data_4BL5 # _model_server_result.job_id H6qJmqpS6G39efQOerpwQA _model_server_result.datetime_utc '2024-11-23 20:19:04' _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 4bl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":902}' # _entry.id 4BL5 # _exptl.entry_id 4BL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 589.342 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 72.54 _cell.angle_beta 72.64 _cell.angle_gamma 60.14 _cell.entry_id 4BL5 _cell.length_a 90.407 _cell.length_b 90.478 _cell.length_c 147.518 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BL5 _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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression H,I,BA,CA,DA,EA,RA 1 1 G,J,Z,AA,FA,GA,SA 2 1 A,E,M,N,U,V,LA,PA 3 1 B,D,O,P,S,T,MA,OA 4 1 K,L,HA,IA,JA,KA,TA,UA 5 1 C,F,Q,R,W,X,Y,NA,QA 6 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 ? 3 N N N ? 3 P N N ? 3 R N N ? 3 T N N ? 3 V N N ? 3 X N N ? 3 AA N N ? 3 CA N N ? 3 EA N N ? 3 GA N N ? 3 IA N N ? 3 KA N N # _chem_comp.formula 'C16 H25 N5 O15 P2' _chem_comp.formula_weight 589.342 _chem_comp.id GFB _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _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 P O1P GFB sing 92 n n O1P HO1P GFB sing 93 n n O3P P GFB doub 94 n n P O5' GFB sing 95 n n P O2P GFB sing 96 n n O2P P1 GFB sing 97 n n O5' C5' GFB sing 98 n n O1 P1 GFB sing 99 n n O1X P1 GFB doub 100 n n P1 O2X GFB sing 101 n n C4' C5' GFB sing 102 n n C5' "H5'A" GFB sing 103 n n C5' H5' GFB sing 104 n n H4' C4' GFB sing 105 n n C3' C4' GFB sing 106 n n C4' O4' GFB sing 107 n n O4' C1' GFB sing 108 n n O3' C3' GFB sing 109 n n C3' C2' GFB sing 110 n n C3' H3' GFB sing 111 n n C2' C1' GFB sing 112 n n H1' C1' GFB sing 113 n n C1' N9 GFB sing 114 n n HO3' O3' GFB sing 115 n n O2' C2' GFB sing 116 n n C2' H2' GFB sing 117 n n O2' HO2' GFB sing 118 n n N9 C4 GFB sing 119 n y N9 C8 GFB sing 120 n y H8 C8 GFB sing 121 n n C8 N7 GFB doub 122 n y N3 C4 GFB sing 123 n n C4 C5 GFB doub 124 n y C5 N7 GFB sing 125 n y C5 C6 GFB sing 126 n n N1 C6 GFB sing 127 n n C6 O6 GFB doub 128 n n C2 N1 GFB sing 129 n n N1 HN1 GFB sing 130 n n N3 C2 GFB doub 131 n n N2 C2 GFB sing 132 n n HN2 N2 GFB sing 133 n n N2 HN2A GFB sing 134 n n C2A C1 GFB sing 135 n n C1 O5 GFB sing 136 n n C1 H1 GFB sing 137 n n C1 O1 GFB sing 138 n n C3 C2A GFB sing 139 n n O2 C2A GFB sing 140 n n H2A C2A GFB sing 141 n n C5A O5 GFB sing 142 n n O3 C3 GFB sing 143 n n C3 H3 GFB sing 144 n n C3 C4A GFB sing 145 n n HO2 O2 GFB sing 146 n n H4A C4A GFB sing 147 n n O4 C4A GFB sing 148 n n C4A C5A GFB sing 149 n n HO3 O3 GFB sing 150 n n C5A H5A GFB sing 151 n n C5A C6A GFB sing 152 n n O4 HO4 GFB sing 153 n n H6A C6A GFB sing 154 n n H6AA C6A GFB sing 155 n n C6A H6AB GFB sing 156 n n O2X HO2X GFB sing 157 n n # _atom_sites.entry_id 4BL5 _atom_sites.fract_transf_matrix[1][1] 0.011061 _atom_sites.fract_transf_matrix[1][2] -0.00635 _atom_sites.fract_transf_matrix[1][3] -0.002335 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012744 _atom_sites.fract_transf_matrix[2][3] -0.002372 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007224 _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 M 2 NAP A 1 901 901 NAP NAP . N 3 GFB A 1 902 902 GFB GFB . O 2 NAP B 1 901 901 NAP NAP . P 3 GFB B 1 902 902 GFB GFB . Q 2 NAP C 1 901 901 NAP NAP . R 3 GFB C 1 902 902 GFB GFB . S 2 NAP D 1 901 901 NAP NAP . T 3 GFB D 1 902 902 GFB GFB . U 2 NAP E 1 901 901 NAP NAP . V 3 GFB E 1 902 902 GFB GFB . W 2 NAP F 1 901 901 NAP NAP . X 3 GFB F 1 902 902 GFB GFB . Y 4 EDO F 1 1321 1321 EDO EDO . Z 2 NAP G 1 901 901 NAP NAP . AA 3 GFB G 1 902 902 GFB GFB . BA 2 NAP H 1 901 901 NAP NAP . CA 3 GFB H 1 902 902 GFB GFB . DA 2 NAP I 1 901 901 NAP NAP . EA 3 GFB I 1 902 902 GFB GFB . FA 2 NAP J 1 901 901 NAP NAP . GA 3 GFB J 1 902 902 GFB GFB . HA 2 NAP K 1 901 901 NAP NAP . IA 3 GFB K 1 902 902 GFB GFB . JA 2 NAP L 1 901 901 NAP NAP . KA 3 GFB L 1 902 902 GFB GFB . LA 5 HOH A 1 2001 2001 HOH HOH . LA 5 HOH A 2 2002 2002 HOH HOH . LA 5 HOH A 3 2003 2003 HOH HOH . LA 5 HOH A 4 2004 2004 HOH HOH . LA 5 HOH A 5 2005 2005 HOH HOH . LA 5 HOH A 6 2006 2006 HOH HOH . LA 5 HOH A 7 2007 2007 HOH HOH . LA 5 HOH A 8 2008 2008 HOH HOH . LA 5 HOH A 9 2009 2009 HOH HOH . LA 5 HOH A 10 2010 2010 HOH HOH . LA 5 HOH A 11 2011 2011 HOH HOH . MA 5 HOH B 1 2001 2001 HOH HOH . MA 5 HOH B 2 2002 2002 HOH HOH . MA 5 HOH B 3 2003 2003 HOH HOH . NA 5 HOH C 1 2001 2001 HOH HOH . NA 5 HOH C 2 2002 2002 HOH HOH . NA 5 HOH C 3 2003 2003 HOH HOH . NA 5 HOH C 4 2004 2004 HOH HOH . NA 5 HOH C 5 2005 2005 HOH HOH . NA 5 HOH C 6 2006 2006 HOH HOH . OA 5 HOH D 1 2001 2001 HOH HOH . OA 5 HOH D 2 2002 2002 HOH HOH . OA 5 HOH D 3 2003 2003 HOH HOH . OA 5 HOH D 4 2004 2004 HOH HOH . OA 5 HOH D 5 2005 2005 HOH HOH . OA 5 HOH D 6 2006 2006 HOH HOH . OA 5 HOH D 7 2007 2007 HOH HOH . PA 5 HOH E 1 2001 2001 HOH HOH . PA 5 HOH E 2 2002 2002 HOH HOH . PA 5 HOH E 3 2003 2003 HOH HOH . PA 5 HOH E 4 2004 2004 HOH HOH . QA 5 HOH F 1 2001 2001 HOH HOH . QA 5 HOH F 2 2002 2002 HOH HOH . RA 5 HOH H 1 2001 2001 HOH HOH . RA 5 HOH H 2 2002 2002 HOH HOH . SA 5 HOH J 1 2001 2001 HOH HOH . SA 5 HOH J 2 2002 2002 HOH HOH . TA 5 HOH K 1 2001 2001 HOH HOH . UA 5 HOH L 1 2001 2001 HOH HOH . UA 5 HOH L 2 2002 2002 HOH HOH . UA 5 HOH L 3 2003 2003 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 O O1P GFB . . . V 3 27.457 -64.433 -88.655 1 45.12 ? O1P GFB 902 E 1 HETATM 2 P P GFB . . . V 3 27.241 -64.568 -87.183 1 45.14 ? P GFB 902 E 1 HETATM 3 O O3P GFB . . . V 3 28.404 -64.714 -86.283 1 42.26 ? O3P GFB 902 E 1 HETATM 4 O O2P GFB . . . V 3 26.473 -63.238 -86.734 1 46.39 ? O2P GFB 902 E 1 HETATM 5 O O5' GFB . . . V 3 26.198 -65.772 -86.979 1 43.37 ? O5' GFB 902 E 1 HETATM 6 P P1 GFB . . . V 3 24.94 -63.049 -86.311 1 50.95 ? P1 GFB 902 E 1 HETATM 7 C C5' GFB . . . V 3 26.236 -66.626 -85.836 1 41.48 ? C5' GFB 902 E 1 HETATM 8 C C4' GFB . . . V 3 25.089 -67.604 -86.054 1 40.34 ? C4' GFB 902 E 1 HETATM 9 O O4' GFB . . . V 3 25.483 -68.665 -86.952 1 40.02 ? O4' GFB 902 E 1 HETATM 10 C C3' GFB . . . V 3 24.762 -68.322 -84.754 1 39.75 ? C3' GFB 902 E 1 HETATM 11 C C1' GFB . . . V 3 25.813 -69.859 -86.139 1 40.9 ? C1' GFB 902 E 1 HETATM 12 O O3' GFB . . . V 3 23.474 -68.933 -84.857 1 39.34 ? O3' GFB 902 E 1 HETATM 13 C C2' GFB . . . V 3 25.843 -69.386 -84.689 1 39.73 ? C2' GFB 902 E 1 HETATM 14 O O2' GFB . . . V 3 25.484 -70.456 -83.785 1 37.59 ? O2' GFB 902 E 1 HETATM 15 N N9 GFB . . . V 3 27.101 -70.452 -86.602 1 42.99 ? N9 GFB 902 E 1 HETATM 16 C C8 GFB . . . V 3 27.241 -71.706 -87.016 1 44.3 ? C8 GFB 902 E 1 HETATM 17 C C4 GFB . . . V 3 28.293 -69.849 -86.706 1 42.91 ? C4 GFB 902 E 1 HETATM 18 N N7 GFB . . . V 3 28.518 -71.887 -87.364 1 45.92 ? N7 GFB 902 E 1 HETATM 19 C C5 GFB . . . V 3 29.159 -70.736 -87.178 1 42.88 ? C5 GFB 902 E 1 HETATM 20 C C6 GFB . . . V 3 30.409 -70.397 -87.381 1 41.77 ? C6 GFB 902 E 1 HETATM 21 O O6 GFB . . . V 3 31.189 -71.231 -87.806 1 42.31 ? O6 GFB 902 E 1 HETATM 22 N N1 GFB . . . V 3 30.836 -69.097 -87.08 1 42.63 ? N1 GFB 902 E 1 HETATM 23 C C2 GFB . . . V 3 29.917 -68.186 -86.593 1 40.37 ? C2 GFB 902 E 1 HETATM 24 N N2 GFB . . . V 3 30.247 -66.941 -86.309 1 40.04 ? N2 GFB 902 E 1 HETATM 25 N N3 GFB . . . V 3 28.674 -68.594 -86.428 1 42.28 ? N3 GFB 902 E 1 HETATM 26 C C1 GFB . . . V 3 26.057 -60.744 -86 1 57.06 ? C1 GFB 902 E 1 HETATM 27 C C2A GFB . . . V 3 26.195 -59.588 -85.096 1 57.27 ? C2A GFB 902 E 1 HETATM 28 O O1 GFB . . . V 3 25.092 -61.673 -85.499 1 51.37 ? O1 GFB 902 E 1 HETATM 29 O O5 GFB . . . V 3 25.556 -60.269 -87.236 1 61.97 ? O5 GFB 902 E 1 HETATM 30 C C3 GFB . . . V 3 27.304 -58.681 -85.638 1 60 ? C3 GFB 902 E 1 HETATM 31 O O2 GFB . . . V 3 26.557 -60.069 -83.791 1 58.47 ? O2 GFB 902 E 1 HETATM 32 C C4A GFB . . . V 3 27.429 -58.594 -87.214 1 61.26 ? C4A GFB 902 E 1 HETATM 33 O O3 GFB . . . V 3 27.114 -57.383 -85.091 1 61.07 ? O3 GFB 902 E 1 HETATM 34 C C5A GFB . . . V 3 26.554 -59.636 -88.04 1 60.25 ? C5A GFB 902 E 1 HETATM 35 O O4 GFB . . . V 3 27.259 -57.212 -87.675 1 60.57 ? O4 GFB 902 E 1 HETATM 36 C C6A GFB . . . V 3 25.858 -59.005 -89.261 1 59.49 ? C6A GFB 902 E 1 HETATM 37 O O1X GFB . . . V 3 24.077 -62.808 -87.499 1 50.06 ? O1X GFB 902 E 1 HETATM 38 O O2X GFB . . . V 3 24.556 -64.103 -85.364 1 51.69 ? O2X GFB 902 E 1 # _model_server_stats.io_time_ms 95 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #