data_5B6Z # _model_server_result.job_id CnjKmq6VjdDSCWJsDA9tBw _model_server_result.datetime_utc '2024-11-13 05:29:15' _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 5b6z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":611}' # _entry.id 5B6Z # _exptl.entry_id 5B6Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 128.255 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description nonane _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 5B6Z _cell.length_a 62.5 _cell.length_b 62.5 _cell.length_c 112 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B6Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,N,O,P,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -62.5 0 0 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -31.25 -54.126588 0 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id N _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 NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 300 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.311 ? covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 300 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.31 ? # _chem_comp.formula 'C9 H20' _chem_comp.formula_weight 128.255 _chem_comp.id DD9 _chem_comp.mon_nstd_flag . _chem_comp.name nonane _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 C2 C1 DD9 sing 144 n n C1 H1 DD9 sing 145 n n C1 H1A DD9 sing 146 n n C1 H1B DD9 sing 147 n n C3 C2 DD9 sing 148 n n C2 H2 DD9 sing 149 n n C2 H2A DD9 sing 150 n n C4 C3 DD9 sing 151 n n C3 H3 DD9 sing 152 n n C3 H3A DD9 sing 153 n n C5 C4 DD9 sing 154 n n C4 H4 DD9 sing 155 n n C4 H4A DD9 sing 156 n n C6 C5 DD9 sing 157 n n C5 H5 DD9 sing 158 n n C5 H5A DD9 sing 159 n n C7 C6 DD9 sing 160 n n C6 H6 DD9 sing 161 n n C6 H6A DD9 sing 162 n n C8 C7 DD9 sing 163 n n C7 H7 DD9 sing 164 n n C7 H7A DD9 sing 165 n n C9 C8 DD9 sing 166 n n C8 H8 DD9 sing 167 n n C8 H8A DD9 sing 168 n n C9 H9 DD9 sing 169 n n C9 H9A DD9 sing 170 n n C9 H9B DD9 sing 171 n n # _atom_sites.entry_id 5B6Z _atom_sites.fract_transf_matrix[1][1] 0.016 _atom_sites.fract_transf_matrix[1][2] 0.009238 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018475 _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] 0.008929 _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 RET A 1 300 300 RET RET . C 3 L2P A 1 600 600 L2P L2P . D 4 TRD A 1 601 601 TRD TRD . E 5 D10 A 1 602 602 D10 D10 . F 6 HP6 A 1 603 603 HP6 HP6 . G 7 OCT A 1 604 604 OCT OCT . H 7 OCT A 1 605 605 OCT OCT . I 8 MYS A 1 606 606 MYS MYS . J 9 UND A 1 607 607 UND UND . K 3 L2P A 1 608 608 L2P L2P . L 3 L2P A 1 609 609 L2P L2P . M 8 MYS A 1 610 610 MYS MYS . N 10 DD9 A 1 611 611 DD9 DD9 . O 11 C14 A 1 612 612 C14 C14 . P 7 OCT A 1 613 613 OCT OCT . Q 9 UND A 1 614 614 UND UND . R 12 HOH A 1 400 400 HOH HOH . R 12 HOH A 2 401 401 HOH HOH . R 12 HOH A 3 402 402 HOH HOH . R 12 HOH A 4 403 403 HOH HOH . R 12 HOH A 5 404 404 HOH HOH . R 12 HOH A 6 405 405 HOH HOH . R 12 HOH A 7 406 406 HOH HOH . R 12 HOH A 8 407 407 HOH HOH . R 12 HOH A 9 408 408 HOH HOH . R 12 HOH A 10 414 414 HOH HOH . R 12 HOH A 11 425 425 HOH HOH . R 12 HOH A 12 424 424 HOH HOH . R 12 HOH A 13 433 433 HOH HOH . R 12 HOH A 14 438 438 HOH HOH . R 12 HOH A 15 441 441 HOH HOH . R 12 HOH A 16 442 442 HOH HOH . R 12 HOH A 17 443 443 HOH HOH . R 12 HOH A 18 451 451 HOH HOH . R 12 HOH A 19 453 453 HOH HOH . R 12 HOH A 20 454 454 HOH HOH . R 12 HOH A 21 455 455 HOH HOH . R 12 HOH A 22 456 456 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 DD9 . . . N 10 -0.534 -21.609 11.996 1 81.59 ? C1 DD9 611 A 1 HETATM 2 C C2 DD9 . . . N 10 -0.123 -21.663 10.526 1 87.76 ? C2 DD9 611 A 1 HETATM 3 C C3 DD9 . . . N 10 -0.896 -20.596 9.754 1 91.79 ? C3 DD9 611 A 1 HETATM 4 C C4 DD9 . . . N 10 -0.284 -20.41 8.366 1 87.41 ? C4 DD9 611 A 1 HETATM 5 C C5 DD9 . . . N 10 -1.285 -19.694 7.46 1 82.49 ? C5 DD9 611 A 1 HETATM 6 C C6 DD9 . . . N 10 -0.786 -18.291 7.123 1 90.49 ? C6 DD9 611 A 1 HETATM 7 C C7 DD9 . . . N 10 -1.977 -17.423 6.724 1 82.79 ? C7 DD9 611 A 1 HETATM 8 C C8 DD9 . . . N 10 -1.498 -16.238 5.89 1 77.74 ? C8 DD9 611 A 1 HETATM 9 C C9 DD9 . . . N 10 -2.632 -15.224 5.754 1 79.17 ? C9 DD9 611 A 1 HETATM 10 H H1 DD9 . . . N 10 -0.329 -20.732 12.357 1 97.91 ? H1 DD9 611 A 1 HETATM 11 H H1A DD9 . . . N 10 -0.047 -22.285 12.493 1 97.91 ? H1A DD9 611 A 1 HETATM 12 H H1B DD9 . . . N 10 -1.487 -21.776 12.072 1 97.91 ? H1B DD9 611 A 1 HETATM 13 H H2 DD9 . . . N 10 -0.328 -22.539 10.163 1 105.31 ? H2 DD9 611 A 1 HETATM 14 H H2A DD9 . . . N 10 0.829 -21.494 10.449 1 105.31 ? H2A DD9 611 A 1 HETATM 15 H H3 DD9 . . . N 10 -0.856 -19.756 10.238 1 110.14 ? H3 DD9 611 A 1 HETATM 16 H H3A DD9 . . . N 10 -1.822 -20.872 9.663 1 110.14 ? H3A DD9 611 A 1 HETATM 17 H H4 DD9 . . . N 10 -0.069 -21.277 7.989 1 104.89 ? H4 DD9 611 A 1 HETATM 18 H H4A DD9 . . . N 10 0.525 -19.879 8.438 1 104.89 ? H4A DD9 611 A 1 HETATM 19 H H5 DD9 . . . N 10 -2.14 -19.63 7.914 1 98.99 ? H5 DD9 611 A 1 HETATM 20 H H5A DD9 . . . N 10 -1.395 -20.201 6.64 1 98.99 ? H5A DD9 611 A 1 HETATM 21 H H6 DD9 . . . N 10 -0.157 -18.338 6.386 1 108.59 ? H6 DD9 611 A 1 HETATM 22 H H6A DD9 . . . N 10 -0.349 -17.906 7.899 1 108.59 ? H6A DD9 611 A 1 HETATM 23 H H7 DD9 . . . N 10 -2.601 -17.952 6.203 1 99.35 ? H7 DD9 611 A 1 HETATM 24 H H7A DD9 . . . N 10 -2.42 -17.097 7.523 1 99.35 ? H7A DD9 611 A 1 HETATM 25 H H8 DD9 . . . N 10 -0.74 -15.819 6.327 1 93.29 ? H8 DD9 611 A 1 HETATM 26 H H8A DD9 . . . N 10 -1.233 -16.548 5.01 1 93.29 ? H8A DD9 611 A 1 HETATM 27 H H9 DD9 . . . N 10 -2.329 -14.47 5.225 1 95.01 ? H9 DD9 611 A 1 HETATM 28 H H9A DD9 . . . N 10 -3.39 -15.643 5.317 1 95.01 ? H9A DD9 611 A 1 HETATM 29 H H9B DD9 . . . N 10 -2.897 -14.915 6.635 1 95.01 ? H9B DD9 611 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #