data_4NTT # _model_server_result.job_id i54FcfkZHWHkGWoRKjK5Xw _model_server_result.datetime_utc '2025-09-07 21:39:03' _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 4ntt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4NTT # _exptl.entry_id 4NTT _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.61 _cell.angle_gamma 90 _cell.entry_id 4NTT _cell.length_a 50.48 _cell.length_b 143.15 _cell.length_c 62.57 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NTT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D 1 1 B,E,F 2 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 ? 2 C N N ? 2 E 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 covale ? covale1 A C TRP 196 A TRP 196 1_555 A N TPO 197 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 197 A TPO 197 1_555 A N LEU 198 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C VAL 337 A VAL 337 1_555 A N SEP 338 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C SEP 338 A SEP 338 1_555 A N ILE 339 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 B C TRP 196 B TRP 196 1_555 B N TPO 197 B TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 B C TPO 197 B TPO 197 1_555 B N LEU 198 B LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 B C VAL 337 B VAL 337 1_555 B N SEP 338 B SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B C SEP 338 B SEP 338 1_555 B N ILE 339 B ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OD2 ASP 184 A ASP 184 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc2 C O2A ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc3 C O3B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc4 B OD2 ASP 184 B ASP 184 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc5 E O2A ADP . B ADP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc6 E O3B ADP . B ADP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? # _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 4NTT _atom_sites.fract_transf_matrix[1][1] 0.01981 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004796 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006986 _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] 0.016444 _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 C 2 ADP A 1 401 355 ADP ADP . D 3 MG A 1 402 1 MG MG . E 2 ADP B 1 401 355 ADP ADP . F 3 MG B 1 402 1 MG MG . # 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 . . . C 2 34.746 49.073 27.211 1 156.27 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 2 35.063 50.529 26.952 1 167.72 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 2 34.719 48.703 28.674 1 150.88 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 2 35.541 48.12 26.348 1 157.02 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 2 32.523 47.461 26.549 1 148.47 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 2 31.156 47.703 25.952 1 150.25 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 2 33.472 46.526 25.837 1 148.7 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 2 33.218 48.899 26.743 1 155.18 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 2 32.342 46.975 28.078 1 146.4 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 2 33.183 45.978 28.667 1 144.99 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 2 32.36 44.774 29.121 1 147.58 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 2 31.317 45.18 30.018 1 152.08 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 2 31.708 44.071 27.936 1 147.42 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 2 32.348 42.816 27.677 1 152 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 2 30.253 43.871 28.329 1 151.12 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 2 29.936 42.475 28.403 1 157.69 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 2 30.074 44.544 29.689 1 156.01 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 2 28.961 45.529 29.595 1 159.79 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 2 29.08 46.821 29.235 1 159.24 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 2 27.876 47.448 29.234 1 168.51 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 2 26.951 46.545 29.598 1 174.19 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 2 25.482 46.542 29.797 1 187.99 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 2 24.757 47.664 29.601 1 198.12 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 2 24.893 45.386 30.182 1 194.61 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 2 25.609 44.261 30.38 1 189.97 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 2 26.947 44.194 30.217 1 177.77 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 2 27.667 45.28 29.834 1 168.93 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #