data_2VAW # _model_server_result.job_id Z9ebKVU8-YUT1CUdPqHVOw _model_server_result.datetime_utc '2024-10-13 14:23:29' _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 2vaw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1317}' # _entry.id 2VAW # _exptl.entry_id 2VAW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 2VAW _cell.length_a 100.658 _cell.length_b 100.658 _cell.length_c 66.319 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VAW _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2VAW _atom_sites.fract_transf_matrix[1][1] 0.009935 _atom_sites.fract_transf_matrix[1][2] 0.005736 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011472 _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] 0.015079 _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 B 2 GDP A 1 1317 1317 GDP GDP . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 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 PB GDP . . . B 2 -35.23 12.055 -13.443 1 41.65 ? PB GDP 1317 A 1 HETATM 2 O O1B GDP . . . B 2 -35.864 12.86 -14.608 1 38.38 ? O1B GDP 1317 A 1 HETATM 3 O O2B GDP . . . B 2 -34.469 10.918 -13.982 1 29.29 ? O2B GDP 1317 A 1 HETATM 4 O O3B GDP . . . B 2 -36.232 11.819 -12.409 1 42.62 ? O3B GDP 1317 A 1 HETATM 5 O O3A GDP . . . B 2 -34.228 13.125 -12.848 1 37.78 ? O3A GDP 1317 A 1 HETATM 6 P PA GDP . . . B 2 -32.65 13.068 -12.791 1 44.49 ? PA GDP 1317 A 1 HETATM 7 O O1A GDP . . . B 2 -32.245 11.807 -12.156 1 43.85 ? O1A GDP 1317 A 1 HETATM 8 O O2A GDP . . . B 2 -32.081 13.472 -14.086 1 40.2 ? O2A GDP 1317 A 1 HETATM 9 O O5' GDP . . . B 2 -32.474 14.279 -11.752 1 44.64 ? O5' GDP 1317 A 1 HETATM 10 C C5' GDP . . . B 2 -33.025 14.147 -10.451 1 47.23 ? C5' GDP 1317 A 1 HETATM 11 C C4' GDP . . . B 2 -32.381 15.11 -9.449 1 48.48 ? C4' GDP 1317 A 1 HETATM 12 O O4' GDP . . . B 2 -31.687 14.312 -8.499 1 48.44 ? O4' GDP 1317 A 1 HETATM 13 C C3' GDP . . . B 2 -31.366 16.103 -9.998 1 47.4 ? C3' GDP 1317 A 1 HETATM 14 O O3' GDP . . . B 2 -31.973 17.369 -10.255 1 44.09 ? O3' GDP 1317 A 1 HETATM 15 C C2' GDP . . . B 2 -30.226 16.112 -8.981 1 47.31 ? C2' GDP 1317 A 1 HETATM 16 O O2' GDP . . . B 2 -30.309 17.14 -7.994 1 45.08 ? O2' GDP 1317 A 1 HETATM 17 C C1' GDP . . . B 2 -30.341 14.739 -8.35 1 47.34 ? C1' GDP 1317 A 1 HETATM 18 N N9 GDP . . . B 2 -29.401 13.717 -8.917 1 50.35 ? N9 GDP 1317 A 1 HETATM 19 C C8 GDP . . . B 2 -28.969 13.466 -10.2 1 47.92 ? C8 GDP 1317 A 1 HETATM 20 N N7 GDP . . . B 2 -28.128 12.489 -10.338 1 44.51 ? N7 GDP 1317 A 1 HETATM 21 C C5 GDP . . . B 2 -27.969 12.03 -9.033 1 45.63 ? C5 GDP 1317 A 1 HETATM 22 C C6 GDP . . . B 2 -27.154 10.951 -8.507 1 43.76 ? C6 GDP 1317 A 1 HETATM 23 O O6 GDP . . . B 2 -26.411 10.197 -9.114 1 38.14 ? O6 GDP 1317 A 1 HETATM 24 N N1 GDP . . . B 2 -27.284 10.808 -7.109 1 48.58 ? N1 GDP 1317 A 1 HETATM 25 C C2 GDP . . . B 2 -28.091 11.593 -6.29 1 53.21 ? C2 GDP 1317 A 1 HETATM 26 N N2 GDP . . . B 2 -28.089 11.306 -4.992 1 54.83 ? N2 GDP 1317 A 1 HETATM 27 N N3 GDP . . . B 2 -28.854 12.607 -6.767 1 53.75 ? N3 GDP 1317 A 1 HETATM 28 C C4 GDP . . . B 2 -28.745 12.769 -8.147 1 50.22 ? C4 GDP 1317 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #