data_4B44 # _model_server_result.job_id O7JhoesVJHcM5aGcAzvIDQ _model_server_result.datetime_utc '2024-10-12 12:19:49' _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 4b44 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1355}' # _entry.id 4B44 # _exptl.entry_id 4B44 _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 90 _cell.entry_id 4B44 _cell.length_a 45.15 _cell.length_b 62.2 _cell.length_c 159.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4B44 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 4B44 _atom_sites.fract_transf_matrix[1][1] 0.022148 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016077 _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] 0.006252 _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 1355 1355 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 . # 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 13.959 9.017 42.627 1 62.34 ? PB GDP 1355 A 1 HETATM 2 O O1B GDP . . . B 2 13.886 7.844 43.549 1 70.37 ? O1B GDP 1355 A 1 HETATM 3 O O2B GDP . . . B 2 14.566 8.607 41.326 1 66.27 ? O2B GDP 1355 A 1 HETATM 4 O O3B GDP . . . B 2 14.833 10.066 43.237 1 65.04 ? O3B GDP 1355 A 1 HETATM 5 O O3A GDP . . . B 2 12.499 9.614 42.39 1 61.38 ? O3A GDP 1355 A 1 HETATM 6 P PA GDP . . . B 2 11.202 8.717 42.641 1 73.79 ? PA GDP 1355 A 1 HETATM 7 O O1A GDP . . . B 2 11.476 7.264 42.412 1 72.19 ? O1A GDP 1355 A 1 HETATM 8 O O2A GDP . . . B 2 10.082 9.196 41.775 1 70.51 ? O2A GDP 1355 A 1 HETATM 9 O O5' GDP . . . B 2 10.771 8.954 44.153 1 69.79 ? O5' GDP 1355 A 1 HETATM 10 C C5' GDP . . . B 2 10.429 7.814 44.922 1 71.97 ? C5' GDP 1355 A 1 HETATM 11 C C4' GDP . . . B 2 9.055 7.987 45.533 1 68.06 ? C4' GDP 1355 A 1 HETATM 12 O O4' GDP . . . B 2 8.851 9.338 45.912 1 73.29 ? O4' GDP 1355 A 1 HETATM 13 C C3' GDP . . . B 2 8.012 7.666 44.496 1 73.84 ? C3' GDP 1355 A 1 HETATM 14 O O3' GDP . . . B 2 7.13 6.684 45.02 1 79.43 ? O3' GDP 1355 A 1 HETATM 15 C C2' GDP . . . B 2 7.235 8.934 44.301 1 71.62 ? C2' GDP 1355 A 1 HETATM 16 O O2' GDP . . . B 2 5.849 8.641 44.157 1 66.91 ? O2' GDP 1355 A 1 HETATM 17 C C1' GDP . . . B 2 7.517 9.691 45.578 1 73.57 ? C1' GDP 1355 A 1 HETATM 18 N N9 GDP . . . B 2 7.376 11.141 45.352 1 74.63 ? N9 GDP 1355 A 1 HETATM 19 C C8 GDP . . . B 2 8.027 11.857 44.433 1 70.34 ? C8 GDP 1355 A 1 HETATM 20 N N7 GDP . . . B 2 7.658 13.152 44.494 1 71.73 ? N7 GDP 1355 A 1 HETATM 21 C C5 GDP . . . B 2 6.756 13.274 45.478 1 77.04 ? C5 GDP 1355 A 1 HETATM 22 C C6 GDP . . . B 2 5.969 14.365 46.078 1 77.59 ? C6 GDP 1355 A 1 HETATM 23 O O6 GDP . . . B 2 6.065 15.528 45.659 1 72.79 ? O6 GDP 1355 A 1 HETATM 24 N N1 GDP . . . B 2 5.149 14.07 47.083 1 79.57 ? N1 GDP 1355 A 1 HETATM 25 C C2 GDP . . . B 2 5.019 12.828 47.559 1 76.59 ? C2 GDP 1355 A 1 HETATM 26 N N2 GDP . . . B 2 4.16 12.622 48.578 1 80.35 ? N2 GDP 1355 A 1 HETATM 27 N N3 GDP . . . B 2 5.709 11.78 47.063 1 73.88 ? N3 GDP 1355 A 1 HETATM 28 C C4 GDP . . . B 2 6.574 11.942 46.041 1 73.8 ? C4 GDP 1355 A 1 # _model_server_stats.io_time_ms 106 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 383 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #