data_3VQY # _model_server_result.job_id ywcBl4mmyPaeld7QuNT1SA _model_server_result.datetime_utc '2025-01-11 12:52:48' _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 3vqy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3VQY # _exptl.entry_id 3VQY _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 3VQY _cell.length_a 103.355 _cell.length_b 103.355 _cell.length_c 70.906 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VQY _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,F _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 51.6775 89.508056 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 OE2 GLU 233 A GLU 396 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc2 A OE1 GLU 233 A GLU 396 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc3 A OG SER 236 A SER 399 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc4 B O1B ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc5 B O1G ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc6 B O2B ANP . A ANP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc7 B O2A ANP . A ANP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc8 D MG MG . A MG 503 1_555 F O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc9 D MG MG . A MG 503 1_555 F O HOH . A HOH 656 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc10 D MG MG . A MG 503 1_555 F O HOH . A HOH 685 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc11 D MG MG . A MG 503 1_555 F O HOH . A HOH 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc12 E MG MG . A MG 504 1_555 F O HOH . A HOH 640 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? # _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 3VQY _atom_sites.fract_transf_matrix[1][1] 0.009675 _atom_sites.fract_transf_matrix[1][2] 0.005586 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011172 _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] 0.014103 _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 LBY A 1 502 501 LBY BLS . D 4 MG A 1 503 701 MG MG . E 4 MG A 1 504 702 MG MG . F 5 HOH A 1 601 1 HOH TIP . F 5 HOH A 2 602 2 HOH TIP . F 5 HOH A 3 603 3 HOH TIP . F 5 HOH A 4 604 4 HOH TIP . F 5 HOH A 5 605 5 HOH TIP . F 5 HOH A 6 606 6 HOH TIP . F 5 HOH A 7 607 7 HOH TIP . F 5 HOH A 8 608 8 HOH TIP . F 5 HOH A 9 609 9 HOH TIP . F 5 HOH A 10 610 10 HOH TIP . F 5 HOH A 11 611 11 HOH TIP . F 5 HOH A 12 612 12 HOH TIP . F 5 HOH A 13 613 13 HOH TIP . F 5 HOH A 14 614 14 HOH TIP . F 5 HOH A 15 615 15 HOH TIP . F 5 HOH A 16 616 17 HOH TIP . F 5 HOH A 17 617 18 HOH TIP . F 5 HOH A 18 618 19 HOH TIP . F 5 HOH A 19 619 20 HOH TIP . F 5 HOH A 20 620 21 HOH TIP . F 5 HOH A 21 621 22 HOH TIP . F 5 HOH A 22 622 23 HOH TIP . F 5 HOH A 23 623 24 HOH TIP . F 5 HOH A 24 624 25 HOH TIP . F 5 HOH A 25 625 26 HOH TIP . F 5 HOH A 26 626 27 HOH TIP . F 5 HOH A 27 627 28 HOH TIP . F 5 HOH A 28 628 29 HOH TIP . F 5 HOH A 29 629 30 HOH TIP . F 5 HOH A 30 630 31 HOH TIP . F 5 HOH A 31 631 32 HOH TIP . F 5 HOH A 32 632 33 HOH TIP . F 5 HOH A 33 633 34 HOH TIP . F 5 HOH A 34 634 35 HOH TIP . F 5 HOH A 35 635 36 HOH TIP . F 5 HOH A 36 636 37 HOH TIP . F 5 HOH A 37 637 38 HOH TIP . F 5 HOH A 38 638 40 HOH TIP . F 5 HOH A 39 639 41 HOH TIP . F 5 HOH A 40 640 42 HOH TIP . F 5 HOH A 41 641 43 HOH TIP . F 5 HOH A 42 642 44 HOH TIP . F 5 HOH A 43 643 45 HOH TIP . F 5 HOH A 44 644 46 HOH TIP . F 5 HOH A 45 645 47 HOH TIP . F 5 HOH A 46 646 48 HOH TIP . F 5 HOH A 47 647 49 HOH TIP . F 5 HOH A 48 648 50 HOH TIP . F 5 HOH A 49 649 51 HOH TIP . F 5 HOH A 50 650 52 HOH TIP . F 5 HOH A 51 651 53 HOH TIP . F 5 HOH A 52 652 54 HOH TIP . F 5 HOH A 53 653 55 HOH TIP . F 5 HOH A 54 654 56 HOH TIP . F 5 HOH A 55 655 57 HOH TIP . F 5 HOH A 56 656 58 HOH TIP . F 5 HOH A 57 657 59 HOH TIP . F 5 HOH A 58 658 60 HOH TIP . F 5 HOH A 59 659 61 HOH TIP . F 5 HOH A 60 660 63 HOH TIP . F 5 HOH A 61 661 67 HOH TIP . F 5 HOH A 62 662 69 HOH TIP . F 5 HOH A 63 663 71 HOH TIP . F 5 HOH A 64 664 72 HOH TIP . F 5 HOH A 65 665 76 HOH TIP . F 5 HOH A 66 666 79 HOH TIP . F 5 HOH A 67 667 81 HOH TIP . F 5 HOH A 68 668 82 HOH TIP . F 5 HOH A 69 669 83 HOH TIP . F 5 HOH A 70 670 86 HOH TIP . F 5 HOH A 71 671 89 HOH TIP . F 5 HOH A 72 672 91 HOH TIP . F 5 HOH A 73 673 93 HOH TIP . F 5 HOH A 74 674 94 HOH TIP . F 5 HOH A 75 675 95 HOH TIP . F 5 HOH A 76 676 96 HOH TIP . F 5 HOH A 77 677 97 HOH TIP . F 5 HOH A 78 678 99 HOH TIP . F 5 HOH A 79 679 100 HOH TIP . F 5 HOH A 80 680 104 HOH TIP . F 5 HOH A 81 681 106 HOH TIP . F 5 HOH A 82 682 109 HOH TIP . F 5 HOH A 83 683 110 HOH TIP . F 5 HOH A 84 684 111 HOH TIP . F 5 HOH A 85 685 113 HOH TIP . F 5 HOH A 86 686 115 HOH TIP . F 5 HOH A 87 687 117 HOH TIP . F 5 HOH A 88 688 119 HOH TIP . F 5 HOH A 89 689 121 HOH TIP . F 5 HOH A 90 690 128 HOH TIP . F 5 HOH A 91 691 131 HOH TIP . F 5 HOH A 92 692 132 HOH TIP . F 5 HOH A 93 693 136 HOH TIP . F 5 HOH A 94 694 141 HOH TIP . F 5 HOH A 95 695 142 HOH TIP . F 5 HOH A 96 696 143 HOH TIP . F 5 HOH A 97 697 146 HOH TIP . F 5 HOH A 98 698 147 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 24.63 24.631 -8.009 1 39.34 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 24.384 25.557 -9.137 1 37.8 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 23.335 24.476 -7.064 1 35.77 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 24.985 23.137 -8.494 1 38.31 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 27.161 25.587 -7.847 1 35.95 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 26.977 26.529 -8.971 1 35.28 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 28.328 24.689 -7.689 1 35.59 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 25.844 25.095 -7.032 1 37.29 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 29.05 27.176 -6.439 1 38.08 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 29.619 27.718 -7.692 1 37.18 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 29.774 26.077 -5.762 1 39.43 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 27.539 26.682 -6.721 1 38.46 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 28.859 28.388 -5.396 1 38.35 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 28.887 28.17 -3.982 1 35.63 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 27.492 28.343 -3.377 1 35.46 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 26.868 29.553 -3.836 1 35.25 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 26.53 27.251 -3.84 1 34.98 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 26.776 26.073 -3.068 1 35.23 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 25.219 27.896 -3.392 1 33.35 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 25.06 27.808 -1.974 1 33.24 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 25.443 29.354 -3.8 1 31.87 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 24.915 29.59 -5.162 1 31.57 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 25.526 29.314 -6.312 1 29.97 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 24.745 29.67 -7.329 1 32.01 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 23.623 30.177 -6.824 1 31.52 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 22.448 30.685 -7.365 1 30.52 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 22.289 30.765 -8.684 1 31 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 21.474 31.1 -6.543 1 30.6 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 21.611 31.039 -5.229 1 31.4 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 22.716 30.562 -4.679 1 30.13 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 23.73 30.126 -5.44 1 30.71 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #