data_2Z4R # _model_server_result.job_id 7PUsGnQvNh5q9pBse3Vqpg _model_server_result.datetime_utc '2024-11-21 18:54:53' _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":"G","auth_seq_id":502}' # _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 . . . G 3 22.356 -39.285 -5.237 1 44.34 ? PB ADP 502 B 1 HETATM 2 O O1B ADP . . . G 3 22.964 -40.445 -4.594 1 43.34 ? O1B ADP 502 B 1 HETATM 3 O O2B ADP . . . G 3 23.311 -38.818 -6.427 1 44.44 ? O2B ADP 502 B 1 HETATM 4 O O3B ADP . . . G 3 22.136 -38.069 -4.185 1 45.24 ? O3B ADP 502 B 1 HETATM 5 P PA ADP . . . G 3 19.95 -40.154 -4.676 1 49.86 ? PA ADP 502 B 1 HETATM 6 O O1A ADP . . . G 3 20.491 -41.317 -3.946 1 45.18 ? O1A ADP 502 B 1 HETATM 7 O O2A ADP . . . G 3 19.673 -38.965 -3.634 1 50.21 ? O2A ADP 502 B 1 HETATM 8 O O3A ADP . . . G 3 20.962 -39.665 -5.839 1 48.2 ? O3A ADP 502 B 1 HETATM 9 O O5' ADP . . . G 3 18.582 -40.487 -5.474 1 53.21 ? O5' ADP 502 B 1 HETATM 10 C C5' ADP . . . G 3 17.673 -40.936 -4.521 1 56.13 ? C5' ADP 502 B 1 HETATM 11 C C4' ADP . . . G 3 16.337 -41.24 -5.161 1 55.23 ? C4' ADP 502 B 1 HETATM 12 O O4' ADP . . . G 3 16.495 -42.198 -6.201 1 52.1 ? O4' ADP 502 B 1 HETATM 13 C C3' ADP . . . G 3 15.455 -41.785 -4.05 1 57.05 ? C3' ADP 502 B 1 HETATM 14 O O3' ADP . . . G 3 14.262 -40.995 -3.891 1 58.8 ? O3' ADP 502 B 1 HETATM 15 C C2' ADP . . . G 3 15.163 -43.238 -4.428 1 57.23 ? C2' ADP 502 B 1 HETATM 16 O O2' ADP . . . G 3 13.736 -43.472 -4.496 1 64.55 ? O2' ADP 502 B 1 HETATM 17 C C1' ADP . . . G 3 15.84 -43.42 -5.799 1 54.84 ? C1' ADP 502 B 1 HETATM 18 N N9 ADP . . . G 3 16.786 -44.552 -5.9 1 51.63 ? N9 ADP 502 B 1 HETATM 19 C C8 ADP . . . G 3 18.141 -44.478 -6.059 1 52.14 ? C8 ADP 502 B 1 HETATM 20 N N7 ADP . . . G 3 18.662 -45.662 -6.151 1 50.22 ? N7 ADP 502 B 1 HETATM 21 C C5 ADP . . . G 3 17.681 -46.571 -6.059 1 51.67 ? C5 ADP 502 B 1 HETATM 22 C C6 ADP . . . G 3 17.629 -47.992 -6.11 1 52.95 ? C6 ADP 502 B 1 HETATM 23 N N6 ADP . . . G 3 18.794 -48.727 -6.301 1 51.73 ? N6 ADP 502 B 1 HETATM 24 N N1 ADP . . . G 3 16.42 -48.606 -5.976 1 52.63 ? N1 ADP 502 B 1 HETATM 25 C C2 ADP . . . G 3 15.289 -47.895 -5.8 1 53.16 ? C2 ADP 502 B 1 HETATM 26 N N3 ADP . . . G 3 15.301 -46.555 -5.758 1 51.4 ? N3 ADP 502 B 1 HETATM 27 C C4 ADP . . . G 3 16.457 -45.868 -5.883 1 51.26 ? C4 ADP 502 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #