data_4LBY # _model_server_result.job_id MeV1dTfIiXb-zaPsa2W5AQ _model_server_result.datetime_utc '2024-10-13 04:21:31' _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 4lby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4LBY # _exptl.entry_id 4LBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 95.85 _cell.angle_gamma 90 _cell.entry_id 4LBY _cell.length_a 147.48 _cell.length_b 98.38 _cell.length_c 39.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,D,E,F,G,H,I,J,K _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 # 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 A OG1 THR 24 A THR 25 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 A OG1 THR 61 A THR 62 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc3 B O1G GNP . A GNP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc4 B O2B GNP . A GNP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc5 C MG MG . A MG 502 1_555 K O HOH . A HOH 657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc6 C MG MG . A MG 502 1_555 K O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 4LBY _atom_sites.fract_transf_matrix[1][1] 0.006781 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000695 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010165 _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] 0.025353 _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 GNP A 1 501 406 GNP GNP . C 3 MG A 1 502 407 MG MG . D 4 NH4 A 1 503 408 NH4 NH4 . E 5 SO4 A 1 504 409 SO4 SO4 . F 5 SO4 A 1 505 410 SO4 SO4 . G 5 SO4 A 1 506 411 SO4 SO4 . H 5 SO4 A 1 507 412 SO4 SO4 . I 5 SO4 A 1 508 413 SO4 SO4 . J 5 SO4 A 1 509 414 SO4 SO4 . K 6 HOH A 1 601 1 HOH HOH . K 6 HOH A 2 602 2 HOH HOH . K 6 HOH A 3 603 3 HOH HOH . K 6 HOH A 4 604 4 HOH HOH . K 6 HOH A 5 605 5 HOH HOH . K 6 HOH A 6 606 6 HOH HOH . K 6 HOH A 7 607 7 HOH HOH . K 6 HOH A 8 608 8 HOH HOH . K 6 HOH A 9 609 9 HOH HOH . K 6 HOH A 10 610 10 HOH HOH . K 6 HOH A 11 611 11 HOH HOH . K 6 HOH A 12 612 12 HOH HOH . K 6 HOH A 13 613 14 HOH HOH . K 6 HOH A 14 614 15 HOH HOH . K 6 HOH A 15 615 17 HOH HOH . K 6 HOH A 16 616 18 HOH HOH . K 6 HOH A 17 617 19 HOH HOH . K 6 HOH A 18 618 20 HOH HOH . K 6 HOH A 19 619 21 HOH HOH . K 6 HOH A 20 620 22 HOH HOH . K 6 HOH A 21 621 23 HOH HOH . K 6 HOH A 22 622 25 HOH HOH . K 6 HOH A 23 623 26 HOH HOH . K 6 HOH A 24 624 27 HOH HOH . K 6 HOH A 25 625 28 HOH HOH . K 6 HOH A 26 626 29 HOH HOH . K 6 HOH A 27 627 30 HOH HOH . K 6 HOH A 28 628 31 HOH HOH . K 6 HOH A 29 629 33 HOH HOH . K 6 HOH A 30 630 36 HOH HOH . K 6 HOH A 31 631 39 HOH HOH . K 6 HOH A 32 632 41 HOH HOH . K 6 HOH A 33 633 43 HOH HOH . K 6 HOH A 34 634 44 HOH HOH . K 6 HOH A 35 635 45 HOH HOH . K 6 HOH A 36 636 47 HOH HOH . K 6 HOH A 37 637 48 HOH HOH . K 6 HOH A 38 638 49 HOH HOH . K 6 HOH A 39 639 50 HOH HOH . K 6 HOH A 40 640 53 HOH HOH . K 6 HOH A 41 641 54 HOH HOH . K 6 HOH A 42 642 56 HOH HOH . K 6 HOH A 43 643 57 HOH HOH . K 6 HOH A 44 644 58 HOH HOH . K 6 HOH A 45 645 59 HOH HOH . K 6 HOH A 46 646 60 HOH HOH . K 6 HOH A 47 647 61 HOH HOH . K 6 HOH A 48 648 62 HOH HOH . K 6 HOH A 49 649 63 HOH HOH . K 6 HOH A 50 650 64 HOH HOH . K 6 HOH A 51 651 65 HOH HOH . K 6 HOH A 52 652 66 HOH HOH . K 6 HOH A 53 653 67 HOH HOH . K 6 HOH A 54 654 69 HOH HOH . K 6 HOH A 55 655 71 HOH HOH . K 6 HOH A 56 656 73 HOH HOH . K 6 HOH A 57 657 74 HOH HOH . K 6 HOH A 58 658 77 HOH HOH . K 6 HOH A 59 659 78 HOH HOH . K 6 HOH A 60 660 79 HOH HOH . K 6 HOH A 61 661 81 HOH HOH . K 6 HOH A 62 662 83 HOH HOH . K 6 HOH A 63 663 84 HOH HOH . K 6 HOH A 64 664 85 HOH HOH . K 6 HOH A 65 665 87 HOH HOH . K 6 HOH A 66 666 88 HOH HOH . K 6 HOH A 67 667 90 HOH HOH . K 6 HOH A 68 668 91 HOH HOH . K 6 HOH A 69 669 92 HOH HOH . K 6 HOH A 70 670 93 HOH HOH . K 6 HOH A 71 671 95 HOH HOH . K 6 HOH A 72 672 96 HOH HOH . K 6 HOH A 73 673 97 HOH HOH . K 6 HOH A 74 674 98 HOH HOH . K 6 HOH A 75 675 99 HOH HOH . K 6 HOH A 76 676 100 HOH HOH . K 6 HOH A 77 677 101 HOH HOH . K 6 HOH A 78 678 102 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 GNP . . . B 2 37.025 2.03 39.573 1 23.35 ? PG GNP 501 A 1 HETATM 2 O O1G GNP . . . B 2 38.449 1.588 39.858 1 14.96 ? O1G GNP 501 A 1 HETATM 3 O O2G GNP . . . B 2 35.951 1.143 40.176 1 20.58 ? O2G GNP 501 A 1 HETATM 4 O O3G GNP . . . B 2 36.884 2.116 38.072 1 26.03 ? O3G GNP 501 A 1 HETATM 5 N N3B GNP . . . B 2 36.856 3.523 40.147 1 16.76 ? N3B GNP 501 A 1 HETATM 6 P PB GNP . . . B 2 37.566 4.12 41.457 1 28.25 ? PB GNP 501 A 1 HETATM 7 O O1B GNP . . . B 2 36.901 3.595 42.671 1 18.92 ? O1B GNP 501 A 1 HETATM 8 O O2B GNP . . . B 2 39.039 3.894 41.356 1 7.69 ? O2B GNP 501 A 1 HETATM 9 O O3A GNP . . . B 2 37.353 5.643 41.508 1 33.52 ? O3A GNP 501 A 1 HETATM 10 P PA GNP . . . B 2 38.274 6.779 41 1 24.45 ? PA GNP 501 A 1 HETATM 11 O O1A GNP . . . B 2 39.465 6.961 41.867 1 20.7 ? O1A GNP 501 A 1 HETATM 12 O O2A GNP . . . B 2 38.533 6.639 39.557 1 27.69 ? O2A GNP 501 A 1 HETATM 13 O O5' GNP . . . B 2 37.398 8.089 41.155 1 27.68 ? O5' GNP 501 A 1 HETATM 14 C C5' GNP . . . B 2 36.154 8.171 40.441 1 23.11 ? C5' GNP 501 A 1 HETATM 15 C C4' GNP . . . B 2 35.681 9.604 40.223 1 22.02 ? C4' GNP 501 A 1 HETATM 16 O O4' GNP . . . B 2 35.341 10.25 41.492 1 31.67 ? O4' GNP 501 A 1 HETATM 17 C C3' GNP . . . B 2 36.669 10.534 39.538 1 24.5 ? C3' GNP 501 A 1 HETATM 18 O O3' GNP . . . B 2 35.968 11.393 38.648 1 29 ? O3' GNP 501 A 1 HETATM 19 C C2' GNP . . . B 2 37.27 11.285 40.727 1 25.92 ? C2' GNP 501 A 1 HETATM 20 O O2' GNP . . . B 2 37.846 12.533 40.396 1 31.72 ? O2' GNP 501 A 1 HETATM 21 C C1' GNP . . . B 2 36.064 11.453 41.643 1 27 ? C1' GNP 501 A 1 HETATM 22 N N9 GNP . . . B 2 36.495 11.543 43.031 1 30.16 ? N9 GNP 501 A 1 HETATM 23 C C8 GNP . . . B 2 37.392 10.715 43.668 1 28.02 ? C8 GNP 501 A 1 HETATM 24 N N7 GNP . . . B 2 37.608 11.026 44.915 1 27.76 ? N7 GNP 501 A 1 HETATM 25 C C5 GNP . . . B 2 36.812 12.148 45.124 1 37.03 ? C5 GNP 501 A 1 HETATM 26 C C6 GNP . . . B 2 36.628 12.943 46.287 1 37.39 ? C6 GNP 501 A 1 HETATM 27 O O6 GNP . . . B 2 37.167 12.805 47.395 1 32.72 ? O6 GNP 501 A 1 HETATM 28 N N1 GNP . . . B 2 35.717 13.979 46.064 1 37.46 ? N1 GNP 501 A 1 HETATM 29 C C2 GNP . . . B 2 35.089 14.214 44.855 1 39.92 ? C2 GNP 501 A 1 HETATM 30 N N2 GNP . . . B 2 34.245 15.249 44.773 1 48.04 ? N2 GNP 501 A 1 HETATM 31 N N3 GNP . . . B 2 35.264 13.49 43.766 1 35.58 ? N3 GNP 501 A 1 HETATM 32 C C4 GNP . . . B 2 36.126 12.473 43.971 1 34.4 ? C4 GNP 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #