data_2C88 # _model_server_result.job_id nUhEdDbnEzrpC8m9x-mUGA _model_server_result.datetime_utc '2024-10-12 15:30:54' _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 2c88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1996}' # _entry.id 2C88 # _exptl.entry_id 2C88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 2C88 _cell.length_a 71.529 _cell.length_b 71.529 _cell.length_c 590.216 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2C88 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PQS _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 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A OE2 GLU 439 A GLU 439 1_555 D MG MG . A MG 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc2 A O LYS 712 A LYS 712 1_555 E NA NA . A NA 1998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A OE1 GLU 732 A GLU 732 1_555 E NA NA . A NA 1998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc4 C O1A ACP . A ACP 1996 1_555 D MG MG . A MG 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc5 C O2B ACP . A ACP 1996 1_555 D MG MG . A MG 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? # _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 2C88 _atom_sites.fract_transf_matrix[1][1] 0.01398 _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] 0.01398 _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] 0.001694 _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 TG1 A 1 1995 1995 TG1 TG1 . C 3 ACP A 1 1996 1996 ACP ACP . D 4 MG A 1 1997 1997 MG MG . E 5 NA A 1 1998 1998 NA NA . # 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 . . . C 3 2.063 33.998 131.448 1 127.57 ? PG ACP 1996 A 1 HETATM 2 O O1G ACP . . . C 3 0.546 33.805 131.387 1 127.45 ? O1G ACP 1996 A 1 HETATM 3 O O2G ACP . . . C 3 2.743 32.964 130.606 1 128.22 ? O2G ACP 1996 A 1 HETATM 4 O O3G ACP . . . C 3 2.482 35.441 131.116 1 127.15 ? O3G ACP 1996 A 1 HETATM 5 P PB ACP . . . C 3 1.776 34.735 134.191 1 124.94 ? PB ACP 1996 A 1 HETATM 6 O O1B ACP . . . C 3 0.47 33.997 134.166 1 124.96 ? O1B ACP 1996 A 1 HETATM 7 O O2B ACP . . . C 3 1.558 36.182 134.03 1 124.91 ? O2B ACP 1996 A 1 HETATM 8 C C3B ACP . . . C 3 2.684 33.977 133.061 1 125.89 ? C3B ACP 1996 A 1 HETATM 9 P PA ACP . . . C 3 3.527 34.353 136.705 1 123.56 ? PA ACP 1996 A 1 HETATM 10 O O1A ACP . . . C 3 4.508 35.496 136.462 1 123.68 ? O1A ACP 1996 A 1 HETATM 11 O O2A ACP . . . C 3 4.107 32.985 136.477 1 123.49 ? O2A ACP 1996 A 1 HETATM 12 O O3A ACP . . . C 3 2.228 34.562 135.779 1 124.29 ? O3A ACP 1996 A 1 HETATM 13 O O5' ACP . . . C 3 2.911 34.75 138.132 1 120.88 ? O5' ACP 1996 A 1 HETATM 14 C C5' ACP . . . C 3 2.184 33.708 138.826 1 116.11 ? C5' ACP 1996 A 1 HETATM 15 C C4' ACP . . . C 3 1.16 33.99 139.957 1 113.54 ? C4' ACP 1996 A 1 HETATM 16 O O4' ACP . . . C 3 1.603 35.135 140.636 1 112.79 ? O4' ACP 1996 A 1 HETATM 17 C C3' ACP . . . C 3 0 34.367 139.133 1 113.13 ? C3' ACP 1996 A 1 HETATM 18 O O3' ACP . . . C 3 -0.817 33.248 138.849 1 112.61 ? O3' ACP 1996 A 1 HETATM 19 C C2' ACP . . . C 3 -0.631 35.548 139.916 1 112.87 ? C2' ACP 1996 A 1 HETATM 20 O O2' ACP . . . C 3 -1.641 35.088 140.804 1 112.37 ? O2' ACP 1996 A 1 HETATM 21 C C1' ACP . . . C 3 0.576 36.137 140.564 1 112.5 ? C1' ACP 1996 A 1 HETATM 22 N N9 ACP . . . C 3 1.217 37.396 139.874 1 111.7 ? N9 ACP 1996 A 1 HETATM 23 C C8 ACP . . . C 3 1.051 37.966 138.641 1 110.96 ? C8 ACP 1996 A 1 HETATM 24 N N7 ACP . . . C 3 1.771 39.049 138.368 1 110.35 ? N7 ACP 1996 A 1 HETATM 25 C C5 ACP . . . C 3 2.436 39.222 139.51 1 110.7 ? C5 ACP 1996 A 1 HETATM 26 C C6 ACP . . . C 3 3.441 40.172 139.976 1 110.93 ? C6 ACP 1996 A 1 HETATM 27 N N6 ACP . . . C 3 3.846 41.214 139.187 1 110.86 ? N6 ACP 1996 A 1 HETATM 28 N N1 ACP . . . C 3 3.982 40.082 141.261 1 110.76 ? N1 ACP 1996 A 1 HETATM 29 C C2 ACP . . . C 3 3.599 39.054 142.095 1 110.99 ? C2 ACP 1996 A 1 HETATM 30 N N3 ACP . . . C 3 2.673 38.097 141.742 1 111.48 ? N3 ACP 1996 A 1 HETATM 31 C C4 ACP . . . C 3 2.147 38.205 140.464 1 111.16 ? C4 ACP 1996 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #