data_5ZBL # _model_server_result.job_id TZRptkhjl2ahFuqr2dAkYQ _model_server_result.datetime_utc '2025-07-03 23:00:46' _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 5zbl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":301}' # _entry.id 5ZBL # _exptl.entry_id 5ZBL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 5ZBL _cell.length_a 70.153 _cell.length_b 70.714 _cell.length_c 190.802 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZBL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,N,O,U,V 1 1 C,D,P,Q,R,S,T,W,X 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 ? 6 P N N ? 6 R N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 5ZBL _atom_sites.fract_transf_matrix[1][1] 0.014255 _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] 0.014141 _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] 0.005241 _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 E 2 EDO A 1 301 5 EDO EDO . F 3 GOL A 1 302 5 GOL GOL . G 4 PO4 A 1 303 1 PO4 PO4 . H 5 SO4 A 1 304 3 SO4 SO4 . I 2 EDO B 1 301 7 EDO EDO . J 2 EDO B 1 302 8 EDO EDO . K 3 GOL B 1 303 1 GOL GOL . L 3 GOL B 1 304 3 GOL GOL . M 4 PO4 B 1 305 2 PO4 PO4 . N 5 SO4 B 1 306 1 SO4 SO4 . O 5 SO4 B 1 307 4 SO4 SO4 . P 6 AMP C 1 301 1 AMP AMP . Q 3 GOL C 1 302 4 GOL GOL . R 6 AMP D 1 301 2 AMP AMP . S 3 GOL D 1 302 2 GOL GOL . T 5 SO4 D 1 303 2 SO4 SO4 . U 7 HOH A 1 401 102 HOH HOH . U 7 HOH A 2 402 28 HOH HOH . U 7 HOH A 3 403 22 HOH HOH . U 7 HOH A 4 404 26 HOH HOH . U 7 HOH A 5 405 1 HOH HOH . U 7 HOH A 6 406 24 HOH HOH . U 7 HOH A 7 407 99 HOH HOH . U 7 HOH A 8 408 6 HOH HOH . U 7 HOH A 9 409 97 HOH HOH . U 7 HOH A 10 410 10 HOH HOH . U 7 HOH A 11 411 95 HOH HOH . U 7 HOH A 12 412 71 HOH HOH . U 7 HOH A 13 413 94 HOH HOH . U 7 HOH A 14 414 39 HOH HOH . U 7 HOH A 15 415 76 HOH HOH . U 7 HOH A 16 416 45 HOH HOH . U 7 HOH A 17 417 103 HOH HOH . U 7 HOH A 18 418 101 HOH HOH . U 7 HOH A 19 419 7 HOH HOH . U 7 HOH A 20 420 82 HOH HOH . U 7 HOH A 21 421 98 HOH HOH . V 7 HOH B 1 401 110 HOH HOH . V 7 HOH B 2 402 118 HOH HOH . V 7 HOH B 3 403 13 HOH HOH . V 7 HOH B 4 404 20 HOH HOH . V 7 HOH B 5 405 67 HOH HOH . V 7 HOH B 6 406 107 HOH HOH . V 7 HOH B 7 407 2 HOH HOH . V 7 HOH B 8 408 50 HOH HOH . V 7 HOH B 9 409 62 HOH HOH . V 7 HOH B 10 410 3 HOH HOH . V 7 HOH B 11 411 73 HOH HOH . V 7 HOH B 12 412 44 HOH HOH . V 7 HOH B 13 413 69 HOH HOH . V 7 HOH B 14 414 25 HOH HOH . V 7 HOH B 15 415 49 HOH HOH . V 7 HOH B 16 416 84 HOH HOH . V 7 HOH B 17 417 75 HOH HOH . V 7 HOH B 18 418 80 HOH HOH . V 7 HOH B 19 419 115 HOH HOH . V 7 HOH B 20 420 104 HOH HOH . V 7 HOH B 21 421 70 HOH HOH . V 7 HOH B 22 422 40 HOH HOH . V 7 HOH B 23 423 111 HOH HOH . W 7 HOH C 1 401 130 HOH HOH . W 7 HOH C 2 402 139 HOH HOH . W 7 HOH C 3 403 32 HOH HOH . W 7 HOH C 4 404 27 HOH HOH . W 7 HOH C 5 405 128 HOH HOH . W 7 HOH C 6 406 41 HOH HOH . W 7 HOH C 7 407 122 HOH HOH . W 7 HOH C 8 408 119 HOH HOH . W 7 HOH C 9 409 79 HOH HOH . W 7 HOH C 10 410 68 HOH HOH . W 7 HOH C 11 411 81 HOH HOH . W 7 HOH C 12 412 15 HOH HOH . W 7 HOH C 13 413 124 HOH HOH . X 7 HOH D 1 401 133 HOH HOH . X 7 HOH D 2 402 55 HOH HOH . X 7 HOH D 3 403 30 HOH HOH . X 7 HOH D 4 404 132 HOH HOH . X 7 HOH D 5 405 36 HOH HOH . X 7 HOH D 6 406 18 HOH HOH . X 7 HOH D 7 407 53 HOH HOH . X 7 HOH D 8 408 61 HOH HOH . X 7 HOH D 9 409 137 HOH HOH . X 7 HOH D 10 410 29 HOH HOH . X 7 HOH D 11 411 37 HOH HOH . X 7 HOH D 12 412 23 HOH HOH . X 7 HOH D 13 413 85 HOH HOH . X 7 HOH D 14 414 47 HOH HOH . X 7 HOH D 15 415 138 HOH HOH . X 7 HOH D 16 416 121 HOH HOH . X 7 HOH D 17 417 131 HOH HOH . X 7 HOH D 18 418 134 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 P AMP . . . R 6 11.56 -20.056 -30.744 1 43.43 ? P AMP 301 D 1 HETATM 2 O O1P AMP . . . R 6 12.877 -19.829 -31.463 1 36.57 ? O1P AMP 301 D 1 HETATM 3 O O2P AMP . . . R 6 11.425 -21.404 -30.117 1 47.13 ? O2P AMP 301 D 1 HETATM 4 O O3P AMP . . . R 6 11.1 -19.015 -29.753 1 44.56 ? O3P AMP 301 D 1 HETATM 5 O O5' AMP . . . R 6 10.481 -19.979 -31.92 1 50.04 ? O5' AMP 301 D 1 HETATM 6 C C5' AMP . . . R 6 10.516 -18.846 -32.82 1 66.65 ? C5' AMP 301 D 1 HETATM 7 C C4' AMP . . . R 6 9.533 -18.876 -34.009 1 73.13 ? C4' AMP 301 D 1 HETATM 8 O O4' AMP . . . R 6 9.559 -20.157 -34.64 1 83.03 ? O4' AMP 301 D 1 HETATM 9 C C3' AMP . . . R 6 8.058 -18.577 -33.668 1 77.27 ? C3' AMP 301 D 1 HETATM 10 O O3' AMP . . . R 6 7.504 -17.648 -34.627 1 63.82 ? O3' AMP 301 D 1 HETATM 11 C C2' AMP . . . R 6 7.36 -19.936 -33.732 1 82.18 ? C2' AMP 301 D 1 HETATM 12 O O2' AMP . . . R 6 5.967 -19.863 -34.096 1 74.25 ? O2' AMP 301 D 1 HETATM 13 C C1' AMP . . . R 6 8.197 -20.586 -34.826 1 86.2 ? C1' AMP 301 D 1 HETATM 14 N N9 AMP . . . R 6 8.138 -22.064 -34.908 1 82.91 ? N9 AMP 301 D 1 HETATM 15 C C8 AMP . . . R 6 8.344 -22.968 -33.937 1 81.81 ? C8 AMP 301 D 1 HETATM 16 N N7 AMP . . . R 6 8.218 -24.229 -34.442 1 81.15 ? N7 AMP 301 D 1 HETATM 17 C C5 AMP . . . R 6 7.934 -24.136 -35.765 1 82.72 ? C5 AMP 301 D 1 HETATM 18 C C6 AMP . . . R 6 7.655 -25.056 -36.915 1 73.5 ? C6 AMP 301 D 1 HETATM 19 N N6 AMP . . . R 6 7.668 -26.402 -36.77 1 68.27 ? N6 AMP 301 D 1 HETATM 20 N N1 AMP . . . R 6 7.377 -24.495 -38.131 1 86.38 ? N1 AMP 301 D 1 HETATM 21 C C2 AMP . . . R 6 7.353 -23.148 -38.317 1 87.58 ? C2 AMP 301 D 1 HETATM 22 N N3 AMP . . . R 6 7.598 -22.271 -37.32 1 88.27 ? N3 AMP 301 D 1 HETATM 23 C C4 AMP . . . R 6 7.885 -22.692 -36.055 1 85.04 ? C4 AMP 301 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #