data_4BUB # _model_server_result.job_id bclul4XX1wM1orbrDGSPUg _model_server_result.datetime_utc '2024-12-21 14:13:59' _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 4bub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1486}' # _entry.id 4BUB # _exptl.entry_id 4BUB _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 90 _cell.angle_gamma 120 _cell.entry_id 4BUB _cell.length_a 74.387 _cell.length_b 74.387 _cell.length_c 441.759 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BUB _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # 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,G 1 1 B,E,F,H 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 MSE 1 A MSE 1 1_555 A N ASN 2 A ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C VAL 58 A VAL 58 1_555 A N MSE 59 A MSE 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 A C MSE 59 A MSE 59 1_555 A N GLU 60 A GLU 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C THR 118 A THR 118 1_555 A N MSE 119 A MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C MSE 119 A MSE 119 1_555 A N MSE 120 A MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 120 A MSE 120 1_555 A N ILE 121 A ILE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 A C HIS 123 A HIS 123 1_555 A N MSE 124 A MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale8 A C MSE 124 A MSE 124 1_555 A N LEU 125 A LEU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 A C ALA 162 A ALA 162 1_555 A N MSE 163 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C MSE 163 A MSE 163 1_555 A N LYS 164 A LYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C PRO 383 A PRO 383 1_555 A N MSE 384 A MSE 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 384 A MSE 384 1_555 A N MSE 385 A MSE 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C MSE 385 A MSE 385 1_555 A N SER 386 A SER 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 A C ILE 411 A ILE 411 1_555 A N MSE 412 A MSE 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale15 A C MSE 412 A MSE 412 1_555 A N GLU 413 A GLU 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 B C MSE 1 B MSE 1 1_555 B N ASN 2 B ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale17 B C VAL 58 B VAL 58 1_555 B N MSE 59 B MSE 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale18 B C MSE 59 B MSE 59 1_555 B N GLU 60 B GLU 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 B C THR 118 B THR 118 1_555 B N MSE 119 B MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale20 B C MSE 119 B MSE 119 1_555 B N MSE 120 B MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale21 B C MSE 120 B MSE 120 1_555 B N ILE 121 B ILE 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale22 B C HIS 123 B HIS 123 1_555 B N MSE 124 B MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale23 B C MSE 124 B MSE 124 1_555 B N LEU 125 B LEU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale24 B C ALA 162 B ALA 162 1_555 B N MSE 163 B MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale25 B C MSE 163 B MSE 163 1_555 B N LYS 164 B LYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale26 B C PRO 383 B PRO 383 1_555 B N MSE 384 B MSE 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale27 B C MSE 384 B MSE 384 1_555 B N MSE 385 B MSE 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale28 B C MSE 385 B MSE 385 1_555 B N SER 386 B SER 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale29 B C ILE 411 B ILE 411 1_555 B N MSE 412 B MSE 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale30 B C MSE 412 B MSE 412 1_555 B N GLU 413 B GLU 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? metalc ? metalc1 C O3B ADP . A ADP 1486 1_555 D MG MG . A MG 1487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc2 B OG1 THR 137 B THR 137 1_555 F MG MG . B MG 1487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc3 E O3B ADP . B ADP 1486 1_555 F MG MG . B MG 1487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc4 E O1B ADP . B ADP 1486 1_555 F MG MG . B MG 1487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? # _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 4BUB _atom_sites.fract_transf_matrix[1][1] 0.013443 _atom_sites.fract_transf_matrix[1][2] 0.007761 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015523 _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] 0.002264 _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 1486 1486 ADP ADP . D 3 MG A 1 1487 1487 MG MG . E 2 ADP B 1 1486 1486 ADP ADP . F 3 MG B 1 1487 1487 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 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 . . . C 2 31.659 -12.961 -3.807 1 111.46 ? PB ADP 1486 A 1 HETATM 2 O O1B ADP . . . C 2 30.179 -13.128 -3.527 1 93.54 ? O1B ADP 1486 A 1 HETATM 3 O O2B ADP . . . C 2 32.025 -12.593 -5.221 1 110.72 ? O2B ADP 1486 A 1 HETATM 4 O O3B ADP . . . C 2 32.413 -12.235 -2.721 1 94.03 ? O3B ADP 1486 A 1 HETATM 5 P PA ADP . . . C 2 31.675 -15.336 -2.555 1 163 ? PA ADP 1486 A 1 HETATM 6 O O1A ADP . . . C 2 32.797 -16.251 -2.093 1 141.53 ? O1A ADP 1486 A 1 HETATM 7 O O2A ADP . . . C 2 31.009 -14.404 -1.564 1 168.57 ? O2A ADP 1486 A 1 HETATM 8 O O3A ADP . . . C 2 32.26 -14.429 -3.726 1 119.02 ? O3A ADP 1486 A 1 HETATM 9 O O5' ADP . . . C 2 30.521 -16.133 -3.362 1 121.34 ? O5' ADP 1486 A 1 HETATM 10 C C5' ADP . . . C 2 29.144 -15.77 -3.236 1 103.5 ? C5' ADP 1486 A 1 HETATM 11 C C4' ADP . . . C 2 28.324 -17.044 -3.354 1 111.75 ? C4' ADP 1486 A 1 HETATM 12 O O4' ADP . . . C 2 28.808 -17.747 -4.496 1 134.79 ? O4' ADP 1486 A 1 HETATM 13 C C3' ADP . . . C 2 28.51 -17.98 -2.165 1 116.01 ? C3' ADP 1486 A 1 HETATM 14 O O3' ADP . . . C 2 27.246 -18.162 -1.516 1 122.72 ? O3' ADP 1486 A 1 HETATM 15 C C2' ADP . . . C 2 29.069 -19.299 -2.71 1 114.97 ? C2' ADP 1486 A 1 HETATM 16 O O2' ADP . . . C 2 28.211 -20.429 -2.487 1 92.13 ? O2' ADP 1486 A 1 HETATM 17 C C1' ADP . . . C 2 29.164 -19.111 -4.209 1 121.31 ? C1' ADP 1486 A 1 HETATM 18 N N9 ADP . . . C 2 30.503 -19.479 -4.783 1 131 ? N9 ADP 1486 A 1 HETATM 19 C C8 ADP . . . C 2 31.716 -19.28 -4.223 1 119.91 ? C8 ADP 1486 A 1 HETATM 20 N N7 ADP . . . C 2 32.709 -19.738 -5.037 1 121.41 ? N7 ADP 1486 A 1 HETATM 21 C C5 ADP . . . C 2 32.138 -20.24 -6.151 1 114.27 ? C5 ADP 1486 A 1 HETATM 22 C C6 ADP . . . C 2 32.597 -20.875 -7.415 1 106.01 ? C6 ADP 1486 A 1 HETATM 23 N N6 ADP . . . C 2 33.91 -21.083 -7.675 1 116.89 ? N6 ADP 1486 A 1 HETATM 24 N N1 ADP . . . C 2 31.67 -21.251 -8.313 1 96.79 ? N1 ADP 1486 A 1 HETATM 25 C C2 ADP . . . C 2 30.362 -21.067 -8.091 1 105.63 ? C2 ADP 1486 A 1 HETATM 26 N N3 ADP . . . C 2 29.875 -20.497 -6.979 1 121.4 ? N3 ADP 1486 A 1 HETATM 27 C C4 ADP . . . C 2 30.692 -20.069 -5.979 1 125.15 ? C4 ADP 1486 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #