data_4PD9 # _model_server_result.job_id u3xTm-_BOcql6xULMSfnvA _model_server_result.datetime_utc '2024-11-23 18:35:59' _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 4pd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PD9 # _exptl.entry_id 4PD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _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 4PD9 _cell.length_a 120.001 _cell.length_b 120.001 _cell.length_c 83.488 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD9 _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 60.0005 -103.923914 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 120.001 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 4PD9 _atom_sites.fract_transf_matrix[1][1] 0.008333 _atom_sites.fract_transf_matrix[1][2] 0.004811 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009622 _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] 0.011978 _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 ADN A 1 501 1 ADN Ar . 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 2 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 O O5' ADN . . . B 2 52.161 -18.787 -1.938 1 61.88 ? O5' ADN 501 A 1 HETATM 2 C C5' ADN . . . B 2 53.386 -18.195 -2.348 1 61.88 ? C5' ADN 501 A 1 HETATM 3 C C4' ADN . . . B 2 53.494 -18.135 -3.851 1 61.88 ? C4' ADN 501 A 1 HETATM 4 O O4' ADN . . . B 2 53.482 -19.479 -4.397 1 61.88 ? O4' ADN 501 A 1 HETATM 5 C C3' ADN . . . B 2 52.355 -17.433 -4.573 1 61.88 ? C3' ADN 501 A 1 HETATM 6 O O3' ADN . . . B 2 52.491 -16.022 -4.577 1 61.88 ? O3' ADN 501 A 1 HETATM 7 C C2' ADN . . . B 2 52.407 -18.052 -5.963 1 61.88 ? C2' ADN 501 A 1 HETATM 8 O O2' ADN . . . B 2 53.44 -17.46 -6.737 1 61.88 ? O2' ADN 501 A 1 HETATM 9 C C1' ADN . . . B 2 52.811 -19.491 -5.638 1 61.88 ? C1' ADN 501 A 1 HETATM 10 N N9 ADN . . . B 2 51.643 -20.385 -5.531 1 61.88 ? N9 ADN 501 A 1 HETATM 11 C C8 ADN . . . B 2 51.086 -20.911 -4.391 1 61.88 ? C8 ADN 501 A 1 HETATM 12 N N7 ADN . . . B 2 50.048 -21.681 -4.615 1 61.88 ? N7 ADN 501 A 1 HETATM 13 C C5 ADN . . . B 2 49.914 -21.661 -5.997 1 61.88 ? C5 ADN 501 A 1 HETATM 14 C C6 ADN . . . B 2 49 -22.28 -6.868 1 61.88 ? C6 ADN 501 A 1 HETATM 15 N N6 ADN . . . B 2 48.007 -23.071 -6.457 1 61.88 ? N6 ADN 501 A 1 HETATM 16 N N1 ADN . . . B 2 49.143 -22.053 -8.193 1 61.88 ? N1 ADN 501 A 1 HETATM 17 C C2 ADN . . . B 2 50.139 -21.259 -8.605 1 61.88 ? C2 ADN 501 A 1 HETATM 18 N N3 ADN . . . B 2 51.06 -20.622 -7.885 1 61.88 ? N3 ADN 501 A 1 HETATM 19 C C4 ADN . . . B 2 50.89 -20.868 -6.574 1 61.88 ? C4 ADN 501 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #