data_8I5X # _model_server_result.job_id ebBMHVCaGwtQPn3Cj1VUNw _model_server_result.datetime_utc '2024-12-05 00:49:15' _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 8i5x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":2009}' # _entry.id 8I5X # _exptl.entry_id 8I5X _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 350.454 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Vinpocetine _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 8I5X _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I5X _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,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 _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 ? _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 9 _struct_asym.id O _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG A 2007 NAG 4 n D NAG 2 D 2 NAG A 2008 NAG 4 n E NAG 1 E 1 NAG A 2009 NAG 4 n E NAG 2 E 2 NAG F 2004 NAG 4 n F NAG 1 F 1 NAG D 1 NAG 4 n F NAG 2 F 2 NAG D 2 NAG # 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 315 A CYS 275 1_555 A SG CYS 364 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 355 A CYS 315 1_555 A SG CYS 370 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 935 A CYS 895 1_555 C SG CYS 55 C CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 937 A CYS 897 1_555 A SG CYS 943 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 975 A CYS 935 1_555 A SG CYS 984 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 1390 A CYS 1350 1_555 A SG CYS 1410 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 1755 A CYS 1715 1_555 A SG CYS 1770 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 323 A ASN 283 1_555 G C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 1392 A ASN 1352 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 1406 A ASN 1366 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 1415 A ASN 1375 1_555 M C1 NAG . A NAG 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B ND2 ASN 93 B ASN 93 1_555 FA C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 GA C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 114 B ASN 114 1_555 HA C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 B ND2 ASN 135 B ASN 135 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C22 H26 N2 O2' _chem_comp.formula_weight 350.454 _chem_comp.id T7F _chem_comp.mon_nstd_flag . _chem_comp.name Vinpocetine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Ethyl apovincaminate' # 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 O02 C20 T7F doub 781 n n C25 C26 T7F sing 782 n n C25 O01 T7F sing 783 n n C20 O01 T7F sing 784 n n C20 C16 T7F sing 785 n n C19 C11 T7F sing 786 n n C11 C05 T7F sing 787 n n C16 C14 T7F doub 788 n n C16 N1 T7F sing 789 n n C23 C24 T7F sing 790 n y C23 C21 T7F doub 791 n y C14 C05 T7F sing 792 n n N1 C21 T7F sing 793 n y N1 C2 T7F sing 794 n y C24 C5 T7F doub 795 n y C21 C3 T7F sing 796 n y C05 C06 T7F sing 797 n n C05 C07 T7F sing 798 n n C06 C2 T7F sing 799 n n C06 N03 T7F sing 800 n n C2 C1 T7F doub 801 n y C5 C4 T7F sing 802 n y C3 C1 T7F sing 803 n y C3 C4 T7F doub 804 n y C1 C15 T7F sing 805 n n C12 C15 T7F sing 806 n n C12 N03 T7F sing 807 n n N03 C09 T7F sing 808 n n C07 C10 T7F sing 809 n n C10 C09 T7F sing 810 n n C5 H1 T7F sing 811 n n C4 H2 T7F sing 812 n n C06 H3 T7F sing 813 n n C07 H4 T7F sing 814 n n C07 H5 T7F sing 815 n n C09 H6 T7F sing 816 n n C09 H7 T7F sing 817 n n C10 H8 T7F sing 818 n n C10 H9 T7F sing 819 n n C11 H10 T7F sing 820 n n C11 H11 T7F sing 821 n n C12 H12 T7F sing 822 n n C12 H13 T7F sing 823 n n C14 H14 T7F sing 824 n n C15 H16 T7F sing 825 n n C15 H17 T7F sing 826 n n C19 H19 T7F sing 827 n n C19 H20 T7F sing 828 n n C19 H21 T7F sing 829 n n C23 H22 T7F sing 830 n n C24 H23 T7F sing 831 n n C25 H24 T7F sing 832 n n C25 H25 T7F sing 833 n n C26 H26 T7F sing 834 n n C26 H27 T7F sing 835 n n C26 H28 T7F sing 836 n n # _atom_sites.entry_id 8I5X _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 G 5 NAG A 1 2001 2006 NAG NAG . H 6 P5S A 1 2002 2012 P5S P5S . I 7 Y01 A 1 2003 2015 Y01 Y01 . J 7 Y01 A 1 2004 2016 Y01 Y01 . K 7 Y01 A 1 2005 2017 Y01 Y01 . L 8 9Z9 A 1 2006 2019 9Z9 9Z9 . M 5 NAG A 1 2007 2021 NAG NAG . N 7 Y01 A 1 2008 2022 Y01 Y01 . O 9 T7F A 1 2009 2024 T7F L3X . P 10 LPE A 1 2010 2010 LPE LPE . Q 11 PCW A 1 2011 2013 PCW PCW . R 10 LPE A 1 2012 2014 LPE LPE . S 10 LPE A 1 2013 2015 LPE LPE . T 11 PCW A 1 2014 2016 PCW PCW . U 11 PCW A 1 2015 2018 PCW PCW . V 10 LPE A 1 2016 2019 LPE LPE . W 10 LPE A 1 2017 2020 LPE LPE . X 10 LPE A 1 2018 2021 LPE LPE . Y 10 LPE A 1 2019 2022 LPE LPE . Z 10 LPE A 1 2020 2023 LPE LPE . AA 10 LPE A 1 2021 2024 LPE LPE . BA 10 LPE A 1 2022 2031 LPE LPE . CA 11 PCW A 1 2023 2035 PCW PCW . DA 11 PCW A 1 2024 2036 PCW PCW . EA 7 Y01 A 1 2025 2040 Y01 Y01 . FA 5 NAG B 1 301 301 NAG NAG . GA 5 NAG B 1 302 302 NAG NAG . HA 5 NAG B 1 303 303 NAG NAG . IA 10 LPE B 1 304 305 LPE LPE . # 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 C5 T7F . . . O 9 144.733 130.22 136.487 1 45.07 ? C5 T7F 2009 A 1 HETATM 2 C C4 T7F . . . O 9 143.586 130.934 136.806 1 46.17 ? C4 T7F 2009 A 1 HETATM 3 C C2 T7F . . . O 9 143.042 134.515 136.257 1 51.13 ? C2 T7F 2009 A 1 HETATM 4 N N1 T7F . . . O 9 144.234 134.19 135.822 1 52.28 ? N1 T7F 2009 A 1 HETATM 5 C C05 T7F . . . O 9 143.562 136.976 136.151 1 52.38 ? C05 T7F 2009 A 1 HETATM 6 C C06 T7F . . . O 9 142.489 135.871 136.175 1 49.32 ? C06 T7F 2009 A 1 HETATM 7 C C07 T7F . . . O 9 143.822 137.605 137.5 1 52.44 ? C07 T7F 2009 A 1 HETATM 8 C C09 T7F . . . O 9 141.908 136.551 138.52 1 48.04 ? C09 T7F 2009 A 1 HETATM 9 C C1 T7F . . . O 9 142.472 133.419 136.722 1 48.42 ? C1 T7F 2009 A 1 HETATM 10 C C10 T7F . . . O 9 142.571 137.886 138.257 1 48.82 ? C10 T7F 2009 A 1 HETATM 11 C C11 T7F . . . O 9 143.08 138.075 135.196 1 50.45 ? C11 T7F 2009 A 1 HETATM 12 C C12 T7F . . . O 9 140.43 134.808 137.042 1 50.33 ? C12 T7F 2009 A 1 HETATM 13 C C14 T7F . . . O 9 144.923 136.425 135.636 1 49.67 ? C14 T7F 2009 A 1 HETATM 14 C C15 T7F . . . O 9 141.182 133.514 137.237 1 45.91 ? C15 T7F 2009 A 1 HETATM 15 C C16 T7F . . . O 9 145.07 135.189 135.261 1 48.14 ? C16 T7F 2009 A 1 HETATM 16 C C19 T7F . . . O 9 144.266 138.883 134.669 1 49.32 ? C19 T7F 2009 A 1 HETATM 17 C C20 T7F . . . O 9 145.909 134.896 134.02 1 50.62 ? C20 T7F 2009 A 1 HETATM 18 C C21 T7F . . . O 9 144.613 132.934 135.942 1 52.08 ? C21 T7F 2009 A 1 HETATM 19 C C23 T7F . . . O 9 145.752 132.21 135.631 1 51.02 ? C23 T7F 2009 A 1 HETATM 20 C C24 T7F . . . O 9 145.809 130.858 135.901 1 48.9 ? C24 T7F 2009 A 1 HETATM 21 C C25 T7F . . . O 9 147.798 133.976 133.024 1 49.51 ? C25 T7F 2009 A 1 HETATM 22 C C26 T7F . . . O 9 148.625 132.771 133.466 1 51.61 ? C26 T7F 2009 A 1 HETATM 23 C C3 T7F . . . O 9 143.506 132.295 136.541 1 50.13 ? C3 T7F 2009 A 1 HETATM 24 N N03 T7F . . . O 9 141.379 136.027 137.277 1 50.67 ? N03 T7F 2009 A 1 HETATM 25 O O01 T7F . . . O 9 147.272 134.621 134.147 1 51.37 ? O01 T7F 2009 A 1 HETATM 26 O O02 T7F . . . O 9 145.401 134.883 132.95 1 53.19 ? O02 T7F 2009 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #