data_2YD9 # _model_server_result.job_id ZOzdyfdQGa7nRrrRRw-TsA _model_server_result.datetime_utc '2024-10-18 01:20:26' _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 2yd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1325}' # _entry.id 2YD9 # _exptl.entry_id 2YD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 282.334 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _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 90 _cell.entry_id 2YD9 _cell.length_a 71.699 _cell.length_b 90.043 _cell.length_c 143.283 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YD9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id L _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 disulf ? disulf1 A SG CYS 28 A CYS 54 1_555 A SG CYS 81 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 130 A CYS 156 1_555 A SG CYS 181 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? disulf ? disulf3 A SG CYS 227 A CYS 253 1_555 A SG CYS 272 A CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 224 A ASN 250 1_555 K C1 NAG . A NAG 1324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 269 A ASN 295 1_555 J C1 NAG . A NAG 1323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _chem_comp.formula 'C11 H26 N2 O6' _chem_comp.formula_weight 282.334 _chem_comp.id B3P _chem_comp.mon_nstd_flag . _chem_comp.name 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _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 C1 C2 B3P sing 70 n n C1 C3 B3P sing 71 n n C1 H11 B3P sing 72 n n C1 H12 B3P sing 73 n n C2 N2 B3P sing 74 n n C2 H21 B3P sing 75 n n C2 H22 B3P sing 76 n n C3 N1 B3P sing 77 n n C3 H31 B3P sing 78 n n C3 H32 B3P sing 79 n n N1 C4 B3P sing 80 n n N1 HN1 B3P sing 81 n n C4 C5 B3P sing 82 n n C4 C6 B3P sing 83 n n C4 C7 B3P sing 84 n n C5 O4 B3P sing 85 n n C5 H51 B3P sing 86 n n C5 H52 B3P sing 87 n n C6 O5 B3P sing 88 n n C6 H61 B3P sing 89 n n C6 H62 B3P sing 90 n n C7 O6 B3P sing 91 n n C7 H71 B3P sing 92 n n C7 H72 B3P sing 93 n n N2 C8 B3P sing 94 n n N2 HN2 B3P sing 95 n n C8 C9 B3P sing 96 n n C8 C10 B3P sing 97 n n C8 C11 B3P sing 98 n n C9 O1 B3P sing 99 n n C9 H91 B3P sing 100 n n C9 H92 B3P sing 101 n n C10 O2 B3P sing 102 n n C10 H101 B3P sing 103 n n C10 H102 B3P sing 104 n n C11 O3 B3P sing 105 n n C11 H111 B3P sing 106 n n C11 H112 B3P sing 107 n n O1 HO1 B3P sing 108 n n O2 HO2 B3P sing 109 n n O3 HO3 B3P sing 110 n n O4 HO4 B3P sing 111 n n O5 HO5 B3P sing 112 n n O6 HO6 B3P sing 113 n n # _atom_sites.entry_id 2YD9 _atom_sites.fract_transf_matrix[1][1] 0.013947 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011106 _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] 0.006979 _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 CL A 1 1315 1315 CL CL . C 2 CL A 1 1316 1316 CL CL . D 2 CL A 1 1317 1317 CL CL . E 2 CL A 1 1318 1318 CL CL . F 3 IOD A 1 1319 1319 IOD IOD . G 3 IOD A 1 1320 1320 IOD IOD . H 3 IOD A 1 1321 1321 IOD IOD . I 3 IOD A 1 1322 1322 IOD IOD . J 4 NAG A 1 1323 1323 NAG NAG . K 4 NAG A 1 1324 1324 NAG NAG . L 5 B3P A 1 1325 1325 B3P B3P . M 6 HOH A 1 2001 2001 HOH HOH . M 6 HOH A 2 2002 2002 HOH HOH . M 6 HOH A 3 2003 2003 HOH HOH . M 6 HOH A 4 2004 2004 HOH HOH . M 6 HOH A 5 2005 2005 HOH HOH . M 6 HOH A 6 2006 2006 HOH HOH . M 6 HOH A 7 2007 2007 HOH HOH . M 6 HOH A 8 2008 2008 HOH HOH . M 6 HOH A 9 2009 2009 HOH HOH . M 6 HOH A 10 2010 2010 HOH HOH . M 6 HOH A 11 2011 2011 HOH HOH . M 6 HOH A 12 2012 2012 HOH HOH . M 6 HOH A 13 2013 2013 HOH HOH . M 6 HOH A 14 2014 2014 HOH HOH . M 6 HOH A 15 2015 2015 HOH HOH . M 6 HOH A 16 2016 2016 HOH HOH . M 6 HOH A 17 2017 2017 HOH HOH . M 6 HOH A 18 2018 2018 HOH HOH . M 6 HOH A 19 2019 2019 HOH HOH . M 6 HOH A 20 2020 2020 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 C C1 B3P . . . L 5 -32.432 -31.765 -3.158 1 55.42 ? C1 B3P 1325 A 1 HETATM 2 C C2 B3P . . . L 5 -31.847 -32.447 -1.917 1 57.32 ? C2 B3P 1325 A 1 HETATM 3 C C3 B3P . . . L 5 -31.574 -30.599 -3.659 1 53.48 ? C3 B3P 1325 A 1 HETATM 4 N N1 B3P . . . L 5 -32.451 -29.6 -4.3 1 52.87 ? N1 B3P 1325 A 1 HETATM 5 C C4 B3P . . . L 5 -31.723 -28.361 -4.649 1 51.14 ? C4 B3P 1325 A 1 HETATM 6 C C5 B3P . . . L 5 -31.459 -27.568 -3.358 1 50.22 ? C5 B3P 1325 A 1 HETATM 7 C C6 B3P . . . L 5 -30.401 -28.693 -5.367 1 49.29 ? C6 B3P 1325 A 1 HETATM 8 C C7 B3P . . . L 5 -32.573 -27.506 -5.595 1 49.48 ? C7 B3P 1325 A 1 HETATM 9 N N2 B3P . . . L 5 -31.398 -33.816 -2.243 1 58.05 ? N2 B3P 1325 A 1 HETATM 10 C C8 B3P . . . L 5 -31.066 -34.537 -1.002 1 55.67 ? C8 B3P 1325 A 1 HETATM 11 C C9 B3P . . . L 5 -31.239 -33.662 0.259 1 53.19 ? C9 B3P 1325 A 1 HETATM 12 C C10 B3P . . . L 5 -29.604 -34.974 -1.07 1 54.32 ? C10 B3P 1325 A 1 HETATM 13 C C11 B3P . . . L 5 -31.936 -35.799 -0.912 1 54.48 ? C11 B3P 1325 A 1 HETATM 14 O O1 B3P . . . L 5 -32.606 -33.583 0.684 1 50.13 ? O1 B3P 1325 A 1 HETATM 15 O O2 B3P . . . L 5 -29.325 -35.55 -2.352 1 51.81 ? O2 B3P 1325 A 1 HETATM 16 O O3 B3P . . . L 5 -31.832 -36.365 0.398 1 56.45 ? O3 B3P 1325 A 1 HETATM 17 O O4 B3P . . . L 5 -30.817 -26.334 -3.667 1 53.07 ? O4 B3P 1325 A 1 HETATM 18 O O5 B3P . . . L 5 -30.658 -29.489 -6.531 1 46.01 ? O5 B3P 1325 A 1 HETATM 19 O O6 B3P . . . L 5 -33.87 -27.325 -5.042 1 54.77 ? O6 B3P 1325 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #