data_3B9R # _model_server_result.job_id r4njD5aDHb8j7sGbI00TRQ _model_server_result.datetime_utc '2024-11-21 14:03:46' _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 3b9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","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 . . . F 5 59.902 -12.554 22.314 1 121.9 ? PG ACP 998 A 1 HETATM 2 O O1G ACP . . . F 5 59.383 -11.048 22.455 1 169.94 ? O1G ACP 998 A 1 HETATM 3 O O2G ACP . . . F 5 60.376 -12.528 20.795 1 261.89 ? O2G ACP 998 A 1 HETATM 4 O O3G ACP . . . F 5 58.784 -13.422 22.618 1 119.28 ? O3G ACP 998 A 1 HETATM 5 P PB ACP . . . F 5 61.934 -14.43 23.485 1 160.04 ? PB ACP 998 A 1 HETATM 6 O O1B ACP . . . F 5 63.157 -14.364 24.278 1 152.68 ? O1B ACP 998 A 1 HETATM 7 O O2B ACP . . . F 5 62.127 -15.096 22.032 1 98.42 ? O2B ACP 998 A 1 HETATM 8 C C3B ACP . . . F 5 61.299 -12.884 23.261 1 279.59 ? C3B ACP 998 A 1 HETATM 9 P PA ACP . . . F 5 61.249 -17.271 24.29 1 148.86 ? PA ACP 998 A 1 HETATM 10 O O1A ACP . . . F 5 61.732 -17.619 25.615 1 142.6 ? O1A ACP 998 A 1 HETATM 11 O O2A ACP . . . F 5 59.743 -17.608 23.988 1 123.63 ? O2A ACP 998 A 1 HETATM 12 O O3A ACP . . . F 5 61.108 -15.659 24.151 1 171.55 ? O3A ACP 998 A 1 HETATM 13 O O5' ACP . . . F 5 62.065 -18.076 23.12 1 128.71 ? O5' ACP 998 A 1 HETATM 14 C C5' ACP . . . F 5 63.403 -17.616 22.819 1 128.07 ? C5' ACP 998 A 1 HETATM 15 C C4' ACP . . . F 5 64.229 -18.604 21.966 1 113.24 ? C4' ACP 998 A 1 HETATM 16 O O4' ACP . . . F 5 63.399 -19.753 22.046 1 81.91 ? O4' ACP 998 A 1 HETATM 17 C C3' ACP . . . F 5 63.98 -18.367 20.466 1 131.19 ? C3' ACP 998 A 1 HETATM 18 O O3' ACP . . . F 5 64.854 -17.689 19.575 1 151.28 ? O3' ACP 998 A 1 HETATM 19 C C2' ACP . . . F 5 63.691 -19.751 19.841 1 115.13 ? C2' ACP 998 A 1 HETATM 20 O O2' ACP . . . F 5 64.717 -19.96 18.884 1 106.67 ? O2' ACP 998 A 1 HETATM 21 C C1' ACP . . . F 5 63.927 -20.7 21.078 1 70.03 ? C1' ACP 998 A 1 HETATM 22 N N9 ACP . . . F 5 63.123 -21.884 21.284 1 68.24 ? N9 ACP 998 A 1 HETATM 23 C C8 ACP . . . F 5 61.731 -21.972 21.573 1 75.5 ? C8 ACP 998 A 1 HETATM 24 N N7 ACP . . . F 5 61.272 -23.208 21.823 1 66.74 ? N7 ACP 998 A 1 HETATM 25 C C5 ACP . . . F 5 62.411 -24.033 21.669 1 71.26 ? C5 ACP 998 A 1 HETATM 26 C C6 ACP . . . F 5 62.619 -25.47 21.772 1 69.11 ? C6 ACP 998 A 1 HETATM 27 N N6 ACP . . . F 5 61.581 -26.327 22.027 1 72.75 ? N6 ACP 998 A 1 HETATM 28 N N1 ACP . . . F 5 63.872 -25.968 21.556 1 63.25 ? N1 ACP 998 A 1 HETATM 29 C C2 ACP . . . F 5 64.866 -25.084 21.254 1 67.87 ? C2 ACP 998 A 1 HETATM 30 N N3 ACP . . . F 5 64.83 -23.743 21.119 1 67.28 ? N3 ACP 998 A 1 HETATM 31 C C4 ACP . . . F 5 63.586 -23.216 21.35 1 66.66 ? C4 ACP 998 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #