data_4HNT # _model_server_result.job_id d5tVKCRVwCEAP3YJCO1YWg _model_server_result.datetime_utc '2024-11-18 06:35:27' _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 4hnt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1201}' # _entry.id 4HNT # _exptl.entry_id 4HNT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 109.86 _cell.angle_gamma 90 _cell.entry_id 4HNT _cell.length_a 96.23 _cell.length_b 256.283 _cell.length_c 126.685 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HNT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,I,J,K,L,M _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 2 _struct_asym.id E _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 OD1 ASP 565 A ASP 572 1_555 F MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 A NZ LYS 735 A LYS 741 1_555 F MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc3 A NE2 HIS 764 A HIS 771 1_555 F MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc4 A NE2 HIS 766 A HIS 773 1_555 F MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc5 B OD1 ASP 565 B ASP 572 1_555 I MN MN . B MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 B NZ LYS 735 B LYS 741 1_555 I MN MN . B MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc7 B NE2 HIS 764 B HIS 771 1_555 I MN MN . B MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc8 B NE2 HIS 766 B HIS 773 1_555 I MN MN . B MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc9 C OD1 ASP 565 C ASP 572 1_555 J MN MN . C MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc10 C NZ LYS 735 C LYS 741 1_555 J MN MN . C MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc11 C NE2 HIS 764 C HIS 771 1_555 J MN MN . C MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc12 C NE2 HIS 766 C HIS 773 1_555 J MN MN . C MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc13 D OD1 ASP 565 D ASP 572 1_555 M MN MN . D MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc14 D NZ LYS 735 D LYS 741 1_555 M MN MN . D MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc15 D NE2 HIS 766 D HIS 773 1_555 M MN MN . D MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4HNT _atom_sites.fract_transf_matrix[1][1] 0.010392 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003754 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003902 _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] 0.008393 _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 E 2 ADP A 1 1201 2100 ADP ADP . F 3 MN A 1 1202 2002 MN MN . G 4 BTI A 1 1203 2000 BTI BNK . H 4 BTI B 1 1201 2000 BTI BNK . I 3 MN B 1 1202 2002 MN MN . J 3 MN C 1 1201 2002 MN MN . K 5 ATP C 1 1202 2100 ATP ATP . L 4 BTI D 1 1201 2000 BTI BNK . M 3 MN D 1 1202 2002 MN MN . # 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 PB ADP . . . E 2 87.367 47.905 1.842 1 110.54 ? PB ADP 1201 A 1 HETATM 2 O O1B ADP . . . E 2 86.059 48.102 1.082 1 110.5 ? O1B ADP 1201 A 1 HETATM 3 O O2B ADP . . . E 2 87.874 49.196 2.478 1 106.87 ? O2B ADP 1201 A 1 HETATM 4 O O3B ADP . . . E 2 87.375 46.674 2.74 1 103.72 ? O3B ADP 1201 A 1 HETATM 5 P PA ADP . . . E 2 88.34 46.383 -0.409 1 110.89 ? PA ADP 1201 A 1 HETATM 6 O O1A ADP . . . E 2 86.935 45.779 -0.378 1 108.22 ? O1A ADP 1201 A 1 HETATM 7 O O2A ADP . . . E 2 89.523 45.42 -0.366 1 106.3 ? O2A ADP 1201 A 1 HETATM 8 O O3A ADP . . . E 2 88.503 47.553 0.725 1 108.75 ? O3A ADP 1201 A 1 HETATM 9 O O5' ADP . . . E 2 88.46 47.332 -1.721 1 103.01 ? O5' ADP 1201 A 1 HETATM 10 C C5' ADP . . . E 2 89.059 48.623 -1.629 1 93.94 ? C5' ADP 1201 A 1 HETATM 11 C C4' ADP . . . E 2 89.398 49.044 -3.047 1 89.3 ? C4' ADP 1201 A 1 HETATM 12 O O4' ADP . . . E 2 90.778 48.8 -3.318 1 88.75 ? O4' ADP 1201 A 1 HETATM 13 C C3' ADP . . . E 2 88.593 48.214 -4.023 1 86.31 ? C3' ADP 1201 A 1 HETATM 14 O O3' ADP . . . E 2 87.68 49.076 -4.689 1 90.76 ? O3' ADP 1201 A 1 HETATM 15 C C2' ADP . . . E 2 89.566 47.684 -5.043 1 86.76 ? C2' ADP 1201 A 1 HETATM 16 O O2' ADP . . . E 2 89.372 48.326 -6.305 1 87.19 ? O2' ADP 1201 A 1 HETATM 17 C C1' ADP . . . E 2 90.945 48.032 -4.523 1 89.29 ? C1' ADP 1201 A 1 HETATM 18 N N9 ADP . . . E 2 91.678 46.751 -4.28 1 91.15 ? N9 ADP 1201 A 1 HETATM 19 C C8 ADP . . . E 2 91.655 46.026 -3.144 1 90.34 ? C8 ADP 1201 A 1 HETATM 20 N N7 ADP . . . E 2 92.41 44.91 -3.244 1 87.98 ? N7 ADP 1201 A 1 HETATM 21 C C5 ADP . . . E 2 92.936 44.898 -4.476 1 90.33 ? C5 ADP 1201 A 1 HETATM 22 C C6 ADP . . . E 2 93.838 44.001 -5.236 1 90.87 ? C6 ADP 1201 A 1 HETATM 23 N N6 ADP . . . E 2 94.329 42.865 -4.679 1 91.67 ? N6 ADP 1201 A 1 HETATM 24 N N1 ADP . . . E 2 94.142 44.349 -6.503 1 90.3 ? N1 ADP 1201 A 1 HETATM 25 C C2 ADP . . . E 2 93.649 45.461 -7.078 1 91.22 ? C2 ADP 1201 A 1 HETATM 26 N N3 ADP . . . E 2 92.817 46.311 -6.451 1 92.88 ? N3 ADP 1201 A 1 HETATM 27 C C4 ADP . . . E 2 92.435 46.095 -5.166 1 91.27 ? C4 ADP 1201 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 257 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #