data_3VFK # _model_server_result.job_id K90WWoNV803nNq-KkL1lRA _model_server_result.datetime_utc '2024-12-07 18:09:17' _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 3vfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":9}' # _entry.id 3VFK # _exptl.entry_id 3VFK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 172.265 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '8-METHYLNONANOIC ACID' _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 109.18 _cell.angle_gamma 90 _cell.entry_id 3VFK _cell.length_a 88.01 _cell.length_b 25.18 _cell.length_c 38.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VFK _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 4 _struct_asym.id D _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 GLY 75 A GLY 75 1_555 A N CCS 76 A CCS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C CCS 76 A CCS 76 1_555 A N LYS 77 A LYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C LYS 77 A LYS 77 1_555 A N DAL 78 A DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C DAL 78 A DAL 78 1_555 A N DAL 79 A DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 B C GHP 1 G GHP 1 1_555 B N 3MY 2 G 3MY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 B C5 GHP 1 G GHP 1 1_555 B OD1 3FG 3 G 3FG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale7 B C 3MY 2 G 3MY 2 1_555 B N 3FG 3 G 3FG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B OBD 3MY 2 G 3MY 2 1_555 B C3 GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale9 B C 3FG 3 G 3FG 3 1_555 B N GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 B C GHP 4 G GHP 4 1_555 B N GHP 5 G GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 B C5 GHP 4 G GHP 4 1_555 B OH OMX 6 G OMX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale12 B O4 GHP 4 G GHP 4 1_555 C C1 GCS . G GCS 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale13 B C GHP 5 G GHP 5 1_555 B N OMX 6 G OMX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C3 GHP 5 G GHP 5 1_555 B CG1 3FG 7 G 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale15 B C OMX 6 G OMX 6 1_555 B N 3FG 7 G 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 B OC OMX 6 G OMX 6 1_555 E C1 NAG . G NAG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale17 B OD1 3FG 7 G 3FG 7 1_555 F C1 MAN . G MAN 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale18 C N2 GCS . G GCS 8 1_555 D C T55 . G T55 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _chem_comp.formula 'C10 H20 O2' _chem_comp.formula_weight 172.265 _chem_comp.id T55 _chem_comp.mon_nstd_flag . _chem_comp.name '8-METHYLNONANOIC 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 OXT C T55 sing 479 n n CAL C T55 sing 480 n n CAL CAK T55 sing 481 n n C O T55 doub 482 n n CAK CAJ T55 sing 483 n n CAJ CAI T55 sing 484 n n CAI CAH T55 sing 485 n n CAH CAG T55 sing 486 n n CAG CAE T55 sing 487 n n CAE CAD T55 sing 488 n n CAE CAF T55 sing 489 n n OXT HXT T55 sing 490 n n CAL HAL1 T55 sing 491 n n CAL HAL2 T55 sing 492 n n CAK HAK1 T55 sing 493 n n CAK HAK2 T55 sing 494 n n CAJ HAJ1 T55 sing 495 n n CAJ HAJ2 T55 sing 496 n n CAI HAI1 T55 sing 497 n n CAI HAI2 T55 sing 498 n n CAH HAH1 T55 sing 499 n n CAH HAH2 T55 sing 500 n n CAG HAG1 T55 sing 501 n n CAG HAG2 T55 sing 502 n n CAE HAE T55 sing 503 n n CAD HAD1 T55 sing 504 n n CAD HAD2 T55 sing 505 n n CAD HAD3 T55 sing 506 n n CAF HAF1 T55 sing 507 n n CAF HAF2 T55 sing 508 n n CAF HAF3 T55 sing 509 n n # _atom_sites.entry_id 3VFK _atom_sites.fract_transf_matrix[1][1] 0.011362 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003952 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.039714 _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] 0.027351 _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 GCS G 1 8 8 GCS GCS . D 4 T55 G 1 9 9 T55 T55 . E 5 NAG G 1 10 10 NAG NAG . F 6 MAN G 1 11 11 MAN MAN . G 7 HOH A 1 201 1 HOH HOH . G 7 HOH A 2 202 2 HOH HOH . G 7 HOH A 3 203 3 HOH HOH . G 7 HOH A 4 204 4 HOH HOH . G 7 HOH A 5 205 5 HOH HOH . G 7 HOH A 6 206 6 HOH HOH . G 7 HOH A 7 207 7 HOH HOH . G 7 HOH A 8 208 8 HOH HOH . G 7 HOH A 9 209 9 HOH HOH . G 7 HOH A 10 210 10 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 CAD T55 . . . D 4 -3.924 22.499 0.784 1 68.04 ? CAD T55 9 G 1 HETATM 2 C CAE T55 . . . D 4 -2.903 21.607 0.078 1 78.21 ? CAE T55 9 G 1 HETATM 3 C CAG T55 . . . D 4 -3.607 20.387 -0.52 1 74.31 ? CAG T55 9 G 1 HETATM 4 C CAH T55 . . . D 4 -4.299 19.56 0.572 1 75.43 ? CAH T55 9 G 1 HETATM 5 C CAI T55 . . . D 4 -4.991 18.371 -0.102 1 79.04 ? CAI T55 9 G 1 HETATM 6 C CAJ T55 . . . D 4 -5.731 17.482 0.904 1 74.64 ? CAJ T55 9 G 1 HETATM 7 C CAK T55 . . . D 4 -4.78 16.881 1.944 1 71.07 ? CAK T55 9 G 1 HETATM 8 C CAL T55 . . . D 4 -5.568 16 2.929 1 65.33 ? CAL T55 9 G 1 HETATM 9 C CAF T55 . . . D 4 -2.236 22.405 -1.042 1 71.79 ? CAF T55 9 G 1 HETATM 10 C C T55 . . . D 4 -6.618 16.827 3.687 1 72.08 ? C T55 9 G 1 HETATM 11 O O T55 . . . D 4 -6.974 17.92 3.252 1 75.67 ? O T55 9 G 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 377 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 11 #