data_2VGB # _model_server_result.job_id pkD16hCFETzCIOZ2ojLSkw _model_server_result.datetime_utc '2024-11-08 08:52:52' _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 2vgb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":580}' # _entry.id 2VGB # _exptl.entry_id 2VGB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.116 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 1,6-di-O-phosphono-beta-D-fructofuranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.46 _cell.angle_gamma 90 _cell.entry_id 2VGB _cell.length_a 74.413 _cell.length_b 172.058 _cell.length_c 85.512 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VGB _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 PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 2 E N N ? 2 I N N ? 2 M N N ? 2 Q 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 metalc ? metalc1 A OD1 ASN 72 A ASN 118 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? metalc ? metalc2 A OG SER 74 A SER 120 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.442 ? metalc ? metalc3 A OD1 ASP 110 A ASP 156 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc4 A O THR 111 A THR 157 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc5 A OE2 GLU 269 A GLU 315 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc6 A OD2 ASP 293 A ASP 339 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc7 F O2P PGA . A PGA 581 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc8 F O1P PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc9 F O2 PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc10 F O4P PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc11 B OD1 ASN 72 B ASN 118 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.208 ? metalc ? metalc12 B OD1 ASP 110 B ASP 156 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc13 B O THR 111 B THR 157 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc14 B OE2 GLU 269 B GLU 315 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? metalc ? metalc15 B OD2 ASP 293 B ASP 339 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc16 J O2P PGA . B PGA 581 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? metalc ? metalc17 J O1 PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc18 J O4P PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc19 J O1P PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc20 C OD1 ASN 72 C ASN 118 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc21 C OD1 ASP 110 C ASP 156 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc22 C O THR 111 C THR 157 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? metalc ? metalc23 C OE2 GLU 269 C GLU 315 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.567 ? metalc ? metalc24 C OD2 ASP 293 C ASP 339 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.72 ? metalc ? metalc25 N O2P PGA . C PGA 581 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? metalc ? metalc26 N O1 PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc27 N O4P PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc28 N O1P PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc29 D OD1 ASN 72 D ASN 118 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc30 D OD1 ASP 110 D ASP 156 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc31 D O THR 111 D THR 157 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc32 D OE2 GLU 269 D GLU 315 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? metalc ? metalc33 D OD2 ASP 293 D ASP 339 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc34 R O2P PGA . D PGA 581 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc35 R O2 PGA . D PGA 581 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc36 R O1P PGA . D PGA 581 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? # _chem_comp.formula 'C6 H14 O12 P2' _chem_comp.formula_weight 340.116 _chem_comp.id FBP _chem_comp.mon_nstd_flag n _chem_comp.name 1,6-di-O-phosphono-beta-D-fructofuranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms BETA-FRUCTOSE-1,6-DIPHOSPHATE;FRUCTOSE-1,6-BISPHOSPHATE;1,6-di-O-phosphono-beta-D-fructose;1,6-di-O-phosphono-D-fructose;1,6-di-O-phosphono-fructose # 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 P1 O1P FBP doub 83 n n P1 O2P FBP sing 84 n n P1 O3P FBP sing 85 n n P1 O1 FBP sing 86 n n O2P HOP2 FBP sing 87 n n O3P HOP3 FBP sing 88 n n O1 C1 FBP sing 89 n n C1 C2 FBP sing 90 n n C1 H11 FBP sing 91 n n C1 H12 FBP sing 92 n n C2 O2 FBP sing 93 n n C2 C3 FBP sing 94 n n C2 O5 FBP sing 95 n n O2 HO2 FBP sing 96 n n C3 O3 FBP sing 97 n n C3 C4 FBP sing 98 n n C3 H3 FBP sing 99 n n O3 HO3 FBP sing 100 n n C4 O4 FBP sing 101 n n C4 C5 FBP sing 102 n n C4 H4 FBP sing 103 n n O4 HO4 FBP sing 104 n n C5 O5 FBP sing 105 n n C5 C6 FBP sing 106 n n C5 H5 FBP sing 107 n n C6 O6 FBP sing 108 n n C6 H61 FBP sing 109 n n C6 H62 FBP sing 110 n n O6 P2 FBP sing 111 n n P2 O4P FBP doub 112 n n P2 O5P FBP sing 113 n n P2 O6P FBP sing 114 n n O5P HOP5 FBP sing 115 n n O6P HOP6 FBP sing 116 n n # _pdbx_chem_comp_identifier.comp_id FBP _pdbx_chem_comp_identifier.identifier b-D-Fruf1PO36PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 2VGB _atom_sites.fract_transf_matrix[1][1] 0.013439 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000577 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005812 _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] 0.011705 _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 FBP A 1 580 580 FBP FBP . F 3 PGA A 1 581 581 PGA PGA . G 4 K A 1 582 582 K K . H 5 MN A 1 583 583 MN MN . I 2 FBP B 1 580 580 FBP FBP . J 3 PGA B 1 581 581 PGA PGA . K 4 K B 1 586 586 K K . L 5 MN B 1 587 587 MN MN . M 2 FBP C 1 580 580 FBP FBP . N 3 PGA C 1 581 581 PGA PGA . O 4 K C 1 590 590 K K . P 5 MN C 1 591 591 MN MN . Q 2 FBP D 1 580 580 FBP FBP . R 3 PGA D 1 581 581 PGA PGA . S 4 K D 1 594 594 K K . T 5 MN D 1 595 595 MN MN . U 6 HOH A 1 2001 2001 HOH HOH . U 6 HOH A 2 2002 2002 HOH HOH . U 6 HOH A 3 2003 2003 HOH HOH . U 6 HOH A 4 2004 2004 HOH HOH . U 6 HOH A 5 2005 2005 HOH HOH . U 6 HOH A 6 2006 2006 HOH HOH . U 6 HOH A 7 2007 2007 HOH HOH . U 6 HOH A 8 2008 2008 HOH HOH . U 6 HOH A 9 2009 2009 HOH HOH . U 6 HOH A 10 2010 2010 HOH HOH . U 6 HOH A 11 2011 2011 HOH HOH . U 6 HOH A 12 2012 2012 HOH HOH . V 6 HOH B 1 2001 2001 HOH HOH . V 6 HOH B 2 2002 2002 HOH HOH . V 6 HOH B 3 2003 2003 HOH HOH . V 6 HOH B 4 2004 2004 HOH HOH . V 6 HOH B 5 2005 2005 HOH HOH . V 6 HOH B 6 2006 2006 HOH HOH . V 6 HOH B 7 2007 2007 HOH HOH . V 6 HOH B 8 2008 2008 HOH HOH . V 6 HOH B 9 2009 2009 HOH HOH . V 6 HOH B 10 2010 2010 HOH HOH . V 6 HOH B 11 2011 2011 HOH HOH . V 6 HOH B 12 2012 2012 HOH HOH . V 6 HOH B 13 2013 2013 HOH HOH . V 6 HOH B 14 2014 2014 HOH HOH . V 6 HOH B 15 2015 2015 HOH HOH . V 6 HOH B 16 2016 2016 HOH HOH . W 6 HOH C 1 2001 2001 HOH HOH . W 6 HOH C 2 2002 2002 HOH HOH . W 6 HOH C 3 2003 2003 HOH HOH . W 6 HOH C 4 2004 2004 HOH HOH . W 6 HOH C 5 2005 2005 HOH HOH . W 6 HOH C 6 2006 2006 HOH HOH . W 6 HOH C 7 2007 2007 HOH HOH . W 6 HOH C 8 2008 2008 HOH HOH . W 6 HOH C 9 2009 2009 HOH HOH . W 6 HOH C 10 2010 2010 HOH HOH . W 6 HOH C 11 2011 2011 HOH HOH . W 6 HOH C 12 2012 2012 HOH HOH . W 6 HOH C 13 2013 2013 HOH HOH . W 6 HOH C 14 2014 2014 HOH HOH . W 6 HOH C 15 2015 2015 HOH HOH . W 6 HOH C 16 2016 2016 HOH HOH . W 6 HOH C 17 2017 2017 HOH HOH . W 6 HOH C 18 2018 2018 HOH HOH . W 6 HOH C 19 2019 2019 HOH HOH . W 6 HOH C 20 2020 2020 HOH HOH . X 6 HOH D 1 2001 2001 HOH HOH . X 6 HOH D 2 2002 2002 HOH HOH . X 6 HOH D 3 2003 2003 HOH HOH . X 6 HOH D 4 2004 2004 HOH HOH . X 6 HOH D 5 2005 2005 HOH HOH . X 6 HOH D 6 2006 2006 HOH HOH . X 6 HOH D 7 2007 2007 HOH HOH . X 6 HOH D 8 2008 2008 HOH HOH . X 6 HOH D 9 2009 2009 HOH HOH . X 6 HOH D 10 2010 2010 HOH HOH . X 6 HOH D 11 2011 2011 HOH HOH . X 6 HOH D 12 2012 2012 HOH HOH . X 6 HOH D 13 2013 2013 HOH HOH . X 6 HOH D 14 2014 2014 HOH HOH . X 6 HOH D 15 2015 2015 HOH HOH . X 6 HOH D 16 2016 2016 HOH HOH . X 6 HOH D 17 2017 2017 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 P P1 FBP . . . Q 2 -8.404 29.186 -7.758 1 70.42 ? P1 FBP 580 D 1 HETATM 2 O O1P FBP . . . Q 2 -8.974 30.381 -7.067 1 72.41 ? O1P FBP 580 D 1 HETATM 3 O O2P FBP . . . Q 2 -9.547 28.365 -8.266 1 71.85 ? O2P FBP 580 D 1 HETATM 4 O O3P FBP . . . Q 2 -7.479 29.563 -8.882 1 71.42 ? O3P FBP 580 D 1 HETATM 5 O O1 FBP . . . Q 2 -7.507 28.339 -6.729 1 74.9 ? O1 FBP 580 D 1 HETATM 6 C C1 FBP . . . Q 2 -7.789 28.225 -5.343 1 76.25 ? C1 FBP 580 D 1 HETATM 7 C C2 FBP . . . Q 2 -6.801 27.301 -4.627 1 76.15 ? C2 FBP 580 D 1 HETATM 8 O O2 FBP . . . Q 2 -7.266 27.122 -3.271 1 76.8 ? O2 FBP 580 D 1 HETATM 9 C C3 FBP . . . Q 2 -5.367 27.787 -4.635 1 76.01 ? C3 FBP 580 D 1 HETATM 10 O O3 FBP . . . Q 2 -5.066 28.438 -3.444 1 77.45 ? O3 FBP 580 D 1 HETATM 11 C C4 FBP . . . Q 2 -4.521 26.552 -4.766 1 75.51 ? C4 FBP 580 D 1 HETATM 12 O O4 FBP . . . Q 2 -3.327 26.852 -5.441 1 73.89 ? O4 FBP 580 D 1 HETATM 13 C C5 FBP . . . Q 2 -5.433 25.683 -5.606 1 76.25 ? C5 FBP 580 D 1 HETATM 14 O O5 FBP . . . Q 2 -6.751 26.046 -5.252 1 76.71 ? O5 FBP 580 D 1 HETATM 15 C C6 FBP . . . Q 2 -5.215 24.176 -5.432 1 75.74 ? C6 FBP 580 D 1 HETATM 16 O O6 FBP . . . Q 2 -4.435 23.803 -6.589 1 73.31 ? O6 FBP 580 D 1 HETATM 17 P P2 FBP . . . Q 2 -4.154 22.284 -7.016 1 69.54 ? P2 FBP 580 D 1 HETATM 18 O O4P FBP . . . Q 2 -4.739 22.024 -8.372 1 72.59 ? O4P FBP 580 D 1 HETATM 19 O O5P FBP . . . Q 2 -2.668 22.098 -7.102 1 71.36 ? O5P FBP 580 D 1 HETATM 20 O O6P FBP . . . Q 2 -4.773 21.333 -6.043 1 71.87 ? O6P FBP 580 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #