data_3B9R # _model_server_result.job_id pezE7NS8qQ4SdJKZ9Rv-rw _model_server_result.datetime_utc '2024-11-21 14:22:10' _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 3b9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":998}' # _entry.id 3B9R # _exptl.entry_id 3B9R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 107.79 _cell.angle_gamma 90 _cell.entry_id 3B9R _cell.length_a 131.98 _cell.length_b 94.43 _cell.length_c 136.18 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B9R _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # 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,K 1 1 B,G,H,I,J,L 2 1 A,C,D,E,F,K 3 1 B,G,H,I,J,L 3 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' 2_545 -x,y-1/2,-z -1 0 0 0 1 0 0 0 -1 0 -47.215 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 J 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 636 A CYS 636 1_555 A SG CYS 675 A CYS 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 A SG CYS 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 B SG CYS 636 B CYS 636 1_555 B SG CYS 675 B CYS 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf4 B SG CYS 876 B CYS 876 1_555 B SG CYS 888 B CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 A OD2 ASP 351 A ASP 351 1_555 D MG MG . A MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 A O THR 353 A THR 353 1_555 D MG MG . A MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 A OD2 ASP 703 A ASP 703 1_555 D MG MG . A MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc4 A O LEU 711 A LEU 711 1_555 E K K . A K 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc5 A O ALA 714 A ALA 714 1_555 E K K . A K 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc6 D MG MG . A MG 996 1_555 K O HOH . A HOH 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc7 D MG MG . A MG 996 1_555 K O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc8 B OD2 ASP 351 B ASP 351 1_555 H MG MG . B MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc9 B O THR 353 B THR 353 1_555 H MG MG . B MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc10 B OD2 ASP 703 B ASP 703 1_555 H MG MG . B MG 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc11 H MG MG . B MG 996 1_555 L O HOH . B HOH 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 3B9R _atom_sites.fract_transf_matrix[1][1] 0.007577 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002432 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01059 _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] 0.007712 _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 ALF A 1 995 2 ALF ALF . D 3 MG A 1 996 1 MG MG2 . E 4 K A 1 997 3 K K1 . F 5 ACP A 1 998 996 ACP ACP . G 2 ALF B 1 995 2 ALF ALF . H 3 MG B 1 996 1 MG MG2 . I 4 K B 1 997 3 K K1 . J 5 ACP B 1 998 996 ACP ACP . K 6 HOH A 1 999 1 HOH HOH . K 6 HOH A 2 1000 2 HOH HOH . K 6 HOH A 3 1001 3 HOH HOH . K 6 HOH A 4 1002 4 HOH HOH . L 6 HOH B 1 999 5 HOH HOH . L 6 HOH B 2 1000 6 HOH HOH . L 6 HOH B 3 1001 7 HOH HOH . L 6 HOH B 4 1002 8 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 ACP . . . J 5 54.356 24.955 41.075 1 211.07 ? PG ACP 998 B 1 HETATM 2 O O1G ACP . . . J 5 53.799 26.243 41.842 1 55.57 ? O1G ACP 998 B 1 HETATM 3 O O2G ACP . . . J 5 53.294 24.743 39.904 1 82.6 ? O2G ACP 998 B 1 HETATM 4 O O3G ACP . . . J 5 54.45 23.89 42.056 1 210.17 ? O3G ACP 998 B 1 HETATM 5 P PB ACP . . . J 5 56.811 26.484 41.179 1 166.26 ? PB ACP 998 B 1 HETATM 6 O O1B ACP . . . J 5 58.159 26.489 40.622 1 163.67 ? O1B ACP 998 B 1 HETATM 7 O O2B ACP . . . J 5 56.867 26.097 42.726 1 101.18 ? O2B ACP 998 B 1 HETATM 8 C C3B ACP . . . J 5 55.873 25.338 40.383 1 206.55 ? C3B ACP 998 B 1 HETATM 9 P PA ACP . . . J 5 56.37 29.471 42.116 1 99 ? PA ACP 998 B 1 HETATM 10 O O1A ACP . . . J 5 57.478 30.338 41.734 1 106.09 ? O1A ACP 998 B 1 HETATM 11 O O2A ACP . . . J 5 54.947 30.041 41.718 1 194.92 ? O2A ACP 998 B 1 HETATM 12 O O3A ACP . . . J 5 56.319 28.058 41.26 1 335.29 ? O3A ACP 998 B 1 HETATM 13 O O5' ACP . . . J 5 56.277 29.459 43.743 1 197.17 ? O5' ACP 998 B 1 HETATM 14 C C5' ACP . . . J 5 57.112 28.603 44.558 1 199.32 ? C5' ACP 998 B 1 HETATM 15 C C4' ACP . . . J 5 57.115 29.044 46.045 1 100.5 ? C4' ACP 998 B 1 HETATM 16 O O4' ACP . . . J 5 56.721 30.418 45.941 1 99.24 ? O4' ACP 998 B 1 HETATM 17 C C3' ACP . . . J 5 55.792 28.611 46.682 1 101.1 ? C3' ACP 998 B 1 HETATM 18 O O3' ACP . . . J 5 55.57 27.455 47.471 1 121.11 ? O3' ACP 998 B 1 HETATM 19 C C2' ACP . . . J 5 55.393 29.811 47.567 1 89.04 ? C2' ACP 998 B 1 HETATM 20 O O2' ACP . . . J 5 55.495 29.415 48.921 1 91.83 ? O2' ACP 998 B 1 HETATM 21 C C1' ACP . . . J 5 56.457 30.931 47.259 1 92.02 ? C1' ACP 998 B 1 HETATM 22 N N9 ACP . . . J 5 55.918 32.264 47.113 1 101.62 ? N9 ACP 998 B 1 HETATM 23 C C8 ACP . . . J 5 54.84 32.717 46.302 1 108.97 ? C8 ACP 998 B 1 HETATM 24 N N7 ACP . . . J 5 54.571 34.025 46.43 1 110.53 ? N7 ACP 998 B 1 HETATM 25 C C5 ACP . . . J 5 55.49 34.486 47.396 1 100.57 ? C5 ACP 998 B 1 HETATM 26 C C6 ACP . . . J 5 55.724 35.776 47.993 1 83.07 ? C6 ACP 998 B 1 HETATM 27 N N6 ACP . . . J 5 54.924 36.821 47.628 1 62.53 ? N6 ACP 998 B 1 HETATM 28 N N1 ACP . . . J 5 56.726 35.915 48.938 1 88.47 ? N1 ACP 998 B 1 HETATM 29 C C2 ACP . . . J 5 57.454 34.814 49.258 1 87.92 ? C2 ACP 998 B 1 HETATM 30 N N3 ACP . . . J 5 57.345 33.552 48.781 1 97.11 ? N3 ACP 998 B 1 HETATM 31 C C4 ACP . . . J 5 56.359 33.402 47.833 1 102.52 ? C4 ACP 998 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #