data_8VBY # _model_server_result.job_id Lc_6pZ8MEMJTC0Cm97RtsQ _model_server_result.datetime_utc '2024-11-14 17:53:56' _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 8vby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":729}' # _entry.id 8VBY # _exptl.entry_id 8VBY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 114.229 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OCTANE _entity.pdbx_number_of_molecules 2 _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 8VBY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _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 ? 13 DA N N ? 13 EA 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 130 A CYS 180 1_555 A SG CYS 139 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 138 A ASN 188 1_555 D C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O VAL 28 A VAL 78 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc2 A OD1 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc3 A OD2 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc4 A NE2 HIS 143 A HIS 193 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc5 A NE2 HIS 325 A HIS 375 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc6 A OE2 GLU 346 A GLU 396 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc7 A O LEU 368 A LEU 418 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc8 A OD1 ASP 371 A ASP 421 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc9 A OG SER 372 A SER 422 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? # _chem_comp.formula 'C8 H18' _chem_comp.formula_weight 114.229 _chem_comp.id OCT _chem_comp.mon_nstd_flag . _chem_comp.name N-OCTANE _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 OCT sing 514 n n C1 H11 OCT sing 515 n n C1 H12 OCT sing 516 n n C1 H13 OCT sing 517 n n C2 C3 OCT sing 518 n n C2 H21 OCT sing 519 n n C2 H22 OCT sing 520 n n C3 C4 OCT sing 521 n n C3 H31 OCT sing 522 n n C3 H32 OCT sing 523 n n C4 C5 OCT sing 524 n n C4 H41 OCT sing 525 n n C4 H42 OCT sing 526 n n C5 C6 OCT sing 527 n n C5 H51 OCT sing 528 n n C5 H52 OCT sing 529 n n C6 C7 OCT sing 530 n n C6 H61 OCT sing 531 n n C6 H62 OCT sing 532 n n C7 C8 OCT sing 533 n n C7 H71 OCT sing 534 n n C7 H72 OCT sing 535 n n C8 H81 OCT sing 536 n n C8 H82 OCT sing 537 n n C8 H83 OCT sing 538 n n # _atom_sites.entry_id 8VBY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 42L A 1 701 701 42L 42L . C 3 A1AAF A 1 702 702 A1AAF MRS . D 4 NAG A 1 703 705 NAG NAG . E 5 Y01 A 1 704 709 Y01 Y01 . F 6 D10 A 1 705 713 D10 D10 . G 7 LNK A 1 706 714 LNK LNK . H 6 D10 A 1 707 715 D10 D10 . I 7 LNK A 1 708 717 LNK LNK . J 7 LNK A 1 709 718 LNK LNK . K 5 Y01 A 1 710 723 Y01 Y01 . L 5 Y01 A 1 711 727 Y01 Y01 . M 8 HP6 A 1 712 728 HP6 HP6 . N 9 ZN A 1 713 729 ZN ZN . O 10 NA A 1 714 730 NA NA . P 8 HP6 A 1 715 732 HP6 HP6 . Q 11 D12 A 1 716 734 D12 D12 . R 11 D12 A 1 717 736 D12 D12 . S 6 D10 A 1 718 738 D10 D10 . T 8 HP6 A 1 719 748 HP6 HP6 . U 8 HP6 A 1 720 749 HP6 HP6 . V 7 LNK A 1 721 750 LNK LNK . W 7 LNK A 1 722 751 LNK LNK . X 7 LNK A 1 723 752 LNK LNK . Y 6 D10 A 1 724 753 D10 D10 . Z 12 MYS A 1 725 754 MYS MYS . AA 11 D12 A 1 726 755 D12 D12 . BA 8 HP6 A 1 727 756 HP6 HP6 . CA 11 D12 A 1 728 758 D12 D12 . DA 13 OCT A 1 729 759 OCT OCT . EA 13 OCT A 1 730 762 OCT OCT . FA 8 HP6 A 1 731 763 HP6 HP6 . GA 7 LNK A 1 732 764 LNK LNK . HA 8 HP6 A 1 733 765 HP6 HP6 . IA 6 D10 A 1 734 766 D10 D10 . JA 6 D10 A 1 735 770 D10 D10 . KA 11 D12 A 1 736 772 D12 D12 . LA 8 HP6 A 1 737 774 HP6 HP6 . MA 5 Y01 A 1 738 776 Y01 Y01 . NA 11 D12 A 1 739 777 D12 D12 . OA 6 D10 A 1 740 778 D10 D10 . PA 6 D10 A 1 741 1 D10 D10 . QA 14 HOH A 1 801 12 HOH HOH . QA 14 HOH A 2 802 11 HOH HOH . QA 14 HOH A 3 803 7 HOH HOH . QA 14 HOH A 4 804 8 HOH HOH . QA 14 HOH A 5 805 3 HOH HOH . QA 14 HOH A 6 806 4 HOH HOH . QA 14 HOH A 7 807 10 HOH HOH . QA 14 HOH A 8 808 9 HOH HOH . QA 14 HOH A 9 809 6 HOH HOH . QA 14 HOH A 10 810 5 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 OCT . . . DA 13 156.084 171.998 150.738 1 54.62 ? C1 OCT 729 A 1 HETATM 2 C C2 OCT . . . DA 13 154.833 171.603 149.965 1 58.32 ? C2 OCT 729 A 1 HETATM 3 C C3 OCT . . . DA 13 154.161 170.358 150.529 1 58.19 ? C3 OCT 729 A 1 HETATM 4 C C4 OCT . . . DA 13 152.951 169.904 149.724 1 61.23 ? C4 OCT 729 A 1 HETATM 5 C C5 OCT . . . DA 13 152.358 168.595 150.23 1 61.37 ? C5 OCT 729 A 1 HETATM 6 C C6 OCT . . . DA 13 151.231 168.061 149.356 1 63.87 ? C6 OCT 729 A 1 HETATM 7 C C7 OCT . . . DA 13 150.006 168.966 149.323 1 60.17 ? C7 OCT 729 A 1 HETATM 8 C C8 OCT . . . DA 13 148.819 168.316 148.625 1 57.86 ? C8 OCT 729 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 8 #