data_2BY4 # _model_server_result.job_id s-R6sbBdcANloMy9vcbTaA _model_server_result.datetime_utc '2024-10-12 15:32:30' _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 2by4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1996}' # _entry.id 2BY4 # _exptl.entry_id 2BY4 _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 2BY4 _cell.length_a 71.739 _cell.length_b 71.739 _cell.length_c 593.656 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BY4 _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,F _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OE2 GLU 439 A GLU 439 1_555 D MG MG . A MG 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc2 C O2B ACP . A ACP 1996 1_555 D MG MG . A MG 1997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _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 2BY4 _atom_sites.fract_transf_matrix[1][1] 0.013939 _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] 0.013939 _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] 0.001684 _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 AD4 A 1 1995 1995 AD4 AD4 . C 3 ACP A 1 1996 1996 ACP ACP . D 4 MG A 1 1997 1997 MG MG . E 4 MG A 1 1998 1998 MG MG . F 5 NA A 1 1999 1999 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 1.741 34.043 131.382 0.5 70.2 ? PG ACP 1996 A 1 HETATM 2 O O1G ACP . . . C 3 0.379 33.398 131.581 0.5 68.65 ? O1G ACP 1996 A 1 HETATM 3 O O2G ACP . . . C 3 2.475 33.353 130.29 0.5 69.59 ? O2G ACP 1996 A 1 HETATM 4 O O3G ACP . . . C 3 1.645 35.557 131.186 0.5 69.61 ? O3G ACP 1996 A 1 HETATM 5 P PB ACP . . . C 3 1.997 34.948 134.06 0.5 73.22 ? PB ACP 1996 A 1 HETATM 6 O O1B ACP . . . C 3 0.675 34.275 134.25 0.5 74.05 ? O1B ACP 1996 A 1 HETATM 7 O O2B ACP . . . C 3 1.817 36.391 133.876 0.5 72.98 ? O2B ACP 1996 A 1 HETATM 8 C C3B ACP . . . C 3 2.676 34.103 132.839 0.5 71.24 ? C3B ACP 1996 A 1 HETATM 9 P PA ACP . . . C 3 3.93 34.318 136.378 0.5 76.44 ? PA ACP 1996 A 1 HETATM 10 O O1A ACP . . . C 3 5.104 35.255 136.128 0.5 75.31 ? O1A ACP 1996 A 1 HETATM 11 O O2A ACP . . . C 3 4.192 32.883 136.012 0.5 75.74 ? O2A ACP 1996 A 1 HETATM 12 O O3A ACP . . . C 3 2.638 34.828 135.581 0.5 74.33 ? O3A ACP 1996 A 1 HETATM 13 O O5' ACP . . . C 3 3.499 34.73 137.874 0.5 73.56 ? O5' ACP 1996 A 1 HETATM 14 C C5' ACP . . . C 3 3.206 33.618 138.755 0.5 71.11 ? C5' ACP 1996 A 1 HETATM 15 C C4' ACP . . . C 3 2.399 33.692 140.096 0.5 70.43 ? C4' ACP 1996 A 1 HETATM 16 O O4' ACP . . . C 3 2.714 34.882 140.768 0.5 70.51 ? O4' ACP 1996 A 1 HETATM 17 C C3' ACP . . . C 3 1.035 33.827 139.567 0.5 70.15 ? C3' ACP 1996 A 1 HETATM 18 O O3' ACP . . . C 3 0.452 32.57 139.341 0.5 69.27 ? O3' ACP 1996 A 1 HETATM 19 C C2' ACP . . . C 3 0.352 34.766 140.588 0.5 69.93 ? C2' ACP 1996 A 1 HETATM 20 O O2' ACP . . . C 3 -0.256 34.002 141.61 0.5 70.27 ? O2' ACP 1996 A 1 HETATM 21 C C1' ACP . . . C 3 1.501 35.602 141.012 0.5 69.83 ? C1' ACP 1996 A 1 HETATM 22 N N9 ACP . . . C 3 1.679 36.967 140.31 0.5 69.47 ? N9 ACP 1996 A 1 HETATM 23 C C8 ACP . . . C 3 1.178 37.454 139.151 0.5 69.46 ? C8 ACP 1996 A 1 HETATM 24 N N7 ACP . . . C 3 1.529 38.686 138.814 0.5 69.29 ? N7 ACP 1996 A 1 HETATM 25 C C5 ACP . . . C 3 2.308 39.021 139.834 0.5 69.32 ? C5 ACP 1996 A 1 HETATM 26 C C6 ACP . . . C 3 3.061 40.207 140.168 0.5 69.52 ? C6 ACP 1996 A 1 HETATM 27 N N6 ACP . . . C 3 3.037 41.291 139.349 0.5 69.96 ? N6 ACP 1996 A 1 HETATM 28 N N1 ACP . . . C 3 3.815 40.267 141.343 0.5 69 ? N1 ACP 1996 A 1 HETATM 29 C C2 ACP . . . C 3 3.859 39.191 142.193 0.5 69.15 ? C2 ACP 1996 A 1 HETATM 30 N N3 ACP . . . C 3 3.179 38.028 141.953 0.5 69.68 ? N3 ACP 1996 A 1 HETATM 31 C C4 ACP . . . C 3 2.44 37.988 140.788 0.5 69.45 ? C4 ACP 1996 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #