data_5ZTF # _model_server_result.job_id 1gdVGVATnYQaQupUOmsz7A _model_server_result.datetime_utc '2024-12-03 23:40:49' _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 5ztf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2001}' # _entry.id 5ZTF # _exptl.entry_id 5ZTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 5ZTF _cell.length_a 165.079 _cell.length_b 84.053 _cell.length_c 118.832 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A O ALA 333 A ALA 305 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc2 A O ILE 335 A ILE 307 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.037 ? metalc ? metalc3 A OE2 GLU 337 A GLU 309 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc4 A OD2 ASP 379 A ASP 351 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc5 A O THR 381 A THR 353 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 A OD1 ASP 730 A ASP 702 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc7 A OD2 ASP 730 A ASP 702 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc8 A OD1 ASN 795 A ASN 767 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc9 A OE2 GLU 798 A GLU 770 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc10 A OD1 ASN 823 A ASN 795 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc11 A OD2 ASP 827 A ASP 799 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc12 A OD1 ASP 827 A ASP 799 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc13 A OD2 ASP 827 A ASP 799 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc14 A OE2 GLU 935 A GLU 907 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc15 B O3G ACP . A ACP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _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 5ZTF _atom_sites.fract_transf_matrix[1][1] 0.006058 _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] 0.011897 _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] 0.008415 _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 B 2 ACP A 1 2001 2001 ACP ACP . C 3 MG A 1 2002 3001 MG MG . D 4 CA A 1 2003 4001 CA CA . E 4 CA A 1 2004 4002 CA CA . # 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 . . . B 2 18.933 9.734 3.045 1 53.55 ? PG ACP 2001 A 1 HETATM 2 O O1G ACP . . . B 2 19.24 11.236 3.084 1 50.95 ? O1G ACP 2001 A 1 HETATM 3 O O2G ACP . . . B 2 17.806 9.422 4.023 1 56.88 ? O2G ACP 2001 A 1 HETATM 4 O O3G ACP . . . B 2 20.155 8.923 3.386 1 59.88 ? O3G ACP 2001 A 1 HETATM 5 P PB ACP . . . B 2 19.487 9.729 0.043 1 60.38 ? PB ACP 2001 A 1 HETATM 6 O O1B ACP . . . B 2 18.686 9.624 -1.204 1 50.29 ? O1B ACP 2001 A 1 HETATM 7 O O2B ACP . . . B 2 20.642 8.792 -0.01 1 47.53 ? O2B ACP 2001 A 1 HETATM 8 C C3B ACP . . . B 2 18.308 9.274 1.388 1 51.78 ? C3B ACP 2001 A 1 HETATM 9 P PA ACP . . . B 2 21.116 11.915 -0.828 1 57.05 ? PA ACP 2001 A 1 HETATM 10 O O1A ACP . . . B 2 21.078 13.385 -0.712 1 57.37 ? O1A ACP 2001 A 1 HETATM 11 O O2A ACP . . . B 2 22.494 11.433 -0.601 1 58.73 ? O2A ACP 2001 A 1 HETATM 12 O O3A ACP . . . B 2 20.077 11.267 0.254 1 50.54 ? O3A ACP 2001 A 1 HETATM 13 O O5' ACP . . . B 2 20.626 11.448 -2.353 1 50.71 ? O5' ACP 2001 A 1 HETATM 14 C C5' ACP . . . B 2 19.443 12.042 -2.869 1 56.62 ? C5' ACP 2001 A 1 HETATM 15 C C4' ACP . . . B 2 19.223 11.447 -4.267 1 49.42 ? C4' ACP 2001 A 1 HETATM 16 O O4' ACP . . . B 2 20.39 11.11 -4.678 1 53.99 ? O4' ACP 2001 A 1 HETATM 17 C C3' ACP . . . B 2 18.456 10.106 -4.148 1 49.88 ? C3' ACP 2001 A 1 HETATM 18 O O3' ACP . . . B 2 17.146 10.265 -4.472 1 59.79 ? O3' ACP 2001 A 1 HETATM 19 C C2' ACP . . . B 2 19.125 9.175 -5.138 1 56.46 ? C2' ACP 2001 A 1 HETATM 20 O O2' ACP . . . B 2 18.2 8.982 -6.316 1 56.7 ? O2' ACP 2001 A 1 HETATM 21 C C1' ACP . . . B 2 20.231 9.768 -5.54 1 56.02 ? C1' ACP 2001 A 1 HETATM 22 N N9 ACP . . . B 2 21.386 8.918 -5.299 1 58.38 ? N9 ACP 2001 A 1 HETATM 23 C C8 ACP . . . B 2 21.829 8.468 -4.103 1 60.85 ? C8 ACP 2001 A 1 HETATM 24 N N7 ACP . . . B 2 22.923 7.709 -4.319 1 58.95 ? N7 ACP 2001 A 1 HETATM 25 C C5 ACP . . . B 2 23.154 7.692 -5.634 1 54.51 ? C5 ACP 2001 A 1 HETATM 26 C C6 ACP . . . B 2 24.132 7.077 -6.378 1 55.86 ? C6 ACP 2001 A 1 HETATM 27 N N6 ACP . . . B 2 25.325 6.192 -6.057 1 63.19 ? N6 ACP 2001 A 1 HETATM 28 N N1 ACP . . . B 2 24.147 7.216 -7.706 1 55.45 ? N1 ACP 2001 A 1 HETATM 29 C C2 ACP . . . B 2 23.19 7.967 -8.325 1 52.63 ? C2 ACP 2001 A 1 HETATM 30 N N3 ACP . . . B 2 22.215 8.58 -7.584 1 55.32 ? N3 ACP 2001 A 1 HETATM 31 C C4 ACP . . . B 2 22.201 8.441 -6.247 1 55.74 ? C4 ACP 2001 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #