data_3VQW # _model_server_result.job_id YnCGneUODjJqAX4V4ZU9GQ _model_server_result.datetime_utc '2025-06-28 15:10:16' _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 3vqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3VQW # _exptl.entry_id 3VQW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 120 _cell.entry_id 3VQW _cell.length_a 105.091 _cell.length_b 105.091 _cell.length_c 70.629 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VQW _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 52.5455 91.011476 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 covale ? covale1 A C ARG 112 A ARG 275 1_555 A N MSE 113 A MSE 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 113 A MSE 276 1_555 A N GLY 114 A GLY 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C PRO 136 A PRO 299 1_555 A N MSE 137 A MSE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 137 A MSE 300 1_555 A N LEU 138 A LEU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 A C THR 180 A THR 343 1_555 A N MSE 181 A MSE 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 181 A MSE 344 1_555 A N LEU 182 A LEU 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C GLN 186 A GLN 349 1_555 A N MSE 187 A MSE 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 187 A MSE 350 1_555 A N GLY 188 A GLY 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale9 A C VAL 227 A VAL 390 1_555 A N MSE 228 A MSE 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 228 A MSE 391 1_555 A N HIS 229 A HIS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OE1 GLU 233 A GLU 396 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc2 A OE2 GLU 233 A GLU 396 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc3 A OG SER 236 A SER 399 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc4 B O1B ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc5 B O1G ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc6 B O2B ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc7 B O1A ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc8 C MG MG . A MG 502 1_555 E O HOH . A HOH 734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 3VQW _atom_sites.fract_transf_matrix[1][1] 0.009516 _atom_sites.fract_transf_matrix[1][2] 0.005494 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010988 _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] 0.014158 _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 ANP A 1 501 301 ANP ANP . C 3 MG A 1 502 401 MG MG . D 3 MG A 1 503 402 MG MG . E 4 HOH A 1 601 1 HOH TIP . E 4 HOH A 2 602 2 HOH TIP . E 4 HOH A 3 603 3 HOH TIP . E 4 HOH A 4 604 4 HOH TIP . E 4 HOH A 5 605 5 HOH TIP . E 4 HOH A 6 606 6 HOH TIP . E 4 HOH A 7 607 7 HOH TIP . E 4 HOH A 8 608 8 HOH TIP . E 4 HOH A 9 609 9 HOH TIP . E 4 HOH A 10 610 10 HOH TIP . E 4 HOH A 11 611 11 HOH TIP . E 4 HOH A 12 612 12 HOH TIP . E 4 HOH A 13 613 13 HOH TIP . E 4 HOH A 14 614 14 HOH TIP . E 4 HOH A 15 615 16 HOH TIP . E 4 HOH A 16 616 17 HOH TIP . E 4 HOH A 17 617 18 HOH TIP . E 4 HOH A 18 618 19 HOH TIP . E 4 HOH A 19 619 20 HOH TIP . E 4 HOH A 20 620 21 HOH TIP . E 4 HOH A 21 621 22 HOH TIP . E 4 HOH A 22 622 23 HOH TIP . E 4 HOH A 23 623 24 HOH TIP . E 4 HOH A 24 624 25 HOH TIP . E 4 HOH A 25 625 26 HOH TIP . E 4 HOH A 26 626 27 HOH TIP . E 4 HOH A 27 627 28 HOH TIP . E 4 HOH A 28 628 29 HOH TIP . E 4 HOH A 29 629 31 HOH TIP . E 4 HOH A 30 630 33 HOH TIP . E 4 HOH A 31 631 34 HOH TIP . E 4 HOH A 32 632 35 HOH TIP . E 4 HOH A 33 633 36 HOH TIP . E 4 HOH A 34 634 38 HOH TIP . E 4 HOH A 35 635 39 HOH TIP . E 4 HOH A 36 636 40 HOH TIP . E 4 HOH A 37 637 41 HOH TIP . E 4 HOH A 38 638 42 HOH TIP . E 4 HOH A 39 639 43 HOH TIP . E 4 HOH A 40 640 44 HOH TIP . E 4 HOH A 41 641 46 HOH TIP . E 4 HOH A 42 642 48 HOH TIP . E 4 HOH A 43 643 49 HOH TIP . E 4 HOH A 44 644 50 HOH TIP . E 4 HOH A 45 645 52 HOH TIP . E 4 HOH A 46 646 54 HOH TIP . E 4 HOH A 47 647 55 HOH TIP . E 4 HOH A 48 648 56 HOH TIP . E 4 HOH A 49 649 59 HOH TIP . E 4 HOH A 50 650 60 HOH TIP . E 4 HOH A 51 651 61 HOH TIP . E 4 HOH A 52 652 62 HOH TIP . E 4 HOH A 53 653 64 HOH TIP . E 4 HOH A 54 654 65 HOH TIP . E 4 HOH A 55 655 66 HOH TIP . E 4 HOH A 56 656 67 HOH TIP . E 4 HOH A 57 657 68 HOH TIP . E 4 HOH A 58 658 69 HOH TIP . E 4 HOH A 59 659 71 HOH TIP . E 4 HOH A 60 660 72 HOH TIP . E 4 HOH A 61 661 73 HOH TIP . E 4 HOH A 62 662 76 HOH TIP . E 4 HOH A 63 663 77 HOH TIP . E 4 HOH A 64 664 78 HOH TIP . E 4 HOH A 65 665 79 HOH TIP . E 4 HOH A 66 666 80 HOH TIP . E 4 HOH A 67 667 82 HOH TIP . E 4 HOH A 68 668 84 HOH TIP . E 4 HOH A 69 669 89 HOH TIP . E 4 HOH A 70 670 91 HOH TIP . E 4 HOH A 71 671 92 HOH TIP . E 4 HOH A 72 672 94 HOH TIP . E 4 HOH A 73 673 97 HOH TIP . E 4 HOH A 74 674 100 HOH TIP . E 4 HOH A 75 675 102 HOH TIP . E 4 HOH A 76 676 103 HOH TIP . E 4 HOH A 77 677 104 HOH TIP . E 4 HOH A 78 678 105 HOH TIP . E 4 HOH A 79 679 108 HOH TIP . E 4 HOH A 80 680 109 HOH TIP . E 4 HOH A 81 681 111 HOH TIP . E 4 HOH A 82 682 113 HOH TIP . E 4 HOH A 83 683 114 HOH TIP . E 4 HOH A 84 684 115 HOH TIP . E 4 HOH A 85 685 116 HOH TIP . E 4 HOH A 86 686 118 HOH TIP . E 4 HOH A 87 687 119 HOH TIP . E 4 HOH A 88 688 120 HOH TIP . E 4 HOH A 89 689 123 HOH TIP . E 4 HOH A 90 690 124 HOH TIP . E 4 HOH A 91 691 126 HOH TIP . E 4 HOH A 92 692 127 HOH TIP . E 4 HOH A 93 693 129 HOH TIP . E 4 HOH A 94 694 131 HOH TIP . E 4 HOH A 95 695 132 HOH TIP . E 4 HOH A 96 696 133 HOH TIP . E 4 HOH A 97 697 134 HOH TIP . E 4 HOH A 98 698 135 HOH TIP . E 4 HOH A 99 699 136 HOH TIP . E 4 HOH A 100 700 137 HOH TIP . E 4 HOH A 101 701 138 HOH TIP . E 4 HOH A 102 702 139 HOH TIP . E 4 HOH A 103 703 140 HOH TIP . E 4 HOH A 104 704 141 HOH TIP . E 4 HOH A 105 705 144 HOH TIP . E 4 HOH A 106 706 146 HOH TIP . E 4 HOH A 107 707 147 HOH TIP . E 4 HOH A 108 708 148 HOH TIP . E 4 HOH A 109 709 149 HOH TIP . E 4 HOH A 110 710 151 HOH TIP . E 4 HOH A 111 711 152 HOH TIP . E 4 HOH A 112 712 153 HOH TIP . E 4 HOH A 113 713 157 HOH TIP . E 4 HOH A 114 714 158 HOH TIP . E 4 HOH A 115 715 160 HOH TIP . E 4 HOH A 116 716 161 HOH TIP . E 4 HOH A 117 717 162 HOH TIP . E 4 HOH A 118 718 164 HOH TIP . E 4 HOH A 119 719 165 HOH TIP . E 4 HOH A 120 720 167 HOH TIP . E 4 HOH A 121 721 168 HOH TIP . E 4 HOH A 122 722 170 HOH TIP . E 4 HOH A 123 723 171 HOH TIP . E 4 HOH A 124 724 172 HOH TIP . E 4 HOH A 125 725 173 HOH TIP . E 4 HOH A 126 726 174 HOH TIP . E 4 HOH A 127 727 175 HOH TIP . E 4 HOH A 128 728 176 HOH TIP . E 4 HOH A 129 729 181 HOH TIP . E 4 HOH A 130 730 182 HOH TIP . E 4 HOH A 131 731 183 HOH TIP . E 4 HOH A 132 732 185 HOH TIP . E 4 HOH A 133 733 187 HOH TIP . E 4 HOH A 134 734 188 HOH TIP . E 4 HOH A 135 735 189 HOH TIP . E 4 HOH A 136 736 190 HOH TIP . E 4 HOH A 137 737 191 HOH TIP . E 4 HOH A 138 738 193 HOH TIP . E 4 HOH A 139 739 194 HOH TIP . E 4 HOH A 140 740 195 HOH TIP . E 4 HOH A 141 741 196 HOH TIP . E 4 HOH A 142 742 197 HOH TIP . E 4 HOH A 143 743 198 HOH TIP . # 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 ANP . . . B 2 24.973 25.424 54.082 1 69.18 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 24.524 26.675 53.433 1 73.69 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 23.848 24.804 55.053 1 38.07 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 25.294 24.265 53.011 1 74.15 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 27.561 26.255 54.184 1 59.33 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 27.276 27.242 53.12 1 59.22 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 28.775 25.409 54.24 1 68.99 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 26.306 25.612 54.995 1 66.81 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 29.407 27.811 55.723 1 62.03 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 30.273 26.626 55.916 1 65.62 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 29.824 28.836 54.742 1 50.24 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 27.916 27.305 55.358 1 67.43 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 29.208 28.522 57.154 1 56.13 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 28.412 27.857 58.136 1 67.89 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 27.924 28.85 59.192 1 71.4 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 27.399 30.012 58.526 1 71.27 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 26.738 28.235 59.937 1 74.04 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 26.451 28.998 61.111 1 85.61 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 25.639 28.486 58.908 1 70.43 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 24.371 28.433 59.565 1 82.68 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 25.963 29.942 58.571 1 61.84 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 25.351 30.328 57.279 1 61.55 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 25.907 30.192 56.076 1 49.39 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 25.062 30.623 55.142 1 55.18 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 23.958 31.04 55.756 1 50.61 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 22.75 31.577 55.329 1 44.25 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 22.53 31.796 54.036 1 43.17 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 21.818 31.888 56.242 1 53 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 22.023 31.698 57.534 1 39.57 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 23.161 31.19 57.975 1 38.67 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 24.138 30.854 57.121 1 58.05 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #