data_4DCV # _model_server_result.job_id ks8gp4HGOa4cQ3brRtBQCA _model_server_result.datetime_utc '2025-01-02 19:38:46' _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 4dcv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 4DCV # _exptl.entry_id 4DCV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 90 _cell.entry_id 4DCV _cell.length_a 62.493 _cell.length_b 66.191 _cell.length_c 111.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DCV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' _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 PG O1G GCP doub 83 n n PG O2G GCP sing 84 n n PG O3G GCP sing 85 n n PG C3B GCP sing 86 n n O2G HOG2 GCP sing 87 n n O3G HOG3 GCP sing 88 n n C3B PB GCP sing 89 n n C3B H3B1 GCP sing 90 n n C3B H3B2 GCP sing 91 n n PB O1B GCP doub 92 n n PB O2B GCP sing 93 n n PB O3A GCP sing 94 n n O2B HOB2 GCP sing 95 n n O3A PA GCP sing 96 n n PA O1A GCP doub 97 n n PA O2A GCP sing 98 n n PA O5' GCP sing 99 n n O2A HOA2 GCP sing 100 n n O5' C5' GCP sing 101 n n C5' C4' GCP sing 102 n n C5' "H5'2" GCP sing 103 n n C5' "H5'1" GCP sing 104 n n C4' O4' GCP sing 105 n n C4' C3' GCP sing 106 n n C4' H4' GCP sing 107 n n O4' C1' GCP sing 108 n n C3' O3' GCP sing 109 n n C3' C2' GCP sing 110 n n C3' H3' GCP sing 111 n n O3' HO3' GCP sing 112 n n C2' O2' GCP sing 113 n n C2' C1' GCP sing 114 n n C2' H2' GCP sing 115 n n O2' HO2' GCP sing 116 n n C1' N9 GCP sing 117 n n C1' H1' GCP sing 118 n n N9 C8 GCP sing 119 n y N9 C4 GCP sing 120 n y C8 N7 GCP doub 121 n y C8 H8 GCP sing 122 n n N7 C5 GCP sing 123 n y C5 C6 GCP sing 124 n y C5 C4 GCP doub 125 n y C6 O6 GCP doub 126 n n C6 N1 GCP sing 127 n y N1 C2 GCP sing 128 n y N1 HN1 GCP sing 129 n n C2 N2 GCP sing 130 n n C2 N3 GCP doub 131 n y N2 HN21 GCP sing 132 n n N2 HN22 GCP sing 133 n n N3 C4 GCP sing 134 n y # _atom_sites.entry_id 4DCV _atom_sites.fract_transf_matrix[1][1] 0.016002 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015108 _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] 0.008949 _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 GCP A 1 500 500 GCP GCP . C 3 HOH A 1 601 1 HOH HOH . C 3 HOH A 2 602 2 HOH HOH . C 3 HOH A 3 603 3 HOH HOH . C 3 HOH A 4 604 4 HOH HOH . C 3 HOH A 5 605 5 HOH HOH . C 3 HOH A 6 606 6 HOH HOH . C 3 HOH A 7 607 7 HOH HOH . C 3 HOH A 8 608 8 HOH HOH . C 3 HOH A 9 609 9 HOH HOH . C 3 HOH A 10 610 10 HOH HOH . C 3 HOH A 11 611 11 HOH HOH . C 3 HOH A 12 612 12 HOH HOH . C 3 HOH A 13 613 13 HOH HOH . C 3 HOH A 14 614 14 HOH HOH . C 3 HOH A 15 615 15 HOH HOH . C 3 HOH A 16 616 16 HOH HOH . C 3 HOH A 17 617 17 HOH HOH . C 3 HOH A 18 618 18 HOH HOH . C 3 HOH A 19 619 19 HOH HOH . C 3 HOH A 20 620 20 HOH HOH . C 3 HOH A 21 621 21 HOH HOH . C 3 HOH A 22 622 22 HOH HOH . C 3 HOH A 23 623 23 HOH HOH . C 3 HOH A 24 624 24 HOH HOH . C 3 HOH A 25 625 25 HOH HOH . C 3 HOH A 26 626 26 HOH HOH . C 3 HOH A 27 627 27 HOH HOH . C 3 HOH A 28 628 28 HOH HOH . C 3 HOH A 29 629 29 HOH HOH . C 3 HOH A 30 630 30 HOH HOH . C 3 HOH A 31 631 31 HOH HOH . C 3 HOH A 32 632 32 HOH HOH . C 3 HOH A 33 633 33 HOH HOH . C 3 HOH A 34 634 34 HOH HOH . C 3 HOH A 35 635 35 HOH HOH . C 3 HOH A 36 636 36 HOH HOH . C 3 HOH A 37 637 37 HOH HOH . C 3 HOH A 38 638 38 HOH HOH . C 3 HOH A 39 639 39 HOH HOH . C 3 HOH A 40 640 40 HOH HOH . C 3 HOH A 41 641 41 HOH HOH . C 3 HOH A 42 642 42 HOH HOH . C 3 HOH A 43 643 43 HOH HOH . C 3 HOH A 44 644 44 HOH HOH . C 3 HOH A 45 645 45 HOH HOH . C 3 HOH A 46 646 46 HOH HOH . C 3 HOH A 47 647 47 HOH HOH . C 3 HOH A 48 648 48 HOH HOH . C 3 HOH A 49 649 49 HOH HOH . C 3 HOH A 50 650 50 HOH HOH . C 3 HOH A 51 651 51 HOH HOH . C 3 HOH A 52 652 52 HOH HOH . C 3 HOH A 53 653 53 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 GCP . . . B 2 -14.452 -6.993 -32.892 1 47.98 ? PG GCP 500 A 1 HETATM 2 O O1G GCP . . . B 2 -13.744 -6.647 -34.192 1 42.49 ? O1G GCP 500 A 1 HETATM 3 O O2G GCP . . . B 2 -13.541 -7.558 -31.815 1 47.21 ? O2G GCP 500 A 1 HETATM 4 O O3G GCP . . . B 2 -15.348 -5.894 -32.353 1 48.94 ? O3G GCP 500 A 1 HETATM 5 C C3B GCP . . . B 2 -15.587 -8.357 -33.309 1 38.58 ? C3B GCP 500 A 1 HETATM 6 P PB GCP . . . B 2 -14.754 -9.946 -33.617 1 36.02 ? PB GCP 500 A 1 HETATM 7 O O1B GCP . . . B 2 -13.547 -9.698 -34.478 1 31.97 ? O1B GCP 500 A 1 HETATM 8 O O2B GCP . . . B 2 -14.595 -10.712 -32.313 1 32.01 ? O2B GCP 500 A 1 HETATM 9 O O3A GCP . . . B 2 -15.775 -10.819 -34.491 1 35.31 ? O3A GCP 500 A 1 HETATM 10 P PA GCP . . . B 2 -17.093 -11.415 -33.777 1 33.44 ? PA GCP 500 A 1 HETATM 11 O O1A GCP . . . B 2 -16.703 -12.625 -32.965 1 36.03 ? O1A GCP 500 A 1 HETATM 12 O O2A GCP . . . B 2 -17.773 -10.248 -33.114 1 40.99 ? O2A GCP 500 A 1 HETATM 13 O O5' GCP . . . B 2 -17.94 -11.843 -35.07 1 34.26 ? O5' GCP 500 A 1 HETATM 14 C C5' GCP . . . B 2 -18.208 -10.874 -36.088 1 31.17 ? C5' GCP 500 A 1 HETATM 15 C C4' GCP . . . B 2 -19.334 -11.369 -36.986 1 30.51 ? C4' GCP 500 A 1 HETATM 16 O O4' GCP . . . B 2 -18.89 -12.473 -37.79 1 32.18 ? O4' GCP 500 A 1 HETATM 17 C C3' GCP . . . B 2 -20.529 -11.884 -36.219 1 30.88 ? C3' GCP 500 A 1 HETATM 18 O O3' GCP . . . B 2 -21.678 -11.521 -36.993 1 30.45 ? O3' GCP 500 A 1 HETATM 19 C C2' GCP . . . B 2 -20.365 -13.393 -36.255 1 32.53 ? C2' GCP 500 A 1 HETATM 20 O O2' GCP . . . B 2 -21.62 -14.062 -36.176 1 36.18 ? O2' GCP 500 A 1 HETATM 21 C C1' GCP . . . B 2 -19.707 -13.633 -37.601 1 31.06 ? C1' GCP 500 A 1 HETATM 22 N N9 GCP . . . B 2 -18.849 -14.834 -37.584 1 32.87 ? N9 GCP 500 A 1 HETATM 23 C C8 GCP . . . B 2 -17.901 -15.098 -36.66 1 31.99 ? C8 GCP 500 A 1 HETATM 24 N N7 GCP . . . B 2 -17.273 -16.272 -36.919 1 31.17 ? N7 GCP 500 A 1 HETATM 25 C C5 GCP . . . B 2 -17.82 -16.782 -38.04 1 34.8 ? C5 GCP 500 A 1 HETATM 26 C C6 GCP . . . B 2 -17.623 -17.997 -38.877 1 35.71 ? C6 GCP 500 A 1 HETATM 27 O O6 GCP . . . B 2 -16.775 -18.865 -38.593 1 40.16 ? O6 GCP 500 A 1 HETATM 28 N N1 GCP . . . B 2 -18.381 -18.16 -39.963 1 37.54 ? N1 GCP 500 A 1 HETATM 29 C C2 GCP . . . B 2 -19.313 -17.26 -40.323 1 35.27 ? C2 GCP 500 A 1 HETATM 30 N N2 GCP . . . B 2 -20.02 -17.527 -41.45 1 32.83 ? N2 GCP 500 A 1 HETATM 31 N N3 GCP . . . B 2 -19.552 -16.121 -39.605 1 32.66 ? N3 GCP 500 A 1 HETATM 32 C C4 GCP . . . B 2 -18.854 -15.826 -38.481 1 33.24 ? C4 GCP 500 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #