data_4KH5 # _model_server_result.job_id foN3S58Eaa3D-KcuyEE0xg _model_server_result.datetime_utc '2024-11-22 19:55:29' _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 4kh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":700}' # _entry.id 4KH5 # _exptl.entry_id 4KH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 426.216 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy(phosphonoamino)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 4KH5 _cell.length_a 73.537 _cell.length_b 150.25 _cell.length_c 240.967 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -120.4835 # 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 E 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 35 A CYS 59 1_555 A SG CYS 64 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 317 A CYS 341 1_555 A SG CYS 328 A CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 332 A CYS 356 1_555 A SG CYS 421 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 341 A CYS 365 1_555 A SG CYS 409 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 372 A CYS 396 1_555 A SG CYS 389 A CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 502 A CYS 526 1_555 A SG CYS 534 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 35 B CYS 59 1_555 B SG CYS 64 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 317 B CYS 341 1_555 B SG CYS 328 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 332 B CYS 356 1_555 B SG CYS 421 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 B SG CYS 341 B CYS 365 1_555 B SG CYS 409 B CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 B SG CYS 372 B CYS 396 1_555 B SG CYS 389 B CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 B SG CYS 502 B CYS 526 1_555 B SG CYS 534 B CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 C O3B AU1 . A AU1 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 C O5' AU1 . A AU1 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc3 E O2A AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc4 E O2A AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 E O2B AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc6 E O2B AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.499 ? # _chem_comp.formula 'C10 H16 N6 O9 P2' _chem_comp.formula_weight 426.216 _chem_comp.id AU1 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Adenosine 5-(alpha,beta-imido)diphosphate' # 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 O2A PA AU1 doub 70 n n O2B PB AU1 doub 71 n n O1B PB AU1 sing 72 n n O1A PA AU1 sing 73 n n PB N3A AU1 sing 74 n n PB O3B AU1 sing 75 n n PA N3A AU1 sing 76 n n PA O5' AU1 sing 77 n n N6 C6 AU1 sing 78 n n N1 C6 AU1 doub 79 n y N1 C2 AU1 sing 80 n y O5' C5' AU1 sing 81 n n C5' C4' AU1 sing 82 n n C6 C5 AU1 sing 83 n y C2 N3 AU1 doub 84 n y N3 C4 AU1 sing 85 n y C5 C4 AU1 doub 86 n y C5 N7 AU1 sing 87 n y O4' C4' AU1 sing 88 n n O4' C1' AU1 sing 89 n n C4 N9 AU1 sing 90 n y N7 C8 AU1 doub 91 n y C4' C3' AU1 sing 92 n n N9 C8 AU1 sing 93 n y N9 C1' AU1 sing 94 n n C1' C2' AU1 sing 95 n n C3' C2' AU1 sing 96 n n C3' O3' AU1 sing 97 n n C2' O2' AU1 sing 98 n n O1A H1 AU1 sing 99 n n N3A H2 AU1 sing 100 n n O1B H3 AU1 sing 101 n n O3B H4 AU1 sing 102 n n C5' H5 AU1 sing 103 n n C5' H6 AU1 sing 104 n n C4' H7 AU1 sing 105 n n C3' H8 AU1 sing 106 n n O3' H9 AU1 sing 107 n n C2' H10 AU1 sing 108 n n O2' H11 AU1 sing 109 n n C1' H12 AU1 sing 110 n n C8 H13 AU1 sing 111 n n C2 H14 AU1 sing 112 n n N6 H15 AU1 sing 113 n n N6 H16 AU1 sing 114 n n # _atom_sites.entry_id 4KH5 _atom_sites.fract_transf_matrix[1][1] 0.013599 _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] 0.006656 _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] 0.00415 _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 AU1 A 1 700 700 AU1 19P . D 3 MG A 1 701 701 MG MG . E 2 AU1 B 1 700 700 AU1 AU1 . F 3 MG B 1 701 701 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 O O1A AU1 . . . C 2 -23.711 -28.626 -35.468 0.8 53.75 ? O1A AU1 700 A 1 HETATM 2 P PA AU1 . . . C 2 -24.202 -27.356 -36.122 0.8 53.58 ? PA AU1 700 A 1 HETATM 3 O O2A AU1 . . . C 2 -25.699 -27.178 -36.039 0.8 53.19 ? O2A AU1 700 A 1 HETATM 4 N N3A AU1 . . . C 2 -23.525 -26.066 -35.145 0.8 54.08 ? N3A AU1 700 A 1 HETATM 5 P PB AU1 . . . C 2 -23.93 -24.38 -35.418 0.8 54.75 ? PB AU1 700 A 1 HETATM 6 O O2B AU1 . . . C 2 -22.644 -23.626 -35.179 0.8 54.37 ? O2B AU1 700 A 1 HETATM 7 O O1B AU1 . . . C 2 -25 -24.071 -34.399 0.8 54.34 ? O1B AU1 700 A 1 HETATM 8 O O3B AU1 . . . C 2 -24.413 -24.312 -36.85 0.8 55.37 ? O3B AU1 700 A 1 HETATM 9 O O5' AU1 . . . C 2 -23.635 -27.133 -37.505 0.8 53.66 ? O5' AU1 700 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 9 #