data_9G9E # _model_server_result.job_id ETBEdqkzcdzeL26D9bILig _model_server_result.datetime_utc '2025-02-22 20:43:36' _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 9g9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":802}' # _entry.id 9G9E # _exptl.entry_id 9G9E _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 506.196 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 9G9E _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9G9E _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,I,J,K,L,M _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 ? 7 J N N ? 7 K 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 disulf ? disulf1 A SG CYS 440 A CYS 421 1_555 A SG CYS 443 A CYS 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc1 A OD2 ASP 549 A ASP 530 1_555 L MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc2 A OD1 ASP 549 A ASP 530 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc3 A O ILE 550 A ILE 531 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc4 A OD1 ASP 603 A ASP 584 1_555 L MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc5 A OD2 ASP 603 A ASP 584 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc6 J O1A ZAN . A ZAN 801 1_555 L MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc7 J O1A ZAN . A ZAN 801 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc8 J O1B ZAN . A ZAN 801 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc9 J O3G ZAN . A ZAN 801 1_555 M MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ZAN _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 C2 N1 ZAN doub 524 n y C2 N3 ZAN sing 525 n y O2' C2' ZAN sing 526 n n N1 C6 ZAN sing 527 n y N3 C4 ZAN doub 528 n y C2' C1' ZAN sing 529 n n C2' C3' ZAN sing 530 n n C6 N6 ZAN sing 531 n n C6 C5 ZAN doub 532 n y C4 C5 ZAN sing 533 n y C4 N9 ZAN sing 534 n y O3' C3' ZAN sing 535 n n C1' N9 ZAN sing 536 n n C1' O4' ZAN sing 537 n n C5 N7 ZAN sing 538 n y C3' C4' ZAN sing 539 n n N9 C8 ZAN sing 540 n y O2B PB ZAN doub 541 n n N7 C8 ZAN doub 542 n y C4' O4' ZAN sing 543 n n C4' C5' ZAN sing 544 n n PB O1B ZAN sing 545 n n PB N3A ZAN sing 546 n n PB O3B ZAN sing 547 n n N3A PA ZAN sing 548 n n O3B PG ZAN sing 549 n n C5' O5' ZAN sing 550 n n O5' PA ZAN sing 551 n n PA O2A ZAN doub 552 n n PA O1A ZAN sing 553 n n O3G PG ZAN doub 554 n n PG O1G ZAN sing 555 n n PG O2G ZAN sing 556 n n O1A H1 ZAN sing 557 n n O1B H2 ZAN sing 558 n n O1G H3 ZAN sing 559 n n O2G H4 ZAN sing 560 n n N3A H5 ZAN sing 561 n n C5' H6 ZAN sing 562 n n C5' H7 ZAN sing 563 n n C4' H8 ZAN sing 564 n n C3' H9 ZAN sing 565 n n O3' H10 ZAN sing 566 n n C2' H11 ZAN sing 567 n n O2' H12 ZAN sing 568 n n C1' H13 ZAN sing 569 n n C8 H14 ZAN sing 570 n n N6 H15 ZAN sing 571 n n N6 H16 ZAN sing 572 n n C2 H17 ZAN sing 573 n n # _atom_sites.entry_id 9G9E _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 J 7 ZAN A 1 801 1 ZAN AN3 . K 7 ZAN A 1 802 2 ZAN AN3 . L 8 MG A 1 803 1 MG MG . M 8 MG A 1 804 2 MG MG . # 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 PA ZAN . . . K 7 159.851 150.182 189.322 1 16.35 ? PA ZAN 802 A 1 HETATM 2 P PB ZAN . . . K 7 157.143 149.143 189.89 1 15.52 ? PB ZAN 802 A 1 HETATM 3 P PG ZAN . . . K 7 156.643 150.98 192.148 1 21.83 ? PG ZAN 802 A 1 HETATM 4 O O1A ZAN . . . K 7 159.115 151.321 188.778 1 14.07 ? O1A ZAN 802 A 1 HETATM 5 O O1B ZAN . . . K 7 156.924 149.068 188.415 1 9.52 ? O1B ZAN 802 A 1 HETATM 6 O O1G ZAN . . . K 7 156.971 152.491 192.257 1 17.04 ? O1G ZAN 802 A 1 HETATM 7 O O2A ZAN . . . K 7 160.971 150.68 190.174 1 31.69 ? O2A ZAN 802 A 1 HETATM 8 O O2B ZAN . . . K 7 156.539 147.96 190.553 1 17.72 ? O2B ZAN 802 A 1 HETATM 9 O O2G ZAN . . . K 7 157.779 150.157 192.754 1 23.63 ? O2G ZAN 802 A 1 HETATM 10 N N3A ZAN . . . K 7 158.833 149.211 190.251 1 28.04 ? N3A ZAN 802 A 1 HETATM 11 O O3B ZAN . . . K 7 156.454 150.553 190.51 1 15.61 ? O3B ZAN 802 A 1 HETATM 12 O O3G ZAN . . . K 7 155.343 150.682 192.878 1 26.79 ? O3G ZAN 802 A 1 HETATM 13 O O5' ZAN . . . K 7 160.437 149.253 188.087 1 9.35 ? O5' ZAN 802 A 1 HETATM 14 C C5' ZAN . . . K 7 160.971 147.996 188.458 1 10.28 ? C5' ZAN 802 A 1 HETATM 15 C C4' ZAN . . . K 7 160.949 147.067 187.196 1 12.49 ? C4' ZAN 802 A 1 HETATM 16 O O4' ZAN . . . K 7 162.368 146.866 186.611 1 17.38 ? O4' ZAN 802 A 1 HETATM 17 C C3' ZAN . . . K 7 160.539 145.659 187.667 1 14.13 ? C3' ZAN 802 A 1 HETATM 18 O O3' ZAN . . . K 7 159.141 145.565 187.749 1 18.43 ? O3' ZAN 802 A 1 HETATM 19 C C2' ZAN . . . K 7 161.028 144.919 186.73 1 13.63 ? C2' ZAN 802 A 1 HETATM 20 O O2' ZAN . . . K 7 160.225 145.009 185.571 1 16.96 ? O2' ZAN 802 A 1 HETATM 21 C C1' ZAN . . . K 7 162.477 145.584 186.392 1 12.7 ? C1' ZAN 802 A 1 HETATM 22 N N9 ZAN . . . K 7 163.773 145.483 187.107 1 10.87 ? N9 ZAN 802 A 1 HETATM 23 C C8 ZAN . . . K 7 163.955 145.08 188.334 1 9.26 ? C8 ZAN 802 A 1 HETATM 24 N N7 ZAN . . . K 7 165.239 145.125 188.627 1 8.18 ? N7 ZAN 802 A 1 HETATM 25 C C5 ZAN . . . K 7 165.886 145.563 187.568 1 7.67 ? C5 ZAN 802 A 1 HETATM 26 C C6 ZAN . . . K 7 167.229 145.819 187.276 1 7.22 ? C6 ZAN 802 A 1 HETATM 27 N N6 ZAN . . . K 7 168.242 145.595 188.25 1 5.69 ? N6 ZAN 802 A 1 HETATM 28 N N1 ZAN . . . K 7 167.535 146.271 186.073 1 10.05 ? N1 ZAN 802 A 1 HETATM 29 C C2 ZAN . . . K 7 166.616 146.485 185.159 1 8.88 ? C2 ZAN 802 A 1 HETATM 30 N N3 ZAN . . . K 7 165.337 146.252 185.407 1 9.02 ? N3 ZAN 802 A 1 HETATM 31 C C4 ZAN . . . K 7 164.947 145.795 186.592 1 9.5 ? C4 ZAN 802 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #