data_4LGD # _model_server_result.job_id wfpnEQOSdiz-afAIg-9qFA _model_server_result.datetime_utc '2025-01-10 23:39:14' _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 4lgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":501}' # _entry.id 4LGD # _exptl.entry_id 4LGD _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.7 _cell.angle_gamma 90 _cell.entry_id 4LGD _cell.length_a 123.403 _cell.length_b 237.136 _cell.length_c 95.862 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 PISA tetrameric 4 software_defined_assembly 5 PISA tetrameric 4 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,K 1 1 C,G,R,S,T,U,V 2 1 D,H,W,X,Y,Z,AA,BA 3 1 B,F,L,M,N,O,P,Q 4 1 A,B,E,F,I,J,K,L,M,N,O,P,Q 5 1 C,D,G,H,R,S,T,U,V,W,X,Y,Z,AA,BA 6 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 I N N ? 3 L N N ? 3 R N N ? 3 W 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 OD2 ASP 165 A ASP 164 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc2 A OD1 ASP 165 A ASP 164 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc3 I O2B ANP . A ANP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 I O1A ANP . A ANP 501 1_555 J MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc5 B OD1 ASP 165 B ASP 164 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc6 B OD2 ASP 165 B ASP 164 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc7 L O2A ANP . B ANP 501 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc8 L O2B ANP . B ANP 501 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc9 C OD2 ASP 122 C ASP 121 1_555 U NA NA . C NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc10 C OD1 ASP 165 C ASP 164 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc11 C OD2 ASP 165 C ASP 164 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc12 R O2B ANP . C ANP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc13 R O1A ANP . C ANP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc14 V NA NA . C NA 505 1_555 H OD1 ASN 15 H ASN 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc15 D OD1 ASP 122 D ASP 121 1_555 BA NA NA . D NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc16 D OD1 ASP 165 D ASP 164 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc17 D OD2 ASP 165 D ASP 164 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc18 W O1A ANP . D ANP 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc19 W O2B ANP . D ANP 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? # _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 4LGD _atom_sites.fract_transf_matrix[1][1] 0.008104 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001531 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004217 _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] 0.010616 _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 I 3 ANP A 1 501 600 ANP ANP . J 4 MG A 1 502 601 MG MG . K 5 SO4 A 1 503 101 SO4 SO4 . L 3 ANP B 1 501 600 ANP ANP . M 4 MG B 1 502 601 MG MG . N 5 SO4 B 1 503 102 SO4 SO4 . O 5 SO4 B 1 504 105 SO4 SO4 . P 5 SO4 B 1 505 107 SO4 SO4 . Q 5 SO4 B 1 506 109 SO4 SO4 . R 3 ANP C 1 501 600 ANP ANP . S 4 MG C 1 502 601 MG MG . T 5 SO4 C 1 503 103 SO4 SO4 . U 6 NA C 1 504 1 NA NA . V 6 NA C 1 505 3 NA NA . W 3 ANP D 1 501 600 ANP ANP . X 4 MG D 1 502 601 MG MG . Y 5 SO4 D 1 503 104 SO4 SO4 . Z 5 SO4 D 1 504 106 SO4 SO4 . AA 5 SO4 D 1 505 108 SO4 SO4 . BA 6 NA D 1 506 2 NA NA . # 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 . . . W 3 16.317 2.634 51.286 1 89.99 ? PG ANP 501 D 1 HETATM 2 O O1G ANP . . . W 3 16.299 2.764 49.802 1 111.88 ? O1G ANP 501 D 1 HETATM 3 O O2G ANP . . . W 3 17.797 2.621 51.765 1 106.84 ? O2G ANP 501 D 1 HETATM 4 O O3G ANP . . . W 3 15.564 3.848 51.908 1 82.38 ? O3G ANP 501 D 1 HETATM 5 P PB ANP . . . W 3 15.902 0.596 53.17 1 69.9 ? PB ANP 501 D 1 HETATM 6 O O1B ANP . . . W 3 17.131 -0.245 53.107 1 86.5 ? O1B ANP 501 D 1 HETATM 7 O O2B ANP . . . W 3 14.692 -0.309 53.546 1 191.58 ? O2B ANP 501 D 1 HETATM 8 N N3B ANP . . . W 3 15.564 1.204 51.658 1 183.68 ? N3B ANP 501 D 1 HETATM 9 P PA ANP . . . W 3 15.298 1.696 55.586 1 85.97 ? PA ANP 501 D 1 HETATM 10 O O1A ANP . . . W 3 13.864 1.394 55.204 1 103.23 ? O1A ANP 501 D 1 HETATM 11 O O2A ANP . . . W 3 15.366 3.03 56.298 1 75.27 ? O2A ANP 501 D 1 HETATM 12 O O3A ANP . . . W 3 16.148 1.724 54.255 1 135.85 ? O3A ANP 501 D 1 HETATM 13 O O5' ANP . . . W 3 15.865 0.568 56.545 1 73.6 ? O5' ANP 501 D 1 HETATM 14 C C5' ANP . . . W 3 17.165 0.672 57.067 1 94.35 ? C5' ANP 501 D 1 HETATM 15 C C4' ANP . . . W 3 17.515 -0.53 57.915 1 94.91 ? C4' ANP 501 D 1 HETATM 16 O O4' ANP . . . W 3 16.482 -0.856 58.795 1 87.36 ? O4' ANP 501 D 1 HETATM 17 C C3' ANP . . . W 3 17.809 -1.741 57.104 1 101.87 ? C3' ANP 501 D 1 HETATM 18 O O3' ANP . . . W 3 19.003 -2.31 57.491 1 115.36 ? O3' ANP 501 D 1 HETATM 19 C C2' ANP . . . W 3 16.693 -2.664 57.365 1 87.98 ? C2' ANP 501 D 1 HETATM 20 O O2' ANP . . . W 3 17.127 -3.967 57.422 1 93.69 ? O2' ANP 501 D 1 HETATM 21 C C1' ANP . . . W 3 16.172 -2.212 58.67 1 66.86 ? C1' ANP 501 D 1 HETATM 22 N N9 ANP . . . W 3 14.741 -2.419 58.76 1 66.22 ? N9 ANP 501 D 1 HETATM 23 C C8 ANP . . . W 3 13.803 -1.758 58.062 1 88.43 ? C8 ANP 501 D 1 HETATM 24 N N7 ANP . . . W 3 12.595 -2.194 58.393 1 67.92 ? N7 ANP 501 D 1 HETATM 25 C C5 ANP . . . W 3 12.713 -3.148 59.313 1 61.12 ? C5 ANP 501 D 1 HETATM 26 C C6 ANP . . . W 3 11.808 -3.937 60.004 1 75.47 ? C6 ANP 501 D 1 HETATM 27 N N6 ANP . . . W 3 10.391 -3.778 59.749 1 79.33 ? N6 ANP 501 D 1 HETATM 28 N N1 ANP . . . W 3 12.255 -4.833 60.894 1 66.27 ? N1 ANP 501 D 1 HETATM 29 C C2 ANP . . . W 3 13.579 -4.986 61.135 1 66.47 ? C2 ANP 501 D 1 HETATM 30 N N3 ANP . . . W 3 14.488 -4.228 60.477 1 60.43 ? N3 ANP 501 D 1 HETATM 31 C C4 ANP . . . W 3 14.091 -3.314 59.571 1 57.06 ? C4 ANP 501 D 1 HETATM 32 H HOG2 ANP . . . W 3 18.258 3.237 51.319 1 128.21 ? HOG2 ANP 501 D 1 HETATM 33 H HOG3 ANP . . . W 3 15.194 4.331 51.259 1 98.85 ? HOG3 ANP 501 D 1 HETATM 34 H HOB2 ANP . . . W 3 14.592 -0.932 52.935 1 229.9 ? HOB2 ANP 501 D 1 HETATM 35 H HNB1 ANP . . . W 3 14.673 1.282 51.553 1 220.42 ? HNB1 ANP 501 D 1 HETATM 36 H "H5'1" ANP . . . W 3 17.801 0.744 56.332 1 113.22 ? "H5'1" ANP 501 D 1 HETATM 37 H "H5'2" ANP . . . W 3 17.221 1.468 57.615 1 113.22 ? "H5'2" ANP 501 D 1 HETATM 38 H H4' ANP . . . W 3 18.303 -0.317 58.436 1 113.9 ? H4' ANP 501 D 1 HETATM 39 H H3' ANP . . . W 3 17.84 -1.506 56.167 1 122.24 ? H3' ANP 501 D 1 HETATM 40 H H2' ANP . . . W 3 16.004 -2.577 56.678 1 105.58 ? H2' ANP 501 D 1 HETATM 41 H HO2' ANP . . . W 3 16.87 -4.396 56.69 1 112.42 ? HO2' ANP 501 D 1 HETATM 42 H H1' ANP . . . W 3 16.624 -2.699 59.382 1 80.23 ? H1' ANP 501 D 1 HETATM 43 H H8 ANP . . . W 3 13.983 -1.063 57.409 1 106.11 ? H8 ANP 501 D 1 HETATM 44 H HN61 ANP . . . W 3 9.785 -4.286 60.206 1 95.2 ? HN61 ANP 501 D 1 HETATM 45 H HN62 ANP . . . W 3 10.106 -3.172 59.135 1 95.2 ? HN62 ANP 501 D 1 HETATM 46 H H2 ANP . . . W 3 13.877 -5.641 61.783 1 79.77 ? H2 ANP 501 D 1 # _model_server_stats.io_time_ms 177 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 155 _model_server_stats.query_time_ms 430 _model_server_stats.encode_time_ms 78 _model_server_stats.element_count 46 #