data_4BN1 # _model_server_result.job_id WgiWmFrcrKwrBHC4FxJ_hA _model_server_result.datetime_utc '2024-11-04 23:13:40' _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 4bn1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1391}' # _entry.id 4BN1 # _exptl.entry_id 4BN1 _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 1 _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 4BN1 _cell.length_a 81.615 _cell.length_b 81.615 _cell.length_c 175.385 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BN1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ARG 168 A ARG 286 1_555 A N TPO 169 A TPO 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 169 A TPO 287 1_555 A N TPO 170 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C TPO 170 A TPO 288 1_555 A N LEU 171 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 143 A ASN 261 1_555 D CA CA . A CA 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc2 A OD2 ASP 156 A ASP 274 1_555 C CA CA . A CA 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc3 A OD1 ASP 156 A ASP 274 1_555 C CA CA . A CA 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc4 A OD2 ASP 156 A ASP 274 1_555 D CA CA . A CA 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc5 B O1B ADP . A ADP 1391 1_555 C CA CA . A CA 1392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc6 B O2B ADP . A ADP 1391 1_555 D CA CA . A CA 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc7 B O1A ADP . A ADP 1391 1_555 D CA CA . A CA 1393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc8 C CA CA . A CA 1392 1_555 E O HOH . A HOH 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc9 C CA CA . A CA 1392 1_555 E O HOH . A HOH 2021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.055 ? metalc ? metalc10 C CA CA . A CA 1392 1_555 E O HOH . A HOH 2044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc11 D CA CA . A CA 1393 1_555 E O HOH . A HOH 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? # _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 4BN1 _atom_sites.fract_transf_matrix[1][1] 0.012253 _atom_sites.fract_transf_matrix[1][2] 0.007074 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014148 _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] 0.005702 _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 B 2 ADP A 1 1391 1391 ADP ADP . C 3 CA A 1 1392 1392 CA CA . D 3 CA A 1 1393 1393 CA CA . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 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 . . . B 2 11.593 -23.456 -5.393 1 43.62 ? PB ADP 1391 A 1 HETATM 2 O O1B ADP . . . B 2 11.895 -23.248 -6.861 1 51.81 ? O1B ADP 1391 A 1 HETATM 3 O O2B ADP . . . B 2 12.72 -23.872 -4.493 1 52.24 ? O2B ADP 1391 A 1 HETATM 4 O O3B ADP . . . B 2 10.793 -22.32 -4.781 1 63.02 ? O3B ADP 1391 A 1 HETATM 5 P PA ADP . . . B 2 10.285 -25.882 -6.47 1 45.01 ? PA ADP 1391 A 1 HETATM 6 O O1A ADP . . . B 2 11.368 -26.9 -6.253 1 58.16 ? O1A ADP 1391 A 1 HETATM 7 O O2A ADP . . . B 2 9.994 -25.489 -7.89 1 49.49 ? O2A ADP 1391 A 1 HETATM 8 O O3A ADP . . . B 2 10.547 -24.693 -5.4 1 61.02 ? O3A ADP 1391 A 1 HETATM 9 O O5' ADP . . . B 2 8.914 -26.386 -5.8 1 41.25 ? O5' ADP 1391 A 1 HETATM 10 C C5' ADP . . . B 2 8.782 -26.366 -4.381 1 41.04 ? C5' ADP 1391 A 1 HETATM 11 C C4' ADP . . . B 2 8.084 -27.624 -3.876 1 41.89 ? C4' ADP 1391 A 1 HETATM 12 O O4' ADP . . . B 2 6.799 -27.784 -4.503 1 53.65 ? O4' ADP 1391 A 1 HETATM 13 C C3' ADP . . . B 2 8.818 -28.924 -4.174 1 43.62 ? C3' ADP 1391 A 1 HETATM 14 O O3' ADP . . . B 2 9.858 -29.246 -3.248 1 35.29 ? O3' ADP 1391 A 1 HETATM 15 C C2' ADP . . . B 2 7.683 -29.934 -4.154 1 43 ? C2' ADP 1391 A 1 HETATM 16 O O2' ADP . . . B 2 7.305 -30.28 -2.813 1 49.76 ? O2' ADP 1391 A 1 HETATM 17 C C1' ADP . . . B 2 6.545 -29.169 -4.797 1 44.78 ? C1' ADP 1391 A 1 HETATM 18 N N9 ADP . . . B 2 6.513 -29.303 -6.279 1 45.2 ? N9 ADP 1391 A 1 HETATM 19 C C8 ADP . . . B 2 7.236 -28.544 -7.137 1 44.07 ? C8 ADP 1391 A 1 HETATM 20 N N7 ADP . . . B 2 6.974 -28.884 -8.426 1 41.28 ? N7 ADP 1391 A 1 HETATM 21 C C5 ADP . . . B 2 6.057 -29.867 -8.407 1 42.39 ? C5 ADP 1391 A 1 HETATM 22 C C6 ADP . . . B 2 5.349 -30.676 -9.421 1 40.26 ? C6 ADP 1391 A 1 HETATM 23 N N6 ADP . . . B 2 5.564 -30.493 -10.745 1 41.59 ? N6 ADP 1391 A 1 HETATM 24 N N1 ADP . . . B 2 4.479 -31.617 -8.989 1 42.61 ? N1 ADP 1391 A 1 HETATM 25 C C2 ADP . . . B 2 4.24 -31.809 -7.68 1 43.31 ? C2 ADP 1391 A 1 HETATM 26 N N3 ADP . . . B 2 4.854 -31.102 -6.712 1 44.64 ? N3 ADP 1391 A 1 HETATM 27 C C4 ADP . . . B 2 5.756 -30.14 -6.996 1 39.2 ? C4 ADP 1391 A 1 HETATM 28 H "H5'1" ADP . . . B 2 8.208 -25.487 -4.082 1 49.25 ? "H5'1" ADP 1391 A 1 HETATM 29 H "H5'2" ADP . . . B 2 9.771 -26.291 -3.925 1 49.25 ? "H5'2" ADP 1391 A 1 HETATM 30 H H4' ADP . . . B 2 7.955 -27.538 -2.788 1 50.26 ? H4' ADP 1391 A 1 HETATM 31 H H3' ADP . . . B 2 9.227 -28.873 -5.193 1 52.34 ? H3' ADP 1391 A 1 HETATM 32 H HO3' ADP . . . B 2 10.272 -30.081 -3.506 1 42.35 ? HO3' ADP 1391 A 1 HETATM 33 H H2' ADP . . . B 2 7.94 -30.82 -4.752 1 51.6 ? H2' ADP 1391 A 1 HETATM 34 H HO2' ADP . . . B 2 8.057 -30.686 -2.361 1 59.71 ? HO2' ADP 1391 A 1 HETATM 35 H H1' ADP . . . B 2 5.59 -29.489 -4.357 1 53.74 ? H1' ADP 1391 A 1 HETATM 36 H H8 ADP . . . B 2 7.933 -27.771 -6.836 1 52.88 ? H8 ADP 1391 A 1 HETATM 37 H HN61 ADP . . . B 2 6.226 -29.797 -11.058 1 49.91 ? HN61 ADP 1391 A 1 HETATM 38 H HN62 ADP . . . B 2 5.073 -31.062 -11.42 1 49.91 ? HN62 ADP 1391 A 1 HETATM 39 H H2 ADP . . . B 2 3.526 -32.57 -7.391 1 51.97 ? H2 ADP 1391 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #