data_4YHJ # _model_server_result.job_id NoaOzd4WAljjySGwc9JV0A _model_server_result.datetime_utc '2024-11-05 03:56:42' _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 4yhj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4YHJ # _exptl.entry_id 4YHJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 426.216 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'AMP PHOSPHORAMIDATE' _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 4YHJ _cell.length_a 104.838 _cell.length_b 104.838 _cell.length_c 221.838 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YHJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H16 N6 O9 P2' _chem_comp.formula_weight 426.216 _chem_comp.id AN2 _chem_comp.mon_nstd_flag . _chem_comp.name 'AMP PHOSPHORAMIDATE' _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 N3B PB AN2 sing 13 n n N3B H3B1 AN2 sing 14 n n N3B H3B2 AN2 sing 15 n n PB O2B AN2 sing 16 n n PB O1B AN2 doub 17 n n PB O3A AN2 sing 18 n n O2B HO2B AN2 sing 19 n n O3A PA AN2 sing 20 n n PA O1A AN2 doub 21 n n PA O2A AN2 sing 22 n n PA O5' AN2 sing 23 n n O2A HO2A AN2 sing 24 n n O5' C5' AN2 sing 25 n n C5' C4' AN2 sing 26 n n C5' "H5'1" AN2 sing 27 n n C5' "H5'2" AN2 sing 28 n n C4' O4' AN2 sing 29 n n C4' C3' AN2 sing 30 n n C4' H4' AN2 sing 31 n n O4' C1' AN2 sing 32 n n C3' O3' AN2 sing 33 n n C3' C2' AN2 sing 34 n n C3' H3' AN2 sing 35 n n O3' HA AN2 sing 36 n n C2' O2' AN2 sing 37 n n C2' C1' AN2 sing 38 n n C2' H2' AN2 sing 39 n n O2' HB AN2 sing 40 n n C1' N9 AN2 sing 41 n n C1' H1' AN2 sing 42 n n N9 C8 AN2 sing 43 n y N9 C4 AN2 sing 44 n y C8 N7 AN2 doub 45 n y C8 H8 AN2 sing 46 n n N7 C5 AN2 sing 47 n y C5 C4 AN2 doub 48 n y C5 C6 AN2 sing 49 n y C4 N3 AN2 sing 50 n y N3 C2 AN2 doub 51 n y C2 N1 AN2 sing 52 n y C2 H2 AN2 sing 53 n n N1 C6 AN2 doub 54 n y C6 N6 AN2 sing 55 n n N6 H6N1 AN2 sing 56 n n N6 H6N2 AN2 sing 57 n n # _atom_sites.entry_id 4YHJ _atom_sites.fract_transf_matrix[1][1] 0.009539 _atom_sites.fract_transf_matrix[1][2] 0.005507 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011014 _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] 0.004508 _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 AN2 A 1 601 1 AN2 AN2 . D 2 AN2 B 1 601 2 AN2 AN2 . E 3 HOH A 1 701 16 HOH HOH . E 3 HOH A 2 702 37 HOH HOH . E 3 HOH A 3 703 34 HOH HOH . E 3 HOH A 4 704 89 HOH HOH . E 3 HOH A 5 705 96 HOH HOH . E 3 HOH A 6 706 45 HOH HOH . E 3 HOH A 7 707 54 HOH HOH . E 3 HOH A 8 708 4 HOH HOH . E 3 HOH A 9 709 5 HOH HOH . E 3 HOH A 10 710 7 HOH HOH . E 3 HOH A 11 711 8 HOH HOH . E 3 HOH A 12 712 9 HOH HOH . E 3 HOH A 13 713 10 HOH HOH . E 3 HOH A 14 714 13 HOH HOH . E 3 HOH A 15 715 14 HOH HOH . E 3 HOH A 16 716 17 HOH HOH . E 3 HOH A 17 717 18 HOH HOH . E 3 HOH A 18 718 24 HOH HOH . E 3 HOH A 19 719 26 HOH HOH . E 3 HOH A 20 720 28 HOH HOH . E 3 HOH A 21 721 33 HOH HOH . E 3 HOH A 22 722 38 HOH HOH . E 3 HOH A 23 723 39 HOH HOH . E 3 HOH A 24 724 41 HOH HOH . E 3 HOH A 25 725 43 HOH HOH . E 3 HOH A 26 726 44 HOH HOH . E 3 HOH A 27 727 46 HOH HOH . E 3 HOH A 28 728 47 HOH HOH . E 3 HOH A 29 729 48 HOH HOH . E 3 HOH A 30 730 49 HOH HOH . E 3 HOH A 31 731 55 HOH HOH . E 3 HOH A 32 732 56 HOH HOH . E 3 HOH A 33 733 57 HOH HOH . E 3 HOH A 34 734 60 HOH HOH . E 3 HOH A 35 735 63 HOH HOH . E 3 HOH A 36 736 65 HOH HOH . E 3 HOH A 37 737 66 HOH HOH . E 3 HOH A 38 738 67 HOH HOH . E 3 HOH A 39 739 68 HOH HOH . E 3 HOH A 40 740 70 HOH HOH . E 3 HOH A 41 741 71 HOH HOH . E 3 HOH A 42 742 76 HOH HOH . E 3 HOH A 43 743 78 HOH HOH . E 3 HOH A 44 744 83 HOH HOH . E 3 HOH A 45 745 87 HOH HOH . E 3 HOH A 46 746 91 HOH HOH . E 3 HOH A 47 747 92 HOH HOH . E 3 HOH A 48 748 93 HOH HOH . E 3 HOH A 49 749 94 HOH HOH . E 3 HOH A 50 750 97 HOH HOH . E 3 HOH A 51 751 100 HOH HOH . E 3 HOH A 52 752 104 HOH HOH . E 3 HOH A 53 753 105 HOH HOH . E 3 HOH A 54 754 106 HOH HOH . E 3 HOH A 55 755 109 HOH HOH . E 3 HOH A 56 756 113 HOH HOH . E 3 HOH A 57 757 117 HOH HOH . E 3 HOH A 58 758 119 HOH HOH . E 3 HOH A 59 759 120 HOH HOH . E 3 HOH A 60 760 121 HOH HOH . E 3 HOH A 61 761 122 HOH HOH . E 3 HOH A 62 762 123 HOH HOH . F 3 HOH B 1 701 3 HOH HOH . F 3 HOH B 2 702 112 HOH HOH . F 3 HOH B 3 703 72 HOH HOH . F 3 HOH B 4 704 75 HOH HOH . F 3 HOH B 5 705 1 HOH HOH . F 3 HOH B 6 706 2 HOH HOH . F 3 HOH B 7 707 6 HOH HOH . F 3 HOH B 8 708 11 HOH HOH . F 3 HOH B 9 709 12 HOH HOH . F 3 HOH B 10 710 15 HOH HOH . F 3 HOH B 11 711 19 HOH HOH . F 3 HOH B 12 712 20 HOH HOH . F 3 HOH B 13 713 21 HOH HOH . F 3 HOH B 14 714 22 HOH HOH . F 3 HOH B 15 715 23 HOH HOH . F 3 HOH B 16 716 25 HOH HOH . F 3 HOH B 17 717 27 HOH HOH . F 3 HOH B 18 718 29 HOH HOH . F 3 HOH B 19 719 30 HOH HOH . F 3 HOH B 20 720 31 HOH HOH . F 3 HOH B 21 721 32 HOH HOH . F 3 HOH B 22 722 35 HOH HOH . F 3 HOH B 23 723 36 HOH HOH . F 3 HOH B 24 724 40 HOH HOH . F 3 HOH B 25 725 42 HOH HOH . F 3 HOH B 26 726 50 HOH HOH . F 3 HOH B 27 727 51 HOH HOH . F 3 HOH B 28 728 52 HOH HOH . F 3 HOH B 29 729 53 HOH HOH . F 3 HOH B 30 730 58 HOH HOH . F 3 HOH B 31 731 59 HOH HOH . F 3 HOH B 32 732 61 HOH HOH . F 3 HOH B 33 733 62 HOH HOH . F 3 HOH B 34 734 64 HOH HOH . F 3 HOH B 35 735 69 HOH HOH . F 3 HOH B 36 736 73 HOH HOH . F 3 HOH B 37 737 74 HOH HOH . F 3 HOH B 38 738 77 HOH HOH . F 3 HOH B 39 739 79 HOH HOH . F 3 HOH B 40 740 80 HOH HOH . F 3 HOH B 41 741 81 HOH HOH . F 3 HOH B 42 742 82 HOH HOH . F 3 HOH B 43 743 84 HOH HOH . F 3 HOH B 44 744 85 HOH HOH . F 3 HOH B 45 745 86 HOH HOH . F 3 HOH B 46 746 88 HOH HOH . F 3 HOH B 47 747 90 HOH HOH . F 3 HOH B 48 748 95 HOH HOH . F 3 HOH B 49 749 98 HOH HOH . F 3 HOH B 50 750 99 HOH HOH . F 3 HOH B 51 751 101 HOH HOH . F 3 HOH B 52 752 102 HOH HOH . F 3 HOH B 53 753 103 HOH HOH . F 3 HOH B 54 754 107 HOH HOH . F 3 HOH B 55 755 108 HOH HOH . F 3 HOH B 56 756 110 HOH HOH . F 3 HOH B 57 757 111 HOH HOH . F 3 HOH B 58 758 114 HOH HOH . F 3 HOH B 59 759 115 HOH HOH . F 3 HOH B 60 760 116 HOH HOH . F 3 HOH B 61 761 118 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 N3B AN2 . . . D 2 20.202 26.544 73.889 1 102.78 ? N3B AN2 601 B 1 HETATM 2 P PB AN2 . . . D 2 21.231 27.628 73.268 1 104.36 ? PB AN2 601 B 1 HETATM 3 O O2B AN2 . . . D 2 22.597 27.157 73.588 1 105.5 ? O2B AN2 601 B 1 HETATM 4 O O1B AN2 . . . D 2 21.133 27.686 71.652 1 103.89 ? O1B AN2 601 B 1 HETATM 5 O O3A AN2 . . . D 2 21.066 29.137 73.876 1 100.11 ? O3A AN2 601 B 1 HETATM 6 P PA AN2 . . . D 2 19.579 29.649 74.298 1 92.93 ? PA AN2 601 B 1 HETATM 7 O O1A AN2 . . . D 2 18.86 30.201 73.124 1 92.23 ? O1A AN2 601 B 1 HETATM 8 O O2A AN2 . . . D 2 18.662 28.504 74.98 1 93.96 ? O2A AN2 601 B 1 HETATM 9 O O5' AN2 . . . D 2 19.809 30.844 75.352 1 84.63 ? O5' AN2 601 B 1 HETATM 10 C C5' AN2 . . . D 2 20.377 30.301 76.546 1 75.9 ? C5' AN2 601 B 1 HETATM 11 C C4' AN2 . . . D 2 19.5 30.717 77.722 1 68.59 ? C4' AN2 601 B 1 HETATM 12 O O4' AN2 . . . D 2 19.298 32.152 77.723 1 64.04 ? O4' AN2 601 B 1 HETATM 13 C C3' AN2 . . . D 2 18.085 30.138 77.551 1 67.94 ? C3' AN2 601 B 1 HETATM 14 O O3' AN2 . . . D 2 18.017 28.772 77.969 1 69.46 ? O3' AN2 601 B 1 HETATM 15 C C2' AN2 . . . D 2 17.278 31.092 78.451 1 66.5 ? C2' AN2 601 B 1 HETATM 16 O O2' AN2 . . . D 2 17.539 30.814 79.828 1 70.47 ? O2' AN2 601 B 1 HETATM 17 C C1' AN2 . . . D 2 17.924 32.448 78.1 1 61.86 ? C1' AN2 601 B 1 HETATM 18 N N9 AN2 . . . D 2 17.162 33.152 77.051 1 54.93 ? N9 AN2 601 B 1 HETATM 19 C C8 AN2 . . . D 2 17.273 32.953 75.698 1 53.17 ? C8 AN2 601 B 1 HETATM 20 N N7 AN2 . . . D 2 16.448 33.733 75.055 1 52.07 ? N7 AN2 601 B 1 HETATM 21 C C5 AN2 . . . D 2 15.745 34.495 75.951 1 49.06 ? C5 AN2 601 B 1 HETATM 22 C C4 AN2 . . . D 2 16.201 34.125 77.24 1 48.71 ? C4 AN2 601 B 1 HETATM 23 N N3 AN2 . . . D 2 15.66 34.733 78.297 1 44.9 ? N3 AN2 601 B 1 HETATM 24 C C2 AN2 . . . D 2 14.719 35.666 78.169 1 43.22 ? C2 AN2 601 B 1 HETATM 25 N N1 AN2 . . . D 2 14.257 36.043 76.986 1 43.48 ? N1 AN2 601 B 1 HETATM 26 C C6 AN2 . . . D 2 14.732 35.491 75.861 1 42.63 ? C6 AN2 601 B 1 HETATM 27 N N6 AN2 . . . D 2 14.217 35.869 74.643 1 35.75 ? N6 AN2 601 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 207 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #