data_5L3W # _model_server_result.job_id nwRhuxyg-M8eHVuG9EEciw _model_server_result.datetime_utc '2024-11-29 16:52:29' _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 5l3w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5L3W # _exptl.entry_id 5L3W _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 5L3W _cell.length_a 144.906 _cell.length_b 144.906 _cell.length_c 49.723 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L3W _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _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,D _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 5L3W _atom_sites.fract_transf_matrix[1][1] 0.006901 _atom_sites.fract_transf_matrix[1][2] 0.003984 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007969 _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] 0.020112 _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 1 401 1 GDP GDP . C 3 SO4 A 1 402 1 SO4 SO4 . D 4 HOH A 1 501 11 HOH HOH . D 4 HOH A 2 502 3 HOH HOH . D 4 HOH A 3 503 1 HOH HOH . D 4 HOH A 4 504 8 HOH HOH . D 4 HOH A 5 505 4 HOH HOH . D 4 HOH A 6 506 32 HOH HOH . D 4 HOH A 7 507 10 HOH HOH . D 4 HOH A 8 508 14 HOH HOH . D 4 HOH A 9 509 27 HOH HOH . D 4 HOH A 10 510 6 HOH HOH . D 4 HOH A 11 511 2 HOH HOH . D 4 HOH A 12 512 17 HOH HOH . D 4 HOH A 13 513 9 HOH HOH . D 4 HOH A 14 514 21 HOH HOH . D 4 HOH A 15 515 7 HOH HOH . D 4 HOH A 16 516 33 HOH HOH . D 4 HOH A 17 517 24 HOH HOH . D 4 HOH A 18 518 22 HOH HOH . D 4 HOH A 19 519 23 HOH HOH . D 4 HOH A 20 520 5 HOH HOH . D 4 HOH A 21 521 13 HOH HOH . D 4 HOH A 22 522 39 HOH HOH . D 4 HOH A 23 523 35 HOH HOH . D 4 HOH A 24 524 19 HOH HOH . D 4 HOH A 25 525 12 HOH HOH . D 4 HOH A 26 526 20 HOH HOH . D 4 HOH A 27 527 29 HOH HOH . D 4 HOH A 28 528 16 HOH HOH . D 4 HOH A 29 529 38 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 18 HOH HOH . D 4 HOH A 32 532 31 HOH HOH . D 4 HOH A 33 533 34 HOH HOH . D 4 HOH A 34 534 15 HOH HOH . D 4 HOH A 35 535 28 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 25 HOH HOH . D 4 HOH A 38 538 40 HOH HOH . D 4 HOH A 39 539 26 HOH HOH . D 4 HOH A 40 540 37 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 79.877 97.216 8.651 1 62.79 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 78.984 97.892 7.637 1 61.67 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 80.949 96.44 7.922 1 72.38 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 79.1 96.245 9.502 1 66.73 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 80.6 98.359 9.518 1 64.27 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 79.952 99.792 9.893 1 56.65 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 79.821 100.724 8.71 1 57.12 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 78.628 99.592 10.601 1 71.11 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 81.061 100.348 10.906 1 63.12 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 81.282 99.697 12.165 1 63.36 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 81.815 100.719 13.163 1 62.18 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 83.097 101.192 12.72 1 60.51 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 80.89 101.93 13.208 1 62.01 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 80.609 102.339 14.552 1 68.38 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 81.665 103.011 12.491 1 59.54 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 81.351 104.309 12.993 1 68.88 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 83.113 102.615 12.739 1 57.41 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 83.989 103.184 11.695 1 60.16 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 83.902 102.979 10.365 1 59.15 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 84.851 103.681 9.7 1 57.33 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 85.574 104.35 10.623 1 60.62 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 86.738 105.269 10.619 1 59.11 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 87.301 105.602 9.558 1 52.91 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 87.167 105.744 11.793 1 64.14 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 86.591 105.413 12.966 1 63.47 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 87.098 105.939 14.11 1 61.41 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 85.527 104.575 13.045 1 64.12 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 84.994 104.025 11.932 1 62.39 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #