data_4PGF # _model_server_result.job_id RNos-qTtB5lNbZQdq7c5jA _model_server_result.datetime_utc '2024-11-28 17:13:59' _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 4pgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 4PGF # _exptl.entry_id 4PGF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _entity.pdbx_number_of_molecules 2 _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 4PGF _cell.length_a 97.597 _cell.length_b 102.74 _cell.length_c 175.018 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PGF _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 97.597 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 covale ? covale1 A C THR 407 A THR 407 1_555 A N ALY 408 A ALY 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C ALY 408 A ALY 408 1_555 A N LEU 409 A LEU 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 B C THR 407 B THR 407 1_555 B N ALY 408 B ALY 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C ALY 408 B ALY 408 1_555 B N LEU 409 B LEU 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 4PGF _atom_sites.fract_transf_matrix[1][1] 0.010246 _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] 0.009733 _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] 0.005714 _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 C 2 NAD A 1 501 501 NAD NAD . D 3 ADN A 1 502 502 ADN ADN . E 2 NAD B 1 501 501 NAD NAD . F 3 ADN B 1 502 502 ADN ADN . G 4 HOH A 1 601 610 HOH HOH . G 4 HOH A 2 602 612 HOH HOH . G 4 HOH A 3 603 601 HOH HOH . G 4 HOH A 4 604 611 HOH HOH . G 4 HOH A 5 605 607 HOH HOH . G 4 HOH A 6 606 606 HOH HOH . G 4 HOH A 7 607 602 HOH HOH . G 4 HOH A 8 608 609 HOH HOH . G 4 HOH A 9 609 613 HOH HOH . G 4 HOH A 10 610 603 HOH HOH . G 4 HOH A 11 611 604 HOH HOH . G 4 HOH A 12 612 608 HOH HOH . G 4 HOH A 13 613 605 HOH HOH . H 4 HOH B 1 601 609 HOH HOH . H 4 HOH B 2 602 608 HOH HOH . H 4 HOH B 3 603 601 HOH HOH . H 4 HOH B 4 604 602 HOH HOH . H 4 HOH B 5 605 606 HOH HOH . H 4 HOH B 6 606 607 HOH HOH . H 4 HOH B 7 607 603 HOH HOH . H 4 HOH B 8 608 611 HOH HOH . H 4 HOH B 9 609 610 HOH HOH . H 4 HOH B 10 610 605 HOH HOH . H 4 HOH B 11 611 604 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 . . . D 3 36.198 -16.323 -61.637 1 60.58 ? O5' ADN 502 A 1 HETATM 2 C C5' ADN . . . D 3 36.514 -15.101 -60.978 1 58.79 ? C5' ADN 502 A 1 HETATM 3 C C4' ADN . . . D 3 35.533 -14.022 -61.35 1 61 ? C4' ADN 502 A 1 HETATM 4 O O4' ADN . . . D 3 34.505 -13.955 -60.34 1 62.79 ? O4' ADN 502 A 1 HETATM 5 C C3' ADN . . . D 3 36.113 -12.599 -61.448 1 59.34 ? C3' ADN 502 A 1 HETATM 6 O O3' ADN . . . D 3 36.06 -12.144 -62.802 1 60.22 ? O3' ADN 502 A 1 HETATM 7 C C2' ADN . . . D 3 35.17 -11.741 -60.57 1 57.95 ? C2' ADN 502 A 1 HETATM 8 O O2' ADN . . . D 3 34.79 -10.512 -61.159 1 56.46 ? O2' ADN 502 A 1 HETATM 9 C C1' ADN . . . D 3 33.962 -12.666 -60.377 1 60.03 ? C1' ADN 502 A 1 HETATM 10 N N9 ADN . . . D 3 33.199 -12.429 -59.145 1 58.02 ? N9 ADN 502 A 1 HETATM 11 C C8 ADN . . . D 3 33.651 -12.201 -57.83 1 57.16 ? C8 ADN 502 A 1 HETATM 12 N N7 ADN . . . D 3 32.649 -12.007 -56.974 1 56.2 ? N7 ADN 502 A 1 HETATM 13 C C5 ADN . . . D 3 31.492 -12.106 -57.746 1 57.27 ? C5 ADN 502 A 1 HETATM 14 C C6 ADN . . . D 3 30.112 -11.986 -57.416 1 59.23 ? C6 ADN 502 A 1 HETATM 15 N N6 ADN . . . D 3 29.731 -11.734 -56.134 1 59.14 ? N6 ADN 502 A 1 HETATM 16 N N1 ADN . . . D 3 29.16 -12.131 -58.402 1 60.46 ? N1 ADN 502 A 1 HETATM 17 C C2 ADN . . . D 3 29.622 -12.386 -59.662 1 60.43 ? C2 ADN 502 A 1 HETATM 18 N N3 ADN . . . D 3 30.891 -12.517 -60.113 1 59.38 ? N3 ADN 502 A 1 HETATM 19 C C4 ADN . . . D 3 31.799 -12.367 -59.1 1 58.06 ? C4 ADN 502 A 1 HETATM 20 H HO5' ADN . . . D 3 35.602 -16.794 -61.051 1 72.7 ? HO5' ADN 502 A 1 HETATM 21 H "H5'1" ADN . . . D 3 37.516 -14.718 -61.296 1 70.54 ? "H5'1" ADN 502 A 1 HETATM 22 H "H5'2" ADN . . . D 3 36.583 -15.24 -59.876 1 70.54 ? "H5'2" ADN 502 A 1 HETATM 23 H H4' ADN . . . D 3 35.029 -14.312 -62.309 1 73.2 ? H4' ADN 502 A 1 HETATM 24 H H3' ADN . . . D 3 37.157 -12.546 -61.043 1 71.21 ? H3' ADN 502 A 1 HETATM 25 H HO3' ADN . . . D 3 35.202 -12.399 -63.144 1 72.27 ? HO3' ADN 502 A 1 HETATM 26 H H2' ADN . . . D 3 35.663 -11.559 -59.58 1 69.54 ? H2' ADN 502 A 1 HETATM 27 H HO2' ADN . . . D 3 34.979 -10.58 -62.097 1 67.75 ? HO2' ADN 502 A 1 HETATM 28 H H1' ADN . . . D 3 33.241 -12.585 -61.239 1 72.04 ? H1' ADN 502 A 1 HETATM 29 H H8 ADN . . . D 3 34.718 -12.197 -57.593 1 68.59 ? H8 ADN 502 A 1 HETATM 30 H HN61 ADN . . . D 3 30.416 -11.59 -55.417 1 70.97 ? HN61 ADN 502 A 1 HETATM 31 H HN62 ADN . . . D 3 28.764 -11.69 -55.895 1 70.97 ? HN62 ADN 502 A 1 HETATM 32 H H2 ADN . . . D 3 28.834 -12.493 -60.425 1 72.51 ? H2 ADN 502 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #