data_2Z4R # _model_server_result.job_id zuxscos9-1idfUJUJNY8oQ _model_server_result.datetime_utc '2024-11-24 05:12:57' _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 2z4r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 2Z4R # _exptl.entry_id 2Z4R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.13 _cell.angle_gamma 90 _cell.entry_id 2Z4R _cell.length_a 133.335 _cell.length_b 221.787 _cell.length_c 55.601 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z4R _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1 B,F,G,K 2 1 C,H,I,L 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I 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 metalc ? metalc1 A OG1 THR 144 A THR 144 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc2 B OG1 THR 144 B THR 144 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 F MG MG . B MG 501 1_555 G O3B ADP . B ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc4 C OG1 THR 144 C THR 144 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc5 H MG MG . C MG 502 1_555 I O3B ADP . C ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? # _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 2Z4R _atom_sites.fract_transf_matrix[1][1] 0.0075 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002169 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004509 _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] 0.018722 _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 D 2 MG A 1 500 500 MG MG . E 3 ADP A 1 501 400 ADP ADP . F 2 MG B 1 501 501 MG MG . G 3 ADP B 1 502 401 ADP ADP . H 2 MG C 1 502 502 MG MG . I 3 ADP C 1 503 402 ADP ADP . J 4 HOH A 1 502 2 HOH HOH . K 4 HOH B 1 503 3 HOH HOH . L 4 HOH C 1 504 1 HOH HOH . L 4 HOH C 2 505 4 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 P PB ADP . . . E 3 40.08 4.04 23.34 1 45.79 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . E 3 41.555 3.88 23.413 1 40.37 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . E 3 39.405 3.483 24.667 1 44.18 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . E 3 39.486 3.259 22.038 1 45.18 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . E 3 40.226 6.37 21.99 1 51.9 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . E 3 41.692 6.312 21.86 1 47.83 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . E 3 39.589 5.724 20.662 1 53.08 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . E 3 39.663 5.575 23.296 1 49.7 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . E 3 39.651 7.856 22.21 1 54.63 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . E 3 40.118 8.614 21.142 1 61.71 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . E 3 39.583 10.024 21.212 1 63.05 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . E 3 39.882 10.679 22.462 1 61.77 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . E 3 40.198 10.769 20.042 1 65.37 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . E 3 39.188 11.253 19.143 1 68.98 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . E 3 41.037 11.883 20.658 1 67.03 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . E 3 40.613 13.186 20.154 1 73.31 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . E 3 40.834 11.742 22.202 1 65.04 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . E 3 42.104 11.481 22.918 1 62 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . E 3 42.498 10.309 23.494 1 62.61 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . E 3 43.666 10.441 24.049 1 62.26 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . E 3 44.099 11.699 23.868 1 62.53 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . E 3 45.267 12.43 24.241 1 63.48 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . E 3 46.276 11.822 24.967 1 62.12 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . E 3 45.366 13.73 23.872 1 63.11 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . E 3 44.394 14.329 23.174 1 62.52 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . E 3 43.286 13.675 22.813 1 60.16 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . E 3 43.1 12.386 23.134 1 61.01 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #