data_3C41 # _model_server_result.job_id V-v665dOkztK-SEmBA5SPw _model_server_result.datetime_utc '2025-07-17 04:09:08' _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 3c41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 3C41 # _exptl.entry_id 3C41 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.901 _cell.angle_gamma 90 _cell.entry_id 3C41 _cell.length_a 48.277 _cell.length_b 82.921 _cell.length_c 68.63 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C41 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 OG SER 43 J SER 41 1_555 C MG MG . J MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc2 D O3G ANP . J ANP 601 1_555 C MG MG . J MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc3 D O2B ANP . J ANP 601 1_555 C MG MG . J MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc4 C MG MG . J MG 603 1_555 G O HOH . J HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc5 C MG MG . J MG 603 1_555 G O HOH . J HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 C MG MG . J MG 603 1_555 H O HOH . K HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc7 G O HOH . J HOH 606 1_555 E MG MG . K MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc8 B OG SER 43 K SER 41 1_555 E MG MG . K MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc9 F O2B ANP . K ANP 602 1_555 E MG MG . K MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc10 F O3G ANP . K ANP 602 1_555 E MG MG . K MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc11 E MG MG . K MG 604 1_555 H O HOH . K HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc12 E MG MG . K MG 604 1_555 H O HOH . K HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _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 3C41 _atom_sites.fract_transf_matrix[1][1] 0.020714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005127 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01206 _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] 0.015011 _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 C 2 MG J 1 603 603 MG MG . D 3 ANP J 1 601 601 ANP ANP . E 2 MG K 1 604 604 MG MG . F 3 ANP K 1 602 602 ANP ANP . G 4 HOH J 1 604 2 HOH HOH . G 4 HOH J 2 605 3 HOH HOH . G 4 HOH J 3 606 4 HOH HOH . G 4 HOH J 4 607 8 HOH HOH . G 4 HOH J 5 608 9 HOH HOH . G 4 HOH J 6 609 11 HOH HOH . G 4 HOH J 7 610 12 HOH HOH . G 4 HOH J 8 611 13 HOH HOH . G 4 HOH J 9 612 14 HOH HOH . G 4 HOH J 10 613 18 HOH HOH . G 4 HOH J 11 614 19 HOH HOH . G 4 HOH J 12 615 22 HOH HOH . G 4 HOH J 13 616 23 HOH HOH . G 4 HOH J 14 617 25 HOH HOH . G 4 HOH J 15 618 26 HOH HOH . G 4 HOH J 16 619 28 HOH HOH . G 4 HOH J 17 620 30 HOH HOH . G 4 HOH J 18 621 32 HOH HOH . G 4 HOH J 19 622 34 HOH HOH . G 4 HOH J 20 623 35 HOH HOH . G 4 HOH J 21 624 36 HOH HOH . G 4 HOH J 22 625 37 HOH HOH . G 4 HOH J 23 626 39 HOH HOH . G 4 HOH J 24 627 40 HOH HOH . G 4 HOH J 25 628 42 HOH HOH . G 4 HOH J 26 629 46 HOH HOH . G 4 HOH J 27 630 47 HOH HOH . G 4 HOH J 28 631 48 HOH HOH . G 4 HOH J 29 632 49 HOH HOH . G 4 HOH J 30 633 50 HOH HOH . G 4 HOH J 31 634 52 HOH HOH . G 4 HOH J 32 635 53 HOH HOH . G 4 HOH J 33 636 55 HOH HOH . G 4 HOH J 34 637 57 HOH HOH . G 4 HOH J 35 638 58 HOH HOH . G 4 HOH J 36 639 59 HOH HOH . G 4 HOH J 37 640 61 HOH HOH . G 4 HOH J 38 641 62 HOH HOH . G 4 HOH J 39 642 63 HOH HOH . G 4 HOH J 40 643 64 HOH HOH . G 4 HOH J 41 644 66 HOH HOH . G 4 HOH J 42 645 68 HOH HOH . G 4 HOH J 43 646 69 HOH HOH . G 4 HOH J 44 647 70 HOH HOH . G 4 HOH J 45 648 72 HOH HOH . G 4 HOH J 46 649 73 HOH HOH . G 4 HOH J 47 650 75 HOH HOH . G 4 HOH J 48 651 77 HOH HOH . G 4 HOH J 49 652 78 HOH HOH . G 4 HOH J 50 653 80 HOH HOH . G 4 HOH J 51 654 82 HOH HOH . G 4 HOH J 52 655 83 HOH HOH . G 4 HOH J 53 656 84 HOH HOH . G 4 HOH J 54 657 85 HOH HOH . G 4 HOH J 55 658 86 HOH HOH . G 4 HOH J 56 659 87 HOH HOH . G 4 HOH J 57 660 89 HOH HOH . G 4 HOH J 58 661 90 HOH HOH . G 4 HOH J 59 662 92 HOH HOH . G 4 HOH J 60 663 96 HOH HOH . G 4 HOH J 61 664 97 HOH HOH . G 4 HOH J 62 665 99 HOH HOH . G 4 HOH J 63 666 101 HOH HOH . G 4 HOH J 64 667 102 HOH HOH . G 4 HOH J 65 668 103 HOH HOH . G 4 HOH J 66 669 104 HOH HOH . G 4 HOH J 67 670 105 HOH HOH . G 4 HOH J 68 671 106 HOH HOH . G 4 HOH J 69 672 110 HOH HOH . G 4 HOH J 70 673 111 HOH HOH . G 4 HOH J 71 674 112 HOH HOH . G 4 HOH J 72 675 114 HOH HOH . G 4 HOH J 73 676 115 HOH HOH . G 4 HOH J 74 677 116 HOH HOH . H 4 HOH K 1 605 1 HOH HOH . H 4 HOH K 2 606 5 HOH HOH . H 4 HOH K 3 607 6 HOH HOH . H 4 HOH K 4 608 7 HOH HOH . H 4 HOH K 5 609 10 HOH HOH . H 4 HOH K 6 610 15 HOH HOH . H 4 HOH K 7 611 16 HOH HOH . H 4 HOH K 8 612 17 HOH HOH . H 4 HOH K 9 613 20 HOH HOH . H 4 HOH K 10 614 21 HOH HOH . H 4 HOH K 11 615 24 HOH HOH . H 4 HOH K 12 616 27 HOH HOH . H 4 HOH K 13 617 29 HOH HOH . H 4 HOH K 14 618 31 HOH HOH . H 4 HOH K 15 619 33 HOH HOH . H 4 HOH K 16 620 38 HOH HOH . H 4 HOH K 17 621 41 HOH HOH . H 4 HOH K 18 622 43 HOH HOH . H 4 HOH K 19 623 44 HOH HOH . H 4 HOH K 20 624 45 HOH HOH . H 4 HOH K 21 625 51 HOH HOH . H 4 HOH K 22 626 54 HOH HOH . H 4 HOH K 23 627 56 HOH HOH . H 4 HOH K 24 628 60 HOH HOH . H 4 HOH K 25 629 65 HOH HOH . H 4 HOH K 26 630 67 HOH HOH . H 4 HOH K 27 631 71 HOH HOH . H 4 HOH K 28 632 74 HOH HOH . H 4 HOH K 29 633 76 HOH HOH . H 4 HOH K 30 634 79 HOH HOH . H 4 HOH K 31 635 81 HOH HOH . H 4 HOH K 32 636 88 HOH HOH . H 4 HOH K 33 637 91 HOH HOH . H 4 HOH K 34 638 93 HOH HOH . H 4 HOH K 35 639 94 HOH HOH . H 4 HOH K 36 640 95 HOH HOH . H 4 HOH K 37 641 98 HOH HOH . H 4 HOH K 38 642 100 HOH HOH . H 4 HOH K 39 643 107 HOH HOH . H 4 HOH K 40 644 108 HOH HOH . H 4 HOH K 41 645 109 HOH HOH . H 4 HOH K 42 646 113 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 . . . F 3 -7.43 7.154 -21.352 1 38.93 ? PG ANP 602 K 1 HETATM 2 O O1G ANP . . . F 3 -8.224 7.714 -20.237 1 40.38 ? O1G ANP 602 K 1 HETATM 3 O O2G ANP . . . F 3 -7.391 7.859 -22.799 1 35.85 ? O2G ANP 602 K 1 HETATM 4 O O3G ANP . . . F 3 -6.118 6.265 -21.068 1 35.15 ? O3G ANP 602 K 1 HETATM 5 P PB ANP . . . F 3 -7.915 5.009 -23.025 1 34.89 ? PB ANP 602 K 1 HETATM 6 O O1B ANP . . . F 3 -7.754 5.803 -24.263 1 36.54 ? O1B ANP 602 K 1 HETATM 7 O O2B ANP . . . F 3 -6.539 4.285 -22.608 1 34.35 ? O2B ANP 602 K 1 HETATM 8 N N3B ANP . . . F 3 -8.401 5.914 -21.765 1 37.45 ? N3B ANP 602 K 1 HETATM 9 P PA ANP . . . F 3 -8.739 2.331 -22.669 1 44.04 ? PA ANP 602 K 1 HETATM 10 O O1A ANP . . . F 3 -8.107 1.473 -23.697 1 48.6 ? O1A ANP 602 K 1 HETATM 11 O O2A ANP . . . F 3 -7.812 2.439 -21.358 1 50.34 ? O2A ANP 602 K 1 HETATM 12 O O3A ANP . . . F 3 -9.008 3.835 -23.186 1 39.39 ? O3A ANP 602 K 1 HETATM 13 O O5' ANP . . . F 3 -10.15 1.757 -22.152 1 50.28 ? O5' ANP 602 K 1 HETATM 14 C C5' ANP . . . F 3 -11.221 1.524 -23.07 1 55.67 ? C5' ANP 602 K 1 HETATM 15 C C4' ANP . . . F 3 -12.445 0.962 -22.343 1 61.08 ? C4' ANP 602 K 1 HETATM 16 O O4' ANP . . . F 3 -12.228 -0.363 -21.825 1 64.02 ? O4' ANP 602 K 1 HETATM 17 C C3' ANP . . . F 3 -12.805 1.829 -21.133 1 63.24 ? C3' ANP 602 K 1 HETATM 18 O O3' ANP . . . F 3 -14.153 2.289 -21.261 1 63.49 ? O3' ANP 602 K 1 HETATM 19 C C2' ANP . . . F 3 -12.719 0.836 -19.974 1 65.25 ? C2' ANP 602 K 1 HETATM 20 O O2' ANP . . . F 3 -13.703 1.175 -18.993 1 68.2 ? O2' ANP 602 K 1 HETATM 21 C C1' ANP . . . F 3 -13.143 -0.426 -20.722 1 65.74 ? C1' ANP 602 K 1 HETATM 22 N N9 ANP . . . F 3 -12.981 -1.641 -19.889 1 67.81 ? N9 ANP 602 K 1 HETATM 23 C C8 ANP . . . F 3 -13.967 -2.3 -19.286 1 68.47 ? C8 ANP 602 K 1 HETATM 24 N N7 ANP . . . F 3 -13.473 -3.35 -18.631 1 67.85 ? N7 ANP 602 K 1 HETATM 25 C C5 ANP . . . F 3 -12.157 -3.364 -18.817 1 69.1 ? C5 ANP 602 K 1 HETATM 26 C C6 ANP . . . F 3 -11.127 -4.193 -18.39 1 69.07 ? C6 ANP 602 K 1 HETATM 27 N N6 ANP . . . F 3 -11.37 -5.241 -17.609 1 67.32 ? N6 ANP 602 K 1 HETATM 28 N N1 ANP . . . F 3 -9.872 -3.914 -18.77 1 70.48 ? N1 ANP 602 K 1 HETATM 29 C C2 ANP . . . F 3 -9.61 -2.869 -19.535 1 69.73 ? C2 ANP 602 K 1 HETATM 30 N N3 ANP . . . F 3 -10.564 -2.058 -19.959 1 69.56 ? N3 ANP 602 K 1 HETATM 31 C C4 ANP . . . F 3 -11.841 -2.275 -19.62 1 68.96 ? C4 ANP 602 K 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #