data_3NTU # _model_server_result.job_id 5OVFGXghxNqVC8OGsrBCeg _model_server_result.datetime_utc '2024-10-18 16:29:13' _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 3ntu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3NTU # _exptl.entry_id 3NTU _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 3NTU _cell.length_a 84.97 _cell.length_b 84.97 _cell.length_c 104.32 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NTU _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 1,2,3,4,5,6 # 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' 2_765 -y+2,x-y+1,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 127.455 73.586179 34.773333 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z+2/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 147.172357 69.546667 4 'crystal symmetry operation' 4_775 -x+2,-y+2,z+1/2 -1 0 0 0 -1 0 0 0 1 84.97 147.172357 52.16 5 'crystal symmetry operation' 5_565 y,-x+y+1,z+5/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 -42.485 73.586179 86.933333 6 'crystal symmetry operation' 6_655 x-y+1,x,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 84.97 0 17.386667 # _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 O GLN 95 A GLN 98 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc2 A OG1 THR 109 A THR 112 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 A O GLU 161 A GLU 164 1_555 E NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc4 A OE2 GLU 161 A GLU 164 1_555 E NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc5 A OD1 ASP 243 A ASP 246 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc6 B O2G ANP . A ANP 401 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc7 B O1B ANP . A ANP 401 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc8 C MG MG . A MG 501 1_555 F O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc9 C MG MG . A MG 501 1_555 F O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc10 C MG MG . A MG 501 1_555 F O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc11 D MG MG . A MG 502 1_555 F O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc12 D MG MG . A MG 502 1_555 F O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc13 D MG MG . A MG 502 1_555 F O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc14 D MG MG . A MG 502 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? # _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 3NTU _atom_sites.fract_transf_matrix[1][1] 0.011769 _atom_sites.fract_transf_matrix[1][2] 0.006795 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01359 _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] 0.009586 _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 1 401 401 ANP ANP . C 3 MG A 1 501 501 MG MG . D 3 MG A 1 502 502 MG MG . E 4 NA A 1 505 505 NA NA . F 5 HOH A 1 601 601 HOH HOH . F 5 HOH A 2 602 602 HOH HOH . F 5 HOH A 3 603 603 HOH HOH . F 5 HOH A 4 604 604 HOH HOH . F 5 HOH A 5 605 605 HOH HOH . F 5 HOH A 6 606 606 HOH HOH . F 5 HOH A 7 607 607 HOH HOH . F 5 HOH A 8 609 609 HOH HOH . F 5 HOH A 9 610 610 HOH HOH . F 5 HOH A 10 611 611 HOH HOH . F 5 HOH A 11 612 612 HOH HOH . F 5 HOH A 12 613 613 HOH HOH . F 5 HOH A 13 614 614 HOH HOH . F 5 HOH A 14 615 615 HOH HOH . F 5 HOH A 15 616 616 HOH HOH . F 5 HOH A 16 617 617 HOH HOH . F 5 HOH A 17 618 618 HOH HOH . F 5 HOH A 18 619 619 HOH HOH . F 5 HOH A 19 620 620 HOH HOH . F 5 HOH A 20 621 621 HOH HOH . F 5 HOH A 21 622 622 HOH HOH . F 5 HOH A 22 623 623 HOH HOH . F 5 HOH A 23 624 624 HOH HOH . F 5 HOH A 24 625 625 HOH HOH . F 5 HOH A 25 626 626 HOH HOH . F 5 HOH A 26 627 627 HOH HOH . F 5 HOH A 27 628 628 HOH HOH . F 5 HOH A 28 629 629 HOH HOH . F 5 HOH A 29 630 630 HOH HOH . F 5 HOH A 30 631 631 HOH HOH . F 5 HOH A 31 632 632 HOH HOH . F 5 HOH A 32 633 633 HOH HOH . F 5 HOH A 33 634 634 HOH HOH . F 5 HOH A 34 635 635 HOH HOH . F 5 HOH A 35 636 636 HOH HOH . F 5 HOH A 36 637 637 HOH HOH . F 5 HOH A 37 638 638 HOH HOH . F 5 HOH A 38 639 639 HOH HOH . F 5 HOH A 39 640 640 HOH HOH . F 5 HOH A 40 641 641 HOH HOH . F 5 HOH A 41 642 642 HOH HOH . F 5 HOH A 42 643 643 HOH HOH . F 5 HOH A 43 644 644 HOH HOH . F 5 HOH A 44 645 645 HOH HOH . F 5 HOH A 45 646 646 HOH HOH . F 5 HOH A 46 647 647 HOH HOH . F 5 HOH A 47 648 648 HOH HOH . F 5 HOH A 48 649 649 HOH HOH . F 5 HOH A 49 650 650 HOH HOH . F 5 HOH A 50 651 651 HOH HOH . F 5 HOH A 51 652 652 HOH HOH . F 5 HOH A 52 653 653 HOH HOH . F 5 HOH A 53 654 654 HOH HOH . F 5 HOH A 54 655 655 HOH HOH . F 5 HOH A 55 656 656 HOH HOH . F 5 HOH A 56 657 657 HOH HOH . F 5 HOH A 57 658 658 HOH HOH . F 5 HOH A 58 659 659 HOH HOH . F 5 HOH A 59 660 660 HOH HOH . F 5 HOH A 60 661 661 HOH HOH . F 5 HOH A 61 662 662 HOH HOH . F 5 HOH A 62 663 663 HOH HOH . F 5 HOH A 63 664 664 HOH HOH . F 5 HOH A 64 665 665 HOH HOH . F 5 HOH A 65 666 666 HOH HOH . F 5 HOH A 66 667 667 HOH HOH . F 5 HOH A 67 668 668 HOH HOH . F 5 HOH A 68 669 669 HOH HOH . F 5 HOH A 69 670 670 HOH HOH . F 5 HOH A 70 671 671 HOH HOH . F 5 HOH A 71 672 672 HOH HOH . F 5 HOH A 72 673 673 HOH HOH . F 5 HOH A 73 674 674 HOH HOH . F 5 HOH A 74 675 675 HOH HOH . F 5 HOH A 75 676 676 HOH HOH . F 5 HOH A 76 677 677 HOH HOH . F 5 HOH A 77 678 678 HOH HOH . F 5 HOH A 78 679 679 HOH HOH . F 5 HOH A 79 680 680 HOH HOH . F 5 HOH A 80 681 681 HOH HOH . F 5 HOH A 81 682 682 HOH HOH . F 5 HOH A 82 683 683 HOH HOH . F 5 HOH A 83 684 684 HOH HOH . F 5 HOH A 84 685 685 HOH HOH . F 5 HOH A 85 686 686 HOH HOH . F 5 HOH A 86 687 687 HOH HOH . F 5 HOH A 87 688 688 HOH HOH . F 5 HOH A 88 689 689 HOH HOH . F 5 HOH A 89 690 690 HOH HOH . F 5 HOH A 90 691 691 HOH HOH . F 5 HOH A 91 692 692 HOH HOH . F 5 HOH A 92 693 693 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 ANP . . . B 2 27.593 60.569 -8.076 1 29.21 ? PG ANP 401 A 1 HETATM 2 O O1G ANP . . . B 2 28.912 61.043 -7.803 1 26.04 ? O1G ANP 401 A 1 HETATM 3 O O2G ANP . . . B 2 27.059 60.08 -6.786 1 29.89 ? O2G ANP 401 A 1 HETATM 4 O O3G ANP . . . B 2 27.058 61.779 -8.662 1 31.01 ? O3G ANP 401 A 1 HETATM 5 P PB ANP . . . B 2 28.151 57.864 -9.005 1 25.74 ? PB ANP 401 A 1 HETATM 6 O O1B ANP . . . B 2 27.567 57.378 -7.734 1 21.19 ? O1B ANP 401 A 1 HETATM 7 O O2B ANP . . . B 2 29.562 57.715 -8.893 1 22.75 ? O2B ANP 401 A 1 HETATM 8 N N3B ANP . . . B 2 27.954 59.44 -9.231 1 25.62 ? N3B ANP 401 A 1 HETATM 9 P PA ANP . . . B 2 26.628 56.052 -10.44 1 27.19 ? PA ANP 401 A 1 HETATM 10 O O1A ANP . . . B 2 27.02 54.854 -9.59 1 27.15 ? O1A ANP 401 A 1 HETATM 11 O O2A ANP . . . B 2 25.328 56.622 -10.044 1 25.42 ? O2A ANP 401 A 1 HETATM 12 O O3A ANP . . . B 2 27.73 57.145 -10.364 1 25.63 ? O3A ANP 401 A 1 HETATM 13 O O5' ANP . . . B 2 26.647 55.549 -11.952 1 27.04 ? O5' ANP 401 A 1 HETATM 14 C C5' ANP . . . B 2 25.897 56.239 -13.066 1 28.73 ? C5' ANP 401 A 1 HETATM 15 C C4' ANP . . . B 2 26.285 55.612 -14.209 1 22.62 ? C4' ANP 401 A 1 HETATM 16 O O4' ANP . . . B 2 25.867 54.193 -14.064 1 27.64 ? O4' ANP 401 A 1 HETATM 17 C C3' ANP . . . B 2 25.376 56.076 -15.388 1 27.43 ? C3' ANP 401 A 1 HETATM 18 O O3' ANP . . . B 2 25.589 57.347 -15.804 1 26.21 ? O3' ANP 401 A 1 HETATM 19 C C2' ANP . . . B 2 25.309 54.838 -16.332 1 25.93 ? C2' ANP 401 A 1 HETATM 20 O O2' ANP . . . B 2 26.65 54.964 -17.042 1 30.12 ? O2' ANP 401 A 1 HETATM 21 C C1' ANP . . . B 2 25.513 53.641 -15.369 1 25.86 ? C1' ANP 401 A 1 HETATM 22 N N9 ANP . . . B 2 24.233 53.067 -15.233 1 26.82 ? N9 ANP 401 A 1 HETATM 23 C C8 ANP . . . B 2 23.259 53.34 -14.262 1 27.3 ? C8 ANP 401 A 1 HETATM 24 N N7 ANP . . . B 2 22.192 52.622 -14.485 1 29.56 ? N7 ANP 401 A 1 HETATM 25 C C5 ANP . . . B 2 22.41 51.866 -15.58 1 27.51 ? C5 ANP 401 A 1 HETATM 26 C C6 ANP . . . B 2 21.641 50.935 -16.287 1 34.27 ? C6 ANP 401 A 1 HETATM 27 N N6 ANP . . . B 2 20.387 50.63 -15.896 1 38.21 ? N6 ANP 401 A 1 HETATM 28 N N1 ANP . . . B 2 22.185 50.335 -17.406 1 32.55 ? N1 ANP 401 A 1 HETATM 29 C C2 ANP . . . B 2 23.48 50.631 -17.848 1 35.78 ? C2 ANP 401 A 1 HETATM 30 N N3 ANP . . . B 2 24.265 51.54 -17.181 1 30.98 ? N3 ANP 401 A 1 HETATM 31 C C4 ANP . . . B 2 23.673 52.128 -16.051 1 28.02 ? C4 ANP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #