data_4NG4 # _model_server_result.job_id WLjD2nDGO3zdemNFw21xjw _model_server_result.datetime_utc '2024-12-26 22:06:17' _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 4ng4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 4NG4 # _exptl.entry_id 4NG4 _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 102.17 _cell.angle_gamma 90 _cell.entry_id 4NG4 _cell.length_a 158.148 _cell.length_b 91.568 _cell.length_c 88.412 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NG4 _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 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_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 1 1 B,F,G 2 1 C,H,I 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 OD1 ASP 301 A ASP 293 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc2 A O PHE 334 A PHE 326 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc3 A OG1 THR 338 A THR 330 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc4 B OD1 ASP 301 B ASP 293 1_555 F MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc5 B O PHE 334 B PHE 326 1_555 F MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc6 B OG1 THR 338 B THR 330 1_555 F MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc7 C OD1 ASP 301 C ASP 293 1_555 H MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc8 C O PHE 334 C PHE 326 1_555 H MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc9 C OG1 THR 338 C THR 330 1_555 H MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? # _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 4NG4 _atom_sites.fract_transf_matrix[1][1] 0.006323 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001364 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010921 _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] 0.011571 _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 1 401 500 MG MG . E 3 ADP A 1 402 600 ADP ADP . F 2 MG B 1 401 500 MG MG . G 3 ADP B 1 402 600 ADP ADP . H 2 MG C 1 401 500 MG MG . I 3 ADP C 1 402 600 ADP ADP . # 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 -8.472 -13.282 31.988 1 64.95 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . E 3 -7.415 -12.211 31.88 1 64.55 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . E 3 -9.768 -12.786 32.597 1 64.53 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . E 3 -8.642 -14.114 30.739 1 64.85 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . E 3 -8.599 -15.569 33.717 1 66.55 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . E 3 -10.077 -15.271 33.79 1 67.34 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . E 3 -8.172 -16.822 32.999 1 67.07 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . E 3 -7.817 -14.317 33.049 1 65.49 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . E 3 -8.077 -15.622 35.251 1 66.67 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . E 3 -7.16 -14.662 35.792 1 66.13 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . E 3 -7.405 -14.463 37.281 1 66 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . E 3 -6.964 -15.624 37.995 1 66.11 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . E 3 -6.648 -13.252 37.831 1 65.94 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . E 3 -7.554 -12.296 38.401 1 65.17 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . E 3 -5.664 -13.818 38.849 1 65.91 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . E 3 -5.633 -13.077 40.072 1 65.35 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . E 3 -6.111 -15.261 39.091 1 66.02 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . E 3 -4.936 -16.181 39.237 1 65.91 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . E 3 -3.972 -16.42 38.315 1 65.24 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . E 3 -3.059 -17.301 38.802 1 65.17 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . E 3 -3.429 -17.646 40.052 1 64.82 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . E 3 -2.916 -18.534 41.125 1 64 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . E 3 -1.782 -19.261 40.967 1 63.31 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . E 3 -3.631 -18.596 42.278 1 64.63 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . E 3 -4.767 -17.889 42.487 1 64.66 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . E 3 -5.282 -17.064 41.555 1 65.14 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . E 3 -4.672 -16.902 40.341 1 65.54 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #