data_3U87 # _model_server_result.job_id J64GTdy3rS-B5REUbkA7IA _model_server_result.datetime_utc '2024-11-02 10:36:43' _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 3u87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 3U87 # _exptl.entry_id 3U87 _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 2 _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 90 _cell.entry_id 3U87 _cell.length_a 127.821 _cell.length_b 127.821 _cell.length_c 125.333 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,O 1 1 B,I,J,K,L,M,N,P 2 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 ? 2 C N N ? 2 I 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 OD1 ASN 161 A ASN 161 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 A OD1 ASP 175 A ASP 175 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 A OD2 ASP 175 A ASP 175 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 A OD2 ASP 175 A ASP 175 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc5 C O2B ANP . A ANP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? metalc ? metalc6 C O3G ANP . A ANP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc7 C O2A ANP . A ANP 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc8 C O1G ANP . A ANP 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc9 E MG MG . A MG 403 1_555 O O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc10 B OD1 ASN 161 B ASN 161 1_555 K MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc11 B OD1 ASP 175 B ASP 175 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc12 B OD2 ASP 175 B ASP 175 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc13 B OD2 ASP 175 B ASP 175 1_555 K MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc14 I O2B ANP . B ANP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc15 I O1B ANP . B ANP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc16 I O2A ANP . B ANP 401 1_555 K MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc17 I O2B ANP . B ANP 401 1_555 K MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? # _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 3U87 _atom_sites.fract_transf_matrix[1][1] 0.007819 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007819 _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] 0.007973 _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 ANP A 1 401 2 ANP ANP . D 3 MG A 1 402 3 MG MG . E 3 MG A 1 403 6 MG MG . F 4 CL A 1 404 7 CL CL . G 5 SO4 A 1 405 9 SO4 SO4 . H 6 GOL A 1 406 12 GOL GOL . I 2 ANP B 1 401 1 ANP ANP . J 3 MG B 1 402 4 MG MG . K 3 MG B 1 403 5 MG MG . L 4 CL B 1 404 8 CL CL . M 5 SO4 B 1 405 10 SO4 SO4 . N 6 GOL B 1 406 11 GOL GOL . O 7 HOH A 1 501 3 HOH HOH . O 7 HOH A 2 502 4 HOH HOH . O 7 HOH A 3 503 6 HOH HOH . O 7 HOH A 4 504 8 HOH HOH . O 7 HOH A 5 505 11 HOH HOH . O 7 HOH A 6 506 13 HOH HOH . O 7 HOH A 7 507 14 HOH HOH . O 7 HOH A 8 508 16 HOH HOH . O 7 HOH A 9 509 17 HOH HOH . O 7 HOH A 10 510 20 HOH HOH . O 7 HOH A 11 511 21 HOH HOH . O 7 HOH A 12 512 23 HOH HOH . O 7 HOH A 13 513 24 HOH HOH . O 7 HOH A 14 514 25 HOH HOH . O 7 HOH A 15 515 28 HOH HOH . O 7 HOH A 16 516 30 HOH HOH . O 7 HOH A 17 517 34 HOH HOH . O 7 HOH A 18 518 36 HOH HOH . O 7 HOH A 19 519 37 HOH HOH . O 7 HOH A 20 520 42 HOH HOH . O 7 HOH A 21 521 43 HOH HOH . O 7 HOH A 22 522 45 HOH HOH . O 7 HOH A 23 523 47 HOH HOH . O 7 HOH A 24 524 48 HOH HOH . O 7 HOH A 25 525 50 HOH HOH . O 7 HOH A 26 526 51 HOH HOH . O 7 HOH A 27 527 53 HOH HOH . O 7 HOH A 28 528 54 HOH HOH . P 7 HOH B 1 501 1 HOH HOH . P 7 HOH B 2 502 2 HOH HOH . P 7 HOH B 3 503 5 HOH HOH . P 7 HOH B 4 504 7 HOH HOH . P 7 HOH B 5 505 9 HOH HOH . P 7 HOH B 6 506 10 HOH HOH . P 7 HOH B 7 507 12 HOH HOH . P 7 HOH B 8 508 15 HOH HOH . P 7 HOH B 9 509 18 HOH HOH . P 7 HOH B 10 510 19 HOH HOH . P 7 HOH B 11 511 22 HOH HOH . P 7 HOH B 12 512 26 HOH HOH . P 7 HOH B 13 513 27 HOH HOH . P 7 HOH B 14 514 29 HOH HOH . P 7 HOH B 15 515 31 HOH HOH . P 7 HOH B 16 516 32 HOH HOH . P 7 HOH B 17 517 33 HOH HOH . P 7 HOH B 18 518 35 HOH HOH . P 7 HOH B 19 519 39 HOH HOH . P 7 HOH B 20 520 40 HOH HOH . P 7 HOH B 21 521 41 HOH HOH . P 7 HOH B 22 522 44 HOH HOH . P 7 HOH B 23 523 49 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 PB ANP . . . I 2 50.568 1.25 98.896 0.83 76.68 ? PB ANP 401 B 1 HETATM 2 O O1B ANP . . . I 2 51.052 1.087 100.358 0.83 78.76 ? O1B ANP 401 B 1 HETATM 3 O O2B ANP . . . I 2 49.537 2.416 98.833 0.83 363.87 ? O2B ANP 401 B 1 HETATM 4 N N3B ANP . . . I 2 51.869 1.574 97.919 0.83 79.42 ? N3B ANP 401 B 1 HETATM 5 P PA ANP . . . I 2 48.298 -0.156 98.532 0.83 65.67 ? PA ANP 401 B 1 HETATM 6 O O1A ANP . . . I 2 47.899 -0.748 99.922 0.83 59.82 ? O1A ANP 401 B 1 HETATM 7 O O2A ANP . . . I 2 47.708 1.278 98.386 0.83 163.43 ? O2A ANP 401 B 1 HETATM 8 O O3A ANP . . . I 2 49.859 -0.074 98.431 0.83 372.26 ? O3A ANP 401 B 1 HETATM 9 O O5' ANP . . . I 2 47.718 -1.099 97.403 0.83 71.17 ? O5' ANP 401 B 1 HETATM 10 C C5' ANP . . . I 2 48.43 -1.31 96.224 0.83 70.02 ? C5' ANP 401 B 1 HETATM 11 C C4' ANP . . . I 2 47.478 -1.857 95.176 0.83 69.66 ? C4' ANP 401 B 1 HETATM 12 O O4' ANP . . . I 2 47.308 -3.227 95.329 0.83 69.76 ? O4' ANP 401 B 1 HETATM 13 C C3' ANP . . . I 2 46.133 -1.239 95.282 0.83 68.67 ? C3' ANP 401 B 1 HETATM 14 O O3' ANP . . . I 2 46.036 -0.107 94.521 0.83 67.11 ? O3' ANP 401 B 1 HETATM 15 C C2' ANP . . . I 2 45.253 -2.286 94.766 0.83 70.02 ? C2' ANP 401 B 1 HETATM 16 O O2' ANP . . . I 2 45.159 -2.269 93.372 0.83 69.98 ? O2' ANP 401 B 1 HETATM 17 C C1' ANP . . . I 2 45.942 -3.509 95.269 0.83 69.09 ? C1' ANP 401 B 1 HETATM 18 N N9 ANP . . . I 2 45.441 -3.905 96.575 0.83 65.84 ? N9 ANP 401 B 1 HETATM 19 C C8 ANP . . . I 2 45.8 -3.369 97.754 0.83 64.02 ? C8 ANP 401 B 1 HETATM 20 N N7 ANP . . . I 2 45.146 -3.959 98.744 0.83 63.64 ? N7 ANP 401 B 1 HETATM 21 C C5 ANP . . . I 2 44.339 -4.896 98.241 0.83 65.9 ? C5 ANP 401 B 1 HETATM 22 C C6 ANP . . . I 2 43.442 -5.805 98.788 0.83 67.84 ? C6 ANP 401 B 1 HETATM 23 N N6 ANP . . . I 2 43.245 -5.848 100.211 0.83 67.78 ? N6 ANP 401 B 1 HETATM 24 N N1 ANP . . . I 2 42.761 -6.641 97.992 0.83 67.82 ? N1 ANP 401 B 1 HETATM 25 C C2 ANP . . . I 2 42.925 -6.626 96.656 0.83 65.88 ? C2 ANP 401 B 1 HETATM 26 N N3 ANP . . . I 2 43.795 -5.754 96.086 0.83 64.55 ? N3 ANP 401 B 1 HETATM 27 C C4 ANP . . . I 2 44.506 -4.886 96.84 0.83 65.28 ? C4 ANP 401 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 450 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 27 #