 704 9 HOH HOH . J 5 HOH B 5 705 10 HOH HOH . J 5 HOH B 6 706 11 HOH HOH . J 5 HOH B 7 707 12 HOH HOH . J 5 HOH B 8 708 13 HOH HOH . J 5 HOH B 9 709 14 HOH HOH . J 5 HOH B 10 710 16 HOH HOH . J 5 HOH B 11 711 20 HOH HOH . J 5 HOH B 12 712 29 HOH HOH . J 5 HOH B 13 713 34 HOH HOH . J 5 HOH B 14 714 35 HOH HOH . J 5 HOH B 15 715 36 HOH HOH . J 5 HOH B 16 716 38 HOH HOH . J 5 HOH B 17 717 44 HOH HOH . J 5 HOH B 18 718 45 HOH HOH . J 5 HOH B 19 719 46 HOH HOH . J 5 HOH B 20 720 48 HOH HOH . J 5 HOH B 21 721 50 HOH HOH . J 5 HOH B 22 722 52 HOH HOH . J 5 HOH B 23 723 53 HOH HOH . J 5 HOH B 24 724 59 HOH HOH . J 5 HOH B 25 725 60 HOH HOH . J 5 HOH B 26 726 62 HOH HOH . J 5 HOH B 27 727 65 HOH HOH . J 5 HOH B 28 728 66 HOH HOH . J 5 HOH B 29 729 69 HOH HOH . J 5 HOH B 30 730 70 HOH HOH . J 5 HOH B 31 731 73 HOH HOH . J 5 HOH B 32 732 75 HOH HOH . J 5 HOH B 33 733 77 HOH HOH . J 5 HOH B 34 734 80 HOH HOH . J 5 HOH B 35 735 84 HOH HOH . J 5 HOH B 36 736 85 HOH HOH . J 5 HOH B 37 737 89 HOH HOH . J 5 HOH B 38 738 91 HOH HOH . J 5 HOH B 39 739 92 HOH HOH . J 5 HOH B 40 740 96 HOH HOH . J 5 HOH B 41 741 97 HOH HOH . J 5 HOH B 42 742 98 HOH HOH . J 5 HOH B 43 743 103 HOH HOH . J 5 HOH B 44 744 105 HOH HOH . J 5 HOH B 45 745 107 HOH HOH . J 5 HOH B 46 746 109 HOH HOH . J 5 HOH B 47 747 117 HOH HOH . J 5 HOH B 48 748 118 HOH HOH . J 5 HOH B 49 749 119 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 N N1 CTP . . . G 3 -40.246 96.369 0.831 1 35.07 ? N1 CTP 500 B 1 HETATM 2 C C2 CTP . . . G 3 -41.019 95.28 1.237 1 34.6 ? C2 CTP 500 B 1 HETATM 3 N N3 CTP . . . G 3 -42.317 95.156 0.8 1 33.71 ? N3 CTP 500 B 1 HETATM 4 C C4 CTP . . . G 3 -42.762 95.968 -0.213 1 34.84 ? C4 CTP 500 B 1 HETATM 5 C C5 CTP . . . G 3 -41.917 96.956 -0.738 1 34.12 ? C5 CTP 500 B 1 HETATM 6 C C6 CTP . . . G 3 -40.745 97.272 -0.068 1 33.73 ? C6 CTP 500 B 1 HETATM 7 O O2 CTP . . . G 3 -40.563 94.403 1.973 1 33.89 ? O2 CTP 500 B 1 HETATM 8 N N4 CTP . . . G 3 -43.998 95.788 -0.676 1 35.51 ? N4 CTP 500 B 1 HETATM 9 C C1' CTP . . . G 3 -38.836 96.442 1.266 1 36.34 ? C1' CTP 500 B 1 HETATM 10 C C2' CTP . . . G 3 -37.871 96.002 0.159 1 37.55 ? C2' CTP 500 B 1 HETATM 11 O O2' CTP . . . G 3 -37.694 94.591 0.097 1 36.97 ? O2' CTP 500 B 1 HETATM 12 C C3' CTP . . . G 3 -36.589 96.768 0.498 1 37.74 ? C3' CTP 500 B 1 HETATM 13 C C4' CTP . . . G 3 -37.053 97.865 1.454 1 37.41 ? C4' CTP 500 B 1 HETATM 14 O O4' CTP . . . G 3 -38.454 97.752 1.619 1 36.45 ? O4' CTP 500 B 1 HETATM 15 O O3' CTP . . . G 3 -35.594 95.992 1.145 1 36.19 ? O3' CTP 500 B 1 HETATM 16 C C5' CTP . . . G 3 -36.647 99.25 0.964 1 38.41 ? C5' CTP 500 B 1 HETATM 17 O O5' CTP . . . G 3 -37.533 99.748 -0.013 1 39.14 ? O5' CTP 500 B 1 HETATM 18 P PA CTP . . . G 3 -37.139 99.947 -1.574 1 39.58 ? PA CTP 500 B 1 HETATM 19 O O1A CTP . . . G 3 -35.676 100.295 -1.753 1 37.24 ? O1A CTP 500 B 1 HETATM 20 O O2A CTP . . . G 3 -38.031 101.051 -2.113 1 39.61 ? O2A CTP 500 B 1 HETATM 21 O O3A CTP . . . G 3 -37.443 98.493 -2.267 1 38.66 ? O3A CTP 500 B 1 HETATM 22 P PB CTP . . . G 3 -38.334 98.262 -3.617 1 36.91 ? PB CTP 500 B 1 HETATM 23 O O1B CTP . . . G 3 -39.757 98.661 -3.307 1 38.56 ? O1B CTP 500 B 1 HETATM 24 O O2B CTP . . . G 3 -38.23 96.829 -4.099 1 36.58 ? O2B CTP 500 B 1 HETATM 25 O O3B CTP . . . G 3 -37.694 99.237 -4.747 1 38.5 ? O3B CTP 500 B 1 HETATM 26 P PG CTP . . . G 3 -38.536 99.975 -5.92 1 38.35 ? PG CTP 500 B 1 HETATM 27 O O1G CTP . . . G 3 -39.636 99.009 -6.349 1 39.12 ? O1G CTP 500 B 1 HETATM 28 O O2G CTP . . . G 3 -37.695 100.247 -7.14 1 37.77 ? O2G CTP 500 B 1 HETATM 29 O O3G CTP . . . G 3 -39.024 101.301 -5.385 1 33.83 ? O3G CTP 500 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #