data_4PD7 # _model_server_result.job_id WhCmVT20VyP5Ne2vXuoPfQ _model_server_result.datetime_utc '2024-11-27 18:03:18' _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 4pd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PD7 # _exptl.entry_id 4PD7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Zebularine _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 120 _cell.entry_id 4PD7 _cell.length_a 119.811 _cell.length_b 119.811 _cell.length_c 82.658 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 59.9055 -103.75937 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 119.811 0 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 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id ZE8 _chem_comp.mon_nstd_flag . _chem_comp.name Zebularine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O2 C2 ZE8 doub 431 n n N3 C2 ZE8 sing 432 n n N3 C4 ZE8 doub 433 n n C2 N1 ZE8 sing 434 n n O2' C2' ZE8 sing 435 n n C4 C5 ZE8 sing 436 n n N1 C1' ZE8 sing 437 n n N1 C6 ZE8 sing 438 n n C2' C1' ZE8 sing 439 n n C2' C3' ZE8 sing 440 n n C1' O4' ZE8 sing 441 n n O4' C4' ZE8 sing 442 n n C6 C5 ZE8 doub 443 n n C3' O3' ZE8 sing 444 n n C3' C4' ZE8 sing 445 n n C4' C5' ZE8 sing 446 n n C5' O5' ZE8 sing 447 n n C4 H1 ZE8 sing 448 n n C5 H2 ZE8 sing 449 n n C6 H3 ZE8 sing 450 n n C1' H4 ZE8 sing 451 n n C2' H5 ZE8 sing 452 n n O2' H6 ZE8 sing 453 n n C3' H7 ZE8 sing 454 n n O3' H8 ZE8 sing 455 n n C4' H9 ZE8 sing 456 n n C5' H10 ZE8 sing 457 n n C5' H11 ZE8 sing 458 n n O5' H12 ZE8 sing 459 n n # _atom_sites.entry_id 4PD7 _atom_sites.fract_transf_matrix[1][1] 0.008346 _atom_sites.fract_transf_matrix[1][2] 0.004819 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009638 _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] 0.012098 _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 ZE8 A 1 501 1 ZE8 ZLN . C 3 NA A 1 502 1 NA NA . D 4 DMU A 1 503 503 DMU DMU . E 5 HOH A 1 601 1 HOH HOH . E 5 HOH A 2 602 1 HOH HOH . E 5 HOH A 3 603 1 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 N N1 ZE8 . . . B 2 51.201 -20.308 -8.609 1 25.56 ? N1 ZE8 501 A 1 HETATM 2 C C2 ZE8 . . . B 2 50.548 -20.602 -9.79 1 25.56 ? C2 ZE8 501 A 1 HETATM 3 O O2 ZE8 . . . B 2 50.887 -20.059 -10.827 1 25.56 ? O2 ZE8 501 A 1 HETATM 4 N N3 ZE8 . . . B 2 49.509 -21.503 -9.804 1 25.56 ? N3 ZE8 501 A 1 HETATM 5 C C4 ZE8 . . . B 2 49.122 -22.12 -8.631 1 25.56 ? C4 ZE8 501 A 1 HETATM 6 C C5 ZE8 . . . B 2 49.815 -21.803 -7.41 1 25.56 ? C5 ZE8 501 A 1 HETATM 7 C C6 ZE8 . . . B 2 50.822 -20.918 -7.427 1 25.56 ? C6 ZE8 501 A 1 HETATM 8 C C1' ZE8 . . . B 2 52.325 -19.327 -8.599 1 25.56 ? C1' ZE8 501 A 1 HETATM 9 C C2' ZE8 . . . B 2 51.863 -17.876 -8.604 1 25.56 ? C2' ZE8 501 A 1 HETATM 10 O O2' ZE8 . . . B 2 52.735 -17.125 -9.423 1 25.56 ? O2' ZE8 501 A 1 HETATM 11 C C3' ZE8 . . . B 2 51.9 -17.487 -7.138 1 25.56 ? C3' ZE8 501 A 1 HETATM 12 O O3' ZE8 . . . B 2 52.224 -16.114 -6.969 1 25.56 ? O3' ZE8 501 A 1 HETATM 13 C C4' ZE8 . . . B 2 52.988 -18.375 -6.555 1 25.56 ? C4' ZE8 501 A 1 HETATM 14 O O4' ZE8 . . . B 2 53.159 -19.496 -7.464 1 25.56 ? O4' ZE8 501 A 1 HETATM 15 C C5' ZE8 . . . B 2 52.906 -18.656 -5.068 1 25.56 ? C5' ZE8 501 A 1 HETATM 16 O O5' ZE8 . . . B 2 51.644 -19.07 -4.561 1 25.56 ? O5' ZE8 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #