data_2Z4R # _model_server_result.job_id utKViNg2hl7SWpZh7oTJkQ _model_server_result.datetime_utc '2024-11-21 19:00:50' _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":"I","auth_seq_id":503}' # _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 . . . I 3 39.562 -72.233 3.892 1 51.69 ? PB ADP 503 C 1 HETATM 2 O O1B ADP . . . I 3 39.076 -70.948 3.377 1 48.31 ? O1B ADP 503 C 1 HETATM 3 O O2B ADP . . . I 3 39.814 -72.125 5.455 1 53.05 ? O2B ADP 503 C 1 HETATM 4 O O3B ADP . . . I 3 40.937 -72.676 3.169 1 47.56 ? O3B ADP 503 C 1 HETATM 5 P PA ADP . . . I 3 38.025 -73.643 2.187 1 53.83 ? PA ADP 503 C 1 HETATM 6 O O1A ADP . . . I 3 37.454 -72.441 1.584 1 51.59 ? O1A ADP 503 C 1 HETATM 7 O O2A ADP . . . I 3 39.302 -74.094 1.311 1 52.59 ? O2A ADP 503 C 1 HETATM 8 O O3A ADP . . . I 3 38.448 -73.372 3.73 1 54.84 ? O3A ADP 503 C 1 HETATM 9 O O5' ADP . . . I 3 36.951 -74.832 2.266 1 56 ? O5' ADP 503 C 1 HETATM 10 C C5' ADP . . . I 3 36.584 -75.062 0.944 1 63.86 ? C5' ADP 503 C 1 HETATM 11 C C4' ADP . . . I 3 35.604 -76.202 0.798 1 65.32 ? C4' ADP 503 C 1 HETATM 12 O O4' ADP . . . I 3 34.402 -76.008 1.576 1 63.53 ? O4' ADP 503 C 1 HETATM 13 C C3' ADP . . . I 3 35.287 -76.27 -0.68 1 66.97 ? C3' ADP 503 C 1 HETATM 14 O O3' ADP . . . I 3 35.637 -77.547 -1.229 1 69.94 ? O3' ADP 503 C 1 HETATM 15 C C2' ADP . . . I 3 33.798 -75.94 -0.792 1 68.14 ? C2' ADP 503 C 1 HETATM 16 O O2' ADP . . . I 3 33.085 -77.012 -1.462 1 75.68 ? O2' ADP 503 C 1 HETATM 17 C C1' ADP . . . I 3 33.309 -75.737 0.667 1 65.7 ? C1' ADP 503 C 1 HETATM 18 N N9 ADP . . . I 3 32.76 -74.386 0.92 1 63.58 ? N9 ADP 503 C 1 HETATM 19 C C8 ADP . . . I 3 33.372 -73.359 1.576 1 64.42 ? C8 ADP 503 C 1 HETATM 20 N N7 ADP . . . I 3 32.593 -72.319 1.635 1 63.54 ? N7 ADP 503 C 1 HETATM 21 C C5 ADP . . . I 3 31.432 -72.605 1.025 1 64.02 ? C5 ADP 503 C 1 HETATM 22 C C6 ADP . . . I 3 30.223 -71.895 0.784 1 64.21 ? C6 ADP 503 C 1 HETATM 23 N N6 ADP . . . I 3 30.073 -70.595 1.234 1 63.05 ? N6 ADP 503 C 1 HETATM 24 N N1 ADP . . . I 3 29.223 -72.518 0.111 1 64.2 ? N1 ADP 503 C 1 HETATM 25 C C2 ADP . . . I 3 29.356 -73.776 -0.325 1 63.99 ? C2 ADP 503 C 1 HETATM 26 N N3 ADP . . . I 3 30.476 -74.476 -0.112 1 63.03 ? N3 ADP 503 C 1 HETATM 27 C C4 ADP . . . I 3 31.522 -73.938 0.548 1 63.63 ? C4 ADP 503 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #