data_2VDB # _model_server_result.job_id fzc7zLRrXteBTKalbxvgag _model_server_result.datetime_utc '2024-10-11 01:20:42' _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 2vdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1590}' # _entry.id 2VDB # _exptl.entry_id 2VDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 172.265 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DECANOIC ACID' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93 _cell.angle_gamma 90 _cell.entry_id 2VDB _cell.length_a 190.507 _cell.length_b 49.462 _cell.length_c 79.933 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PQS _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 disulf ? disulf1 A SG CYS 48 A CYS 53 1_555 A SG CYS 57 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? disulf ? disulf2 A SG CYS 70 A CYS 75 1_555 A SG CYS 86 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 85 A CYS 90 1_555 A SG CYS 96 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 119 A CYS 124 1_555 A SG CYS 164 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 163 A CYS 168 1_555 A SG CYS 172 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf6 A SG CYS 195 A CYS 200 1_555 A SG CYS 241 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 240 A CYS 245 1_555 A SG CYS 248 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf8 A SG CYS 260 A CYS 265 1_555 A SG CYS 274 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf9 A SG CYS 273 A CYS 278 1_555 A SG CYS 284 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf10 A SG CYS 311 A CYS 316 1_555 A SG CYS 356 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 A SG CYS 355 A CYS 360 1_555 A SG CYS 364 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 A SG CYS 387 A CYS 392 1_555 A SG CYS 433 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 A SG CYS 432 A CYS 437 1_555 A SG CYS 443 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf14 A SG CYS 456 A CYS 461 1_555 A SG CYS 472 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf15 A SG CYS 471 A CYS 476 1_555 A SG CYS 482 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf16 A SG CYS 509 A CYS 514 1_555 A SG CYS 554 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 A SG CYS 553 A CYS 558 1_555 A SG CYS 562 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _chem_comp.formula 'C10 H20 O2' _chem_comp.formula_weight 172.265 _chem_comp.id DKA _chem_comp.mon_nstd_flag . _chem_comp.name 'DECANOIC ACID' _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 O1 DKA doub 83 n n C1 C2 DKA sing 84 n n C1 O2 DKA sing 85 n n C2 C3 DKA sing 86 n n C2 H21 DKA sing 87 n n C2 H22 DKA sing 88 n n C3 C4 DKA sing 89 n n C3 H31 DKA sing 90 n n C3 H32 DKA sing 91 n n C4 C5 DKA sing 92 n n C4 H41 DKA sing 93 n n C4 H42 DKA sing 94 n n C5 C6 DKA sing 95 n n C5 H51 DKA sing 96 n n C5 H52 DKA sing 97 n n C6 C7 DKA sing 98 n n C6 H61 DKA sing 99 n n C6 H62 DKA sing 100 n n C7 C8 DKA sing 101 n n C7 H71 DKA sing 102 n n C7 H72 DKA sing 103 n n C8 C9 DKA sing 104 n n C8 H81 DKA sing 105 n n C8 H82 DKA sing 106 n n C9 C10 DKA sing 107 n n C9 H91 DKA sing 108 n n C9 H92 DKA sing 109 n n C10 H101 DKA sing 110 n n C10 H102 DKA sing 111 n n C10 H103 DKA sing 112 n n O2 HO2 DKA sing 113 n n # _atom_sites.entry_id 2VDB _atom_sites.fract_transf_matrix[1][1] 0.005249 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000275 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020218 _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] 0.012528 _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 3 DKA A 1 1585 1585 DKA DKA . D 3 DKA A 1 1586 1586 DKA DKA . E 3 DKA A 1 1587 1587 DKA DKA . F 3 DKA A 1 1588 1588 DKA DKA . G 3 DKA A 1 1589 1589 DKA DKA . H 3 DKA A 1 1590 1590 DKA DKA . I 4 NPS A 1 1591 1591 NPS NPS . # 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 DKA . . . H 3 33.038 -9.137 17.628 1 57.67 ? C1 DKA 1590 A 1 HETATM 2 O O1 DKA . . . H 3 32.181 -8.232 17.398 1 57.73 ? O1 DKA 1590 A 1 HETATM 3 C C2 DKA . . . H 3 34.449 -8.75 18.024 1 56.86 ? C2 DKA 1590 A 1 HETATM 4 C C3 DKA . . . H 3 34.629 -8.868 19.526 1 56.95 ? C3 DKA 1590 A 1 HETATM 5 C C4 DKA . . . H 3 35.837 -8.071 20.005 1 56.68 ? C4 DKA 1590 A 1 HETATM 6 C C5 DKA . . . H 3 35.748 -7.897 21.513 1 56.93 ? C5 DKA 1590 A 1 HETATM 7 C C6 DKA . . . H 3 35.808 -6.437 21.947 1 57.27 ? C6 DKA 1590 A 1 HETATM 8 C C7 DKA . . . H 3 34.499 -5.705 21.644 1 57.65 ? C7 DKA 1590 A 1 HETATM 9 C C8 DKA . . . H 3 34.405 -4.374 22.383 1 56.96 ? C8 DKA 1590 A 1 HETATM 10 C C9 DKA . . . H 3 33.965 -4.623 23.823 1 57.57 ? C9 DKA 1590 A 1 HETATM 11 C C10 DKA . . . H 3 32.873 -5.674 23.925 1 56.54 ? C10 DKA 1590 A 1 HETATM 12 O O2 DKA . . . H 3 32.786 -10.361 17.527 1 57.02 ? O2 DKA 1590 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 12 #