data_6VPG # _model_server_result.job_id WjU8VBz92nFw6BTXWJteqA _model_server_result.datetime_utc '2024-11-07 05:36:12' _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 6vpg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6VPG # _exptl.entry_id 6VPG _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 90 _cell.entry_id 6VPG _cell.length_a 83.562 _cell.length_b 83.562 _cell.length_c 114.516 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VPG _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _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 covale ? covale1 A C ARG 189 A ARG 286 1_555 A N TPO 190 A TPO 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 190 A TPO 287 1_555 A N TPO 191 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C TPO 191 A TPO 288 1_555 A N LEU 192 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASP 177 A ASP 274 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc2 B O2B ANP . A ANP 401 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _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 6VPG _atom_sites.fract_transf_matrix[1][1] 0.011967 _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] 0.011967 _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] 0.008732 _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 1 ANP ANP . C 3 GOL A 1 402 1 GOL GOL . D 4 CL A 1 403 1 CL CL . E 4 CL A 1 404 2 CL CL . F 5 MG A 1 405 1 MG MG . G 6 HOH A 1 501 32 HOH HOH . G 6 HOH A 2 502 51 HOH HOH . G 6 HOH A 3 503 22 HOH HOH . G 6 HOH A 4 504 61 HOH HOH . G 6 HOH A 5 505 25 HOH HOH . G 6 HOH A 6 506 60 HOH HOH . G 6 HOH A 7 507 53 HOH HOH . G 6 HOH A 8 508 63 HOH HOH . G 6 HOH A 9 509 16 HOH HOH . G 6 HOH A 10 510 55 HOH HOH . G 6 HOH A 11 511 17 HOH HOH . G 6 HOH A 12 512 23 HOH HOH . G 6 HOH A 13 513 35 HOH HOH . G 6 HOH A 14 514 46 HOH HOH . G 6 HOH A 15 515 62 HOH HOH . G 6 HOH A 16 516 21 HOH HOH . G 6 HOH A 17 517 15 HOH HOH . G 6 HOH A 18 518 28 HOH HOH . G 6 HOH A 19 519 6 HOH HOH . G 6 HOH A 20 520 3 HOH HOH . G 6 HOH A 21 521 34 HOH HOH . G 6 HOH A 22 522 45 HOH HOH . G 6 HOH A 23 523 19 HOH HOH . G 6 HOH A 24 524 56 HOH HOH . G 6 HOH A 25 525 54 HOH HOH . G 6 HOH A 26 526 37 HOH HOH . G 6 HOH A 27 527 49 HOH HOH . G 6 HOH A 28 528 8 HOH HOH . G 6 HOH A 29 529 59 HOH HOH . G 6 HOH A 30 530 58 HOH HOH . G 6 HOH A 31 531 40 HOH HOH . G 6 HOH A 32 532 2 HOH HOH . G 6 HOH A 33 533 29 HOH HOH . G 6 HOH A 34 534 57 HOH HOH . G 6 HOH A 35 535 10 HOH HOH . G 6 HOH A 36 536 31 HOH HOH . G 6 HOH A 37 537 52 HOH HOH . G 6 HOH A 38 538 13 HOH HOH . G 6 HOH A 39 539 1 HOH HOH . G 6 HOH A 40 540 50 HOH HOH . G 6 HOH A 41 541 24 HOH HOH . G 6 HOH A 42 542 5 HOH HOH . G 6 HOH A 43 543 27 HOH HOH . G 6 HOH A 44 544 7 HOH HOH . G 6 HOH A 45 545 26 HOH HOH . G 6 HOH A 46 546 9 HOH HOH . G 6 HOH A 47 547 14 HOH HOH . G 6 HOH A 48 548 20 HOH HOH . G 6 HOH A 49 549 41 HOH HOH . G 6 HOH A 50 550 42 HOH HOH . G 6 HOH A 51 551 39 HOH HOH . G 6 HOH A 52 552 18 HOH HOH . G 6 HOH A 53 553 36 HOH HOH . G 6 HOH A 54 554 11 HOH HOH . G 6 HOH A 55 555 48 HOH HOH . G 6 HOH A 56 556 33 HOH HOH . G 6 HOH A 57 557 4 HOH HOH . G 6 HOH A 58 558 38 HOH HOH . G 6 HOH A 59 559 30 HOH HOH . G 6 HOH A 60 560 43 HOH HOH . G 6 HOH A 61 561 12 HOH HOH . G 6 HOH A 62 562 47 HOH HOH . G 6 HOH A 63 563 44 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 -13.583 28.919 8.005 1 214.3 ? PG ANP 401 A 1 HETATM 2 O O1G ANP . . . B 2 -14.676 29.93 7.853 1 214.04 ? O1G ANP 401 A 1 HETATM 3 O O2G ANP . . . B 2 -14.125 27.525 7.501 1 215.38 ? O2G ANP 401 A 1 HETATM 4 O O3G ANP . . . B 2 -13.147 28.84 9.527 1 213.27 ? O3G ANP 401 A 1 HETATM 5 P PB ANP . . . B 2 -11.059 28.183 7.124 1 207.22 ? PB ANP 401 A 1 HETATM 6 O O1B ANP . . . B 2 -10.5 27.955 5.757 1 206.12 ? O1B ANP 401 A 1 HETATM 7 O O2B ANP . . . B 2 -9.917 28.619 8.093 1 208.52 ? O2B ANP 401 A 1 HETATM 8 N N3B ANP . . . B 2 -12.24 29.377 7.075 1 211.04 ? N3B ANP 401 A 1 HETATM 9 P PA ANP . . . B 2 -10.807 25.814 8.443 1 188.81 ? PA ANP 401 A 1 HETATM 10 O O1A ANP . . . B 2 -9.854 25.039 7.61 1 188.23 ? O1A ANP 401 A 1 HETATM 11 O O2A ANP . . . B 2 -10.123 26.643 9.533 1 191.25 ? O2A ANP 401 A 1 HETATM 12 O O3A ANP . . . B 2 -11.683 26.836 7.596 1 199.94 ? O3A ANP 401 A 1 HETATM 13 O O5' ANP . . . B 2 -11.887 24.824 9.03 1 173.65 ? O5' ANP 401 A 1 HETATM 14 C C5' ANP . . . B 2 -13.101 25.377 9.563 1 158.39 ? C5' ANP 401 A 1 HETATM 15 C C4' ANP . . . B 2 -14.051 24.267 9.929 1 142.02 ? C4' ANP 401 A 1 HETATM 16 O O4' ANP . . . B 2 -13.318 23.038 10.119 1 131.24 ? O4' ANP 401 A 1 HETATM 17 C C3' ANP . . . B 2 -14.815 24.489 11.229 1 135.03 ? C3' ANP 401 A 1 HETATM 18 O O3' ANP . . . B 2 -16.008 25.228 10.992 1 135.86 ? O3' ANP 401 A 1 HETATM 19 C C2' ANP . . . B 2 -15.1 23.06 11.695 1 126.79 ? C2' ANP 401 A 1 HETATM 20 O O2' ANP . . . B 2 -16.286 22.541 11.105 1 125 ? O2' ANP 401 A 1 HETATM 21 C C1' ANP . . . B 2 -13.864 22.302 11.199 1 119.23 ? C1' ANP 401 A 1 HETATM 22 N N9 ANP . . . B 2 -12.823 22.127 12.207 1 100.1 ? N9 ANP 401 A 1 HETATM 23 C C8 ANP . . . B 2 -11.568 22.676 12.204 1 96.7 ? C8 ANP 401 A 1 HETATM 24 N N7 ANP . . . B 2 -10.836 22.345 13.242 1 96.86 ? N7 ANP 401 A 1 HETATM 25 C C5 ANP . . . B 2 -11.673 21.522 13.98 1 95.19 ? C5 ANP 401 A 1 HETATM 26 C C6 ANP . . . B 2 -11.494 20.838 15.2 1 83.44 ? C6 ANP 401 A 1 HETATM 27 N N6 ANP . . . B 2 -10.369 20.88 15.917 1 76.3 ? N6 ANP 401 A 1 HETATM 28 N N1 ANP . . . B 2 -12.529 20.1 15.662 1 82.12 ? N1 ANP 401 A 1 HETATM 29 C C2 ANP . . . B 2 -13.658 20.056 14.949 1 85.86 ? C2 ANP 401 A 1 HETATM 30 N N3 ANP . . . B 2 -13.94 20.655 13.789 1 92.22 ? N3 ANP 401 A 1 HETATM 31 C C4 ANP . . . B 2 -12.9 21.378 13.356 1 96.47 ? C4 ANP 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #