data_3VW2 # _model_server_result.job_id fQKn5ivF6uJPXfLSwDG3Cg _model_server_result.datetime_utc '2024-10-14 18:29:35' _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 3vw2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":301}' # _entry.id 3VW2 # _exptl.entry_id 3VW2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 336.361 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BERBERINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 104.97 _cell.angle_beta 97.74 _cell.angle_gamma 90.04 _cell.entry_id 3VW2 _cell.length_a 43.817 _cell.length_b 54.623 _cell.length_c 92.291 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VW2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C20 H18 N O4 1' _chem_comp.formula_weight 336.361 _chem_comp.id BER _chem_comp.mon_nstd_flag . _chem_comp.name BERBERINE _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 BER sing 70 n y C1 N1 BER doub 71 n y C1 C3 BER sing 72 n y C2 C4 BER doub 73 n y C2 C5 BER sing 74 n y N1 C6 BER sing 75 n y N1 C7 BER sing 76 n n C3 C8 BER doub 77 n y C3 H31 BER sing 78 n n C4 C9 BER sing 79 n y C4 C10 BER sing 80 n n C5 C11 BER doub 81 n y C5 H51 BER sing 82 n n C6 C12 BER doub 83 n y C6 H61 BER sing 84 n n C7 C10 BER sing 85 n n C7 H71 BER sing 86 n n C7 H72 BER sing 87 n n C8 C12 BER sing 88 n y C8 C13 BER sing 89 n y C9 C14 BER doub 90 n y C9 H91 BER sing 91 n n C10 H101 BER sing 92 n n C10 H102 BER sing 93 n n C11 C14 BER sing 94 n y C11 O1 BER sing 95 n n C12 C15 BER sing 96 n y C13 C16 BER doub 97 n y C13 H131 BER sing 98 n n C14 O2 BER sing 99 n n O1 C17 BER sing 100 n n C15 C18 BER doub 101 n y C15 O3 BER sing 102 n n C16 C18 BER sing 103 n y C16 H161 BER sing 104 n n O2 C17 BER sing 105 n n C17 H171 BER sing 106 n n C17 H172 BER sing 107 n n C18 O4 BER sing 108 n n O3 C19 BER sing 109 n n O4 C20 BER sing 110 n n C19 H191 BER sing 111 n n C19 H192 BER sing 112 n n C19 H193 BER sing 113 n n C20 H201 BER sing 114 n n C20 H202 BER sing 115 n n C20 H203 BER sing 116 n n # _atom_sites.entry_id 3VW2 _atom_sites.fract_transf_matrix[1][1] 0.022822 _atom_sites.fract_transf_matrix[1][2] 0.000015 _atom_sites.fract_transf_matrix[1][3] 0.003215 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018307 _atom_sites.fract_transf_matrix[2][3] 0.004945 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011327 _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 E 2 BER A 1 301 301 BER BER . F 3 SO4 A 1 302 302 SO4 SO4 . G 2 BER B 1 301 301 BER BER . H 3 SO4 B 1 302 302 SO4 SO4 . I 2 BER C 1 301 301 BER BER . J 3 SO4 C 1 302 302 SO4 SO4 . K 2 BER D 1 301 301 BER BER . L 3 SO4 D 1 302 302 SO4 SO4 . M 4 HOH A 1 401 401 HOH HOH . M 4 HOH A 2 402 402 HOH HOH . M 4 HOH A 3 403 403 HOH HOH . M 4 HOH A 4 404 404 HOH HOH . M 4 HOH A 5 405 405 HOH HOH . M 4 HOH A 6 406 406 HOH HOH . M 4 HOH A 7 407 407 HOH HOH . M 4 HOH A 8 408 408 HOH HOH . M 4 HOH A 9 409 409 HOH HOH . M 4 HOH A 10 410 410 HOH HOH . M 4 HOH A 11 411 411 HOH HOH . M 4 HOH A 12 412 413 HOH HOH . M 4 HOH A 13 413 414 HOH HOH . M 4 HOH A 14 414 415 HOH HOH . M 4 HOH A 15 415 416 HOH HOH . M 4 HOH A 16 416 417 HOH HOH . M 4 HOH A 17 417 418 HOH HOH . M 4 HOH A 18 418 419 HOH HOH . M 4 HOH A 19 419 420 HOH HOH . M 4 HOH A 20 420 411 HOH HOH . M 4 HOH A 21 421 412 HOH HOH . M 4 HOH A 22 422 407 HOH HOH . N 4 HOH B 1 401 401 HOH HOH . N 4 HOH B 2 402 402 HOH HOH . N 4 HOH B 3 403 403 HOH HOH . N 4 HOH B 4 404 404 HOH HOH . N 4 HOH B 5 405 405 HOH HOH . N 4 HOH B 6 406 406 HOH HOH . N 4 HOH B 7 407 407 HOH HOH . N 4 HOH B 8 408 409 HOH HOH . N 4 HOH B 9 409 400 HOH HOH . N 4 HOH B 10 410 411 HOH HOH . N 4 HOH B 11 411 412 HOH HOH . N 4 HOH B 12 412 413 HOH HOH . N 4 HOH B 13 413 414 HOH HOH . N 4 HOH B 14 414 415 HOH HOH . N 4 HOH B 15 415 416 HOH HOH . N 4 HOH B 16 416 413 HOH HOH . O 4 HOH C 1 401 412 HOH HOH . O 4 HOH C 2 402 408 HOH HOH . O 4 HOH C 3 403 401 HOH HOH . O 4 HOH C 4 404 402 HOH HOH . O 4 HOH C 5 405 403 HOH HOH . O 4 HOH C 6 406 404 HOH HOH . O 4 HOH C 7 407 405 HOH HOH . O 4 HOH C 8 408 406 HOH HOH . O 4 HOH C 9 409 407 HOH HOH . O 4 HOH C 10 410 408 HOH HOH . O 4 HOH C 11 411 409 HOH HOH . O 4 HOH C 12 412 410 HOH HOH . O 4 HOH C 13 413 414 HOH HOH . O 4 HOH C 14 414 415 HOH HOH . O 4 HOH C 15 415 416 HOH HOH . O 4 HOH C 16 416 417 HOH HOH . P 4 HOH D 1 401 401 HOH HOH . P 4 HOH D 2 402 402 HOH HOH . P 4 HOH D 3 403 403 HOH HOH . P 4 HOH D 4 404 404 HOH HOH . P 4 HOH D 5 405 405 HOH HOH . P 4 HOH D 6 406 406 HOH HOH . P 4 HOH D 7 407 408 HOH HOH . P 4 HOH D 8 408 409 HOH HOH . P 4 HOH D 9 409 400 HOH HOH . P 4 HOH D 10 410 411 HOH HOH . P 4 HOH D 11 411 412 HOH HOH . P 4 HOH D 12 412 413 HOH HOH . P 4 HOH D 13 413 414 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 BER . . . K 2 -2.928 -2.719 20.063 1 57 ? C1 BER 301 D 1 HETATM 2 C C2 BER . . . K 2 -2.619 -2.021 21.28 1 59.11 ? C2 BER 301 D 1 HETATM 3 N N1 BER . . . K 2 -2.022 -2.788 19.12 1 61.17 ? N1 BER 301 D 1 HETATM 4 C C3 BER . . . K 2 -4.286 -3.288 19.998 1 58.59 ? C3 BER 301 D 1 HETATM 5 C C4 BER . . . K 2 -1.289 -1.42 21.433 1 59.23 ? C4 BER 301 D 1 HETATM 6 C C5 BER . . . K 2 -3.588 -1.964 22.229 1 62.67 ? C5 BER 301 D 1 HETATM 7 C C6 BER . . . K 2 -2.232 -3.441 17.975 1 62.02 ? C6 BER 301 D 1 HETATM 8 C C7 BER . . . K 2 -0.824 -2.235 19.268 1 59.49 ? C7 BER 301 D 1 HETATM 9 C C8 BER . . . K 2 -4.399 -4.209 18.855 1 60.92 ? C8 BER 301 D 1 HETATM 10 C C9 BER . . . K 2 -0.943 -0.752 22.57 1 59.39 ? C9 BER 301 D 1 HETATM 11 C C10 BER . . . K 2 -0.412 -1.557 20.394 1 58.93 ? C10 BER 301 D 1 HETATM 12 C C11 BER . . . K 2 -3.222 -1.294 23.348 1 64.5 ? C11 BER 301 D 1 HETATM 13 C C12 BER . . . K 2 -3.54 -4.083 17.668 1 63.24 ? C12 BER 301 D 1 HETATM 14 C C13 BER . . . K 2 -5.32 -5.139 18.86 1 62.69 ? C13 BER 301 D 1 HETATM 15 C C14 BER . . . K 2 -1.923 -0.707 23.514 1 63.37 ? C14 BER 301 D 1 HETATM 16 O O1 BER . . . K 2 -3.939 -1.061 24.447 1 69.4 ? O1 BER 301 D 1 HETATM 17 C C15 BER . . . K 2 -3.345 -5.461 17.137 1 66.49 ? C15 BER 301 D 1 HETATM 18 C C16 BER . . . K 2 -5.659 -5.713 17.598 1 63.29 ? C16 BER 301 D 1 HETATM 19 O O2 BER . . . K 2 -1.901 -0.126 24.718 1 67.5 ? O2 BER 301 D 1 HETATM 20 C C17 BER . . . K 2 -3.152 -0.298 25.359 1 69.19 ? C17 BER 301 D 1 HETATM 21 C C18 BER . . . K 2 -4.685 -5.888 16.755 1 65.5 ? C18 BER 301 D 1 HETATM 22 O O3 BER . . . K 2 -2.597 -5.399 15.947 1 71.71 ? O3 BER 301 D 1 HETATM 23 O O4 BER . . . K 2 -4.893 -6.452 15.469 1 69.64 ? O4 BER 301 D 1 HETATM 24 C C19 BER . . . K 2 -1.483 -4.55 16.104 1 73.28 ? C19 BER 301 D 1 HETATM 25 C C20 BER . . . K 2 -5.095 -7.839 15.382 1 72.17 ? C20 BER 301 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #