data_2VMY # _model_server_result.job_id vAt6ygp-c522HdOHgZYOAw _model_server_result.datetime_utc '2024-11-24 16:52:08' _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 2vmy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":505}' # _entry.id 2VMY # _exptl.entry_id 2VMY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 473.439 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid' _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 90.33 _cell.angle_gamma 90 _cell.entry_id 2VMY _cell.length_a 57.382 _cell.length_b 103.483 _cell.length_c 61.959 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VMY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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,J,K _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 ? 4 E N N ? 4 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 covale ? covale1 D C4A PLP . A PLP 501 1_555 C N GLY . A GLY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.233 ? covale ? covale2 G C4A PLP . B PLP 501 1_555 F N GLY . B GLY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.23 ? # _chem_comp.formula 'C20 H23 N7 O7' _chem_comp.formula_weight 473.439 _chem_comp.id FFO _chem_comp.mon_nstd_flag . _chem_comp.name 'N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[6S]-5-FORMYL-TETRAHYDROFOLATE;6S-FOLINIC ACID' # 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 N1 C2 FFO doub 83 n n N1 C8A FFO sing 84 n n C2 NA2 FFO sing 85 n n C2 N3 FFO sing 86 n n NA2 HN21 FFO sing 87 n n NA2 HN22 FFO sing 88 n n N3 C4 FFO sing 89 n n N3 H22 FFO sing 90 n n C4 O4 FFO doub 91 n n C4 C4A FFO sing 92 n n C4A N5 FFO sing 93 n n C4A C8A FFO doub 94 n n N5 C6 FFO sing 95 n n N5 C5A FFO sing 96 n n C6 C7 FFO sing 97 n n C6 C9 FFO sing 98 n n C6 H6 FFO sing 99 n n C7 N8 FFO sing 100 n n C7 H7 FFO sing 101 n n C7 H23 FFO sing 102 n n N8 C8A FFO sing 103 n n N8 H24 FFO sing 104 n n C9 N10 FFO sing 105 n n C9 H91 FFO sing 106 n n C9 H92 FFO sing 107 n n N10 C14 FFO sing 108 n n N10 HN0 FFO sing 109 n n C11 C12 FFO doub 110 n y C11 C16 FFO sing 111 n y C11 C FFO sing 112 n n C12 C13 FFO sing 113 n y C12 H12 FFO sing 114 n n C13 C14 FFO doub 115 n y C13 H13 FFO sing 116 n n C14 C15 FFO sing 117 n y C15 C16 FFO doub 118 n y C15 H15 FFO sing 119 n n C16 H16 FFO sing 120 n n C O FFO doub 121 n n C N FFO sing 122 n n N CA FFO sing 123 n n N HN FFO sing 124 n n CA CB FFO sing 125 n n CA CT FFO sing 126 n n CA HA FFO sing 127 n n CB CG FFO sing 128 n n CB HB1 FFO sing 129 n n CB HB2 FFO sing 130 n n CG CD FFO sing 131 n n CG HG1 FFO sing 132 n n CG HG2 FFO sing 133 n n CD OE1 FFO doub 134 n n CD OE2 FFO sing 135 n n OE2 HOE2 FFO sing 136 n n CT O1 FFO doub 137 n n CT O2 FFO sing 138 n n O2 HO2 FFO sing 139 n n C5A O5B FFO doub 140 n n C5A H5A FFO sing 141 n n # _atom_sites.entry_id 2VMY _atom_sites.fract_transf_matrix[1][1] 0.017427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0001 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009663 _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] 0.01614 _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 2 GLY A 1 502 502 GLY GLY . D 3 PLP A 1 501 501 PLP PLP . E 4 FFO A 1 505 505 FFO FFO . F 2 GLY B 1 502 502 GLY GLY . G 3 PLP B 1 501 501 PLP PLP . H 4 FFO B 1 505 505 FFO FFO . I 5 MRD B 1 701 701 MRD MRD . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . K 6 HOH B 1 2001 2001 HOH HOH . K 6 HOH B 2 2002 2002 HOH HOH . K 6 HOH B 3 2003 2003 HOH HOH . K 6 HOH B 4 2004 2004 HOH HOH . K 6 HOH B 5 2005 2005 HOH HOH . K 6 HOH B 6 2006 2006 HOH HOH . K 6 HOH B 7 2007 2007 HOH HOH . K 6 HOH B 8 2008 2008 HOH HOH . K 6 HOH B 9 2009 2009 HOH HOH . K 6 HOH B 10 2010 2010 HOH HOH . K 6 HOH B 11 2011 2011 HOH HOH . K 6 HOH B 12 2012 2012 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 N N1 FFO . . . E 4 24.201 28.816 7.182 1 60.02 ? N1 FFO 505 A 1 HETATM 2 C C2 FFO . . . E 4 25.341 28.256 6.734 1 60.11 ? C2 FFO 505 A 1 HETATM 3 N NA2 FFO . . . E 4 26.051 28.842 5.775 1 59.97 ? NA2 FFO 505 A 1 HETATM 4 N N3 FFO . . . E 4 25.784 27.044 7.274 1 60.01 ? N3 FFO 505 A 1 HETATM 5 C C4 FFO . . . E 4 25.042 26.422 8.281 1 59.85 ? C4 FFO 505 A 1 HETATM 6 O O4 FFO . . . E 4 25.482 25.239 8.809 1 59.86 ? O4 FFO 505 A 1 HETATM 7 C C4A FFO . . . E 4 23.865 27.028 8.72 1 60.03 ? C4A FFO 505 A 1 HETATM 8 N N5 FFO . . . E 4 23.055 26.491 9.736 1 60.42 ? N5 FFO 505 A 1 HETATM 9 C C6 FFO . . . E 4 22.324 27.423 10.623 1 60.43 ? C6 FFO 505 A 1 HETATM 10 C C7 FFO . . . E 4 21.568 28.453 9.766 1 60.33 ? C7 FFO 505 A 1 HETATM 11 N N8 FFO . . . E 4 22.282 28.846 8.607 1 60.14 ? N8 FFO 505 A 1 HETATM 12 C C8A FFO . . . E 4 23.468 28.234 8.152 1 60.05 ? C8A FFO 505 A 1 HETATM 13 C C9 FFO . . . E 4 23.279 28.152 11.59 1 60.39 ? C9 FFO 505 A 1 HETATM 14 N N10 FFO . . . E 4 23.802 27.226 12.612 1 60.81 ? N10 FFO 505 A 1 HETATM 15 C C11 FFO . . . E 4 27.511 27.703 14.4 1 60.97 ? C11 FFO 505 A 1 HETATM 16 C C12 FFO . . . E 4 27.306 28.121 13.084 1 60.98 ? C12 FFO 505 A 1 HETATM 17 C C13 FFO . . . E 4 26.061 27.966 12.474 1 60.97 ? C13 FFO 505 A 1 HETATM 18 C C14 FFO . . . E 4 25.004 27.391 13.18 1 60.9 ? C14 FFO 505 A 1 HETATM 19 C C15 FFO . . . E 4 25.21 26.973 14.498 1 60.7 ? C15 FFO 505 A 1 HETATM 20 C C16 FFO . . . E 4 26.455 27.127 15.108 1 60.71 ? C16 FFO 505 A 1 HETATM 21 C C FFO . . . E 4 28.895 27.892 15.048 1 60.99 ? C FFO 505 A 1 HETATM 22 O O FFO . . . E 4 29.92 27.88 14.365 1 60.96 ? O FFO 505 A 1 HETATM 23 N N FFO . . . E 4 28.879 28.074 16.369 1 61.25 ? N FFO 505 A 1 HETATM 24 C CA FFO . . . E 4 30.097 28.287 17.179 1 61.56 ? CA FFO 505 A 1 HETATM 25 C CB FFO . . . E 4 30.345 29.789 17.425 1 61.47 ? CB FFO 505 A 1 HETATM 26 C CG FFO . . . E 4 29.038 30.589 17.505 1 62.04 ? CG FFO 505 A 1 HETATM 27 C CD FFO . . . E 4 29.111 31.724 18.526 1 62.77 ? CD FFO 505 A 1 HETATM 28 O OE1 FFO . . . E 4 29.206 32.887 18.072 1 62.99 ? OE1 FFO 505 A 1 HETATM 29 O OE2 FFO . . . E 4 29.06 31.405 19.736 1 63.27 ? OE2 FFO 505 A 1 HETATM 30 C CT FFO . . . E 4 29.97 27.561 18.524 1 61.63 ? CT FFO 505 A 1 HETATM 31 O O1 FFO . . . E 4 31.028 27.398 19.17 1 62.14 ? O1 FFO 505 A 1 HETATM 32 O O2 FFO . . . E 4 28.829 27.186 18.876 1 61.38 ? O2 FFO 505 A 1 HETATM 33 C C5A FFO . . . E 4 22.919 25.027 9.929 1 60.86 ? C5A FFO 505 A 1 HETATM 34 O O5B FFO . . . E 4 21.868 24.539 10.336 1 61.75 ? O5B FFO 505 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 34 #