data_4PL5 # _model_server_result.job_id kIA7navwScg4102Pphb67A _model_server_result.datetime_utc '2024-11-16 14:44:12' _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 4pl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1001}' # _entry.id 4PL5 # _exptl.entry_id 4PL5 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.49 _cell.angle_gamma 90 _cell.entry_id 4PL5 _cell.length_a 319.22 _cell.length_b 63.03 _cell.length_c 140.78 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PL5 _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J 1 1 C,D,K,L,M,N 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 E N N ? 2 H N N ? 2 K N N ? 2 M 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 B NZ LYS 365 A LYS 907 1_555 G C01 31L . A 31L 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.243 ? metalc ? metalc1 A OD1 ASN 151 B ASN 693 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc2 A OD2 ASP 169 B ASP 711 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc3 E O2A ADP . B ADP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc4 E O3A ADP . B ADP 1001 1_555 F MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc5 B OD1 ASN 151 A ASN 693 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc6 B OD2 ASP 169 A ASP 711 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc7 H O2B ADP . A ADP 1002 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc8 H O2A ADP . A ADP 1002 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc9 C OD1 ASN 151 C ASN 693 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc10 K O3A ADP . C ADP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc11 D OD1 ASN 151 D ASN 693 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc12 M O1B ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc13 M O1A ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc14 M O3A ADP . D ADP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? # _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 46 n n PB O2B ADP sing 47 n n PB O3B ADP sing 48 n n PB O3A ADP sing 49 n n O2B HOB2 ADP sing 50 n n O3B HOB3 ADP sing 51 n n PA O1A ADP doub 52 n n PA O2A ADP sing 53 n n PA O3A ADP sing 54 n n PA O5' ADP sing 55 n n O2A HOA2 ADP sing 56 n n O5' C5' ADP sing 57 n n C5' C4' ADP sing 58 n n C5' "H5'1" ADP sing 59 n n C5' "H5'2" ADP sing 60 n n C4' O4' ADP sing 61 n n C4' C3' ADP sing 62 n n C4' H4' ADP sing 63 n n O4' C1' ADP sing 64 n n C3' O3' ADP sing 65 n n C3' C2' ADP sing 66 n n C3' H3' ADP sing 67 n n O3' HO3' ADP sing 68 n n C2' O2' ADP sing 69 n n C2' C1' ADP sing 70 n n C2' H2' ADP sing 71 n n O2' HO2' ADP sing 72 n n C1' N9 ADP sing 73 n n C1' H1' ADP sing 74 n n N9 C8 ADP sing 75 n y N9 C4 ADP sing 76 n y C8 N7 ADP doub 77 n y C8 H8 ADP sing 78 n n N7 C5 ADP sing 79 n y C5 C6 ADP sing 80 n y C5 C4 ADP doub 81 n y C6 N6 ADP sing 82 n n C6 N1 ADP doub 83 n y N6 HN61 ADP sing 84 n n N6 HN62 ADP sing 85 n n N1 C2 ADP sing 86 n y C2 N3 ADP doub 87 n y C2 H2 ADP sing 88 n n N3 C4 ADP sing 89 n y # _atom_sites.entry_id 4PL5 _atom_sites.fract_transf_matrix[1][1] 0.003133 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000524 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015865 _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] 0.007202 _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 E 2 ADP B 1 1001 1 ADP ADP . F 3 MG B 1 1002 1 MG MG . G 4 31L A 1 1001 401 31L 573 . H 2 ADP A 1 1002 1 ADP ADP . I 3 MG A 1 1003 1 MG MG . J 5 PEU A 1 1004 1 PEU PEU . K 2 ADP C 1 1001 1 ADP ADP . L 3 MG C 1 1002 1 MG MG . M 2 ADP D 1 1001 1 ADP ADP . N 3 MG D 1 1002 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 . . . M 2 33.58 -7.395 149.938 1 125.42 ? PB ADP 1001 D 1 HETATM 2 O O1B ADP . . . M 2 34.752 -7.617 149.018 1 125.75 ? O1B ADP 1001 D 1 HETATM 3 O O2B ADP . . . M 2 32.482 -6.52 149.378 1 119 ? O2B ADP 1001 D 1 HETATM 4 O O3B ADP . . . M 2 33.102 -8.64 150.641 1 131.95 ? O3B ADP 1001 D 1 HETATM 5 P PA ADP . . . M 2 35.488 -6.945 151.998 1 84.21 ? PA ADP 1001 D 1 HETATM 6 O O1A ADP . . . M 2 36.705 -7.109 151.127 1 85.83 ? O1A ADP 1001 D 1 HETATM 7 O O2A ADP . . . M 2 35.097 -8.001 153.009 1 78.89 ? O2A ADP 1001 D 1 HETATM 8 O O3A ADP . . . M 2 34.213 -6.507 151.111 1 184.05 ? O3A ADP 1001 D 1 HETATM 9 O O5' ADP . . . M 2 35.652 -5.543 152.726 1 109.51 ? O5' ADP 1001 D 1 HETATM 10 C C5' ADP . . . M 2 34.64 -4.584 152.441 1 110.81 ? C5' ADP 1001 D 1 HETATM 11 C C4' ADP . . . M 2 35.263 -3.263 152.795 1 108.39 ? C4' ADP 1001 D 1 HETATM 12 O O4' ADP . . . M 2 36.558 -3.563 153.304 1 102.45 ? O4' ADP 1001 D 1 HETATM 13 C C3' ADP . . . M 2 35.443 -2.406 151.564 1 108.13 ? C3' ADP 1001 D 1 HETATM 14 O O3' ADP . . . M 2 34.502 -1.332 151.617 1 115.51 ? O3' ADP 1001 D 1 HETATM 15 C C2' ADP . . . M 2 36.85 -1.865 151.669 1 100.36 ? C2' ADP 1001 D 1 HETATM 16 O O2' ADP . . . M 2 36.779 -0.489 152.056 1 99.55 ? O2' ADP 1001 D 1 HETATM 17 C C1' ADP . . . M 2 37.519 -2.653 152.781 1 95.84 ? C1' ADP 1001 D 1 HETATM 18 N N9 ADP . . . M 2 38.685 -3.417 152.268 1 85.86 ? N9 ADP 1001 D 1 HETATM 19 C C8 ADP . . . M 2 38.677 -4.68 151.783 1 79.21 ? C8 ADP 1001 D 1 HETATM 20 N N7 ADP . . . M 2 39.929 -5.071 151.408 1 71.45 ? N7 ADP 1001 D 1 HETATM 21 C C5 ADP . . . M 2 40.762 -4.035 151.663 1 74.61 ? C5 ADP 1001 D 1 HETATM 22 C C6 ADP . . . M 2 42.215 -3.752 151.515 1 73 ? C6 ADP 1001 D 1 HETATM 23 N N6 ADP . . . M 2 43.063 -4.681 151.006 1 72.06 ? N6 ADP 1001 D 1 HETATM 24 N N1 ADP . . . M 2 42.675 -2.536 151.909 1 68.12 ? N1 ADP 1001 D 1 HETATM 25 C C2 ADP . . . M 2 41.857 -1.593 152.419 1 64 ? C2 ADP 1001 D 1 HETATM 26 N N3 ADP . . . M 2 40.533 -1.774 152.581 1 67.23 ? N3 ADP 1001 D 1 HETATM 27 C C4 ADP . . . M 2 39.938 -2.95 152.231 1 77.78 ? C4 ADP 1001 D 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 27 #