data_2B92 # _model_server_result.job_id YXClLlkAtdzXFOlgmbT35g _model_server_result.datetime_utc '2024-11-22 16:01:45' _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 2b92 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":593}' # _entry.id 2B92 # _exptl.entry_id 2B92 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 2B92 _cell.length_a 148.82 _cell.length_b 103.921 _cell.length_c 55.485 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2B92 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 G 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 OG SER 63 A SER 52 1_555 C MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 A OG1 THR 86 A THR 75 1_555 C MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 D O3B GDP . A GDP 593 1_555 E AL AF3 . A AF3 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc4 D O2B GDP . A GDP 593 1_555 E AL AF3 . A AF3 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.421 ? metalc ? metalc5 D O2B GDP . A GDP 593 1_555 C MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc6 E F1 AF3 . A AF3 594 1_555 C MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc7 E AL AF3 . A AF3 594 1_555 C MG MG . A MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.358 ? metalc ? metalc8 E AL AF3 . A AF3 594 1_555 I O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc9 B OG SER 63 B SER 52 1_555 F MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc10 B OG1 THR 86 B THR 75 1_555 F MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc11 G O3B GDP . B GDP 593 1_555 H AL AF3 . B AF3 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc12 G O2B GDP . B GDP 593 1_555 H AL AF3 . B AF3 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.332 ? metalc ? metalc13 G O2B GDP . B GDP 593 1_555 F MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc14 H F3 AF3 . B AF3 594 1_555 F MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc15 H AL AF3 . B AF3 594 1_555 F MG MG . B MG 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.253 ? metalc ? metalc16 H AL AF3 . B AF3 594 1_555 J O HOH . B HOH 599 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 2B92 _atom_sites.fract_transf_matrix[1][1] 0.00672 _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] 0.009623 _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] 0.018023 _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 C 2 MG A 1 595 595 MG MG . D 3 GDP A 1 593 593 GDP GDP . E 4 AF3 A 1 594 594 AF3 AF3 . F 2 MG B 1 595 595 MG MG . G 3 GDP B 1 593 593 GDP GDP . H 4 AF3 B 1 594 594 AF3 AF3 . I 5 HOH A 1 596 3 HOH HOH . I 5 HOH A 2 597 4 HOH HOH . I 5 HOH A 3 598 5 HOH HOH . I 5 HOH A 4 599 6 HOH HOH . I 5 HOH A 5 600 7 HOH HOH . I 5 HOH A 6 601 9 HOH HOH . I 5 HOH A 7 602 10 HOH HOH . I 5 HOH A 8 603 12 HOH HOH . I 5 HOH A 9 604 13 HOH HOH . J 5 HOH B 1 596 1 HOH HOH . J 5 HOH B 2 597 2 HOH HOH . J 5 HOH B 3 598 8 HOH HOH . J 5 HOH B 4 599 11 HOH HOH . J 5 HOH B 5 600 14 HOH HOH . J 5 HOH B 6 601 15 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 . . . G 3 79.714 37.079 10.47 1 47.88 ? PB GDP 593 B 1 HETATM 2 O O1B GDP . . . G 3 80.07 35.797 9.998 1 53.21 ? O1B GDP 593 B 1 HETATM 3 O O2B GDP . . . G 3 80.757 38 10.498 1 48.79 ? O2B GDP 593 B 1 HETATM 4 O O3B GDP . . . G 3 78.639 37.664 9.798 1 47.31 ? O3B GDP 593 B 1 HETATM 5 O O3A GDP . . . G 3 79.182 36.991 12.018 1 55.83 ? O3A GDP 593 B 1 HETATM 6 P PA GDP . . . G 3 79.923 37.851 13.217 1 55.42 ? PA GDP 593 B 1 HETATM 7 O O1A GDP . . . G 3 81.339 37.443 13.425 1 56.66 ? O1A GDP 593 B 1 HETATM 8 O O2A GDP . . . G 3 79.767 39.41 12.804 1 55.79 ? O2A GDP 593 B 1 HETATM 9 O O5' GDP . . . G 3 79.018 37.645 14.529 1 51.06 ? O5' GDP 593 B 1 HETATM 10 C C5' GDP . . . G 3 77.625 37.729 14.425 1 47.51 ? C5' GDP 593 B 1 HETATM 11 C C4' GDP . . . G 3 76.959 37.303 15.727 1 51.05 ? C4' GDP 593 B 1 HETATM 12 O O4' GDP . . . G 3 77.245 35.835 16.003 1 55.26 ? O4' GDP 593 B 1 HETATM 13 C C3' GDP . . . G 3 77.558 38.061 16.914 1 53.12 ? C3' GDP 593 B 1 HETATM 14 O O3' GDP . . . G 3 76.532 38.316 17.894 1 53.09 ? O3' GDP 593 B 1 HETATM 15 C C2' GDP . . . G 3 78.561 37.099 17.479 1 51.76 ? C2' GDP 593 B 1 HETATM 16 O O2' GDP . . . G 3 78.783 37.4 18.866 1 51.51 ? O2' GDP 593 B 1 HETATM 17 C C1' GDP . . . G 3 77.856 35.792 17.357 1 51.23 ? C1' GDP 593 B 1 HETATM 18 N N9 GDP . . . G 3 78.785 34.629 17.396 1 48.48 ? N9 GDP 593 B 1 HETATM 19 C C8 GDP . . . G 3 80.135 34.667 17.281 1 51.08 ? C8 GDP 593 B 1 HETATM 20 N N7 GDP . . . G 3 80.599 33.396 17.301 1 51.72 ? N7 GDP 593 B 1 HETATM 21 C C5 GDP . . . G 3 79.552 32.582 17.387 1 49.96 ? C5 GDP 593 B 1 HETATM 22 C C6 GDP . . . G 3 79.439 31.217 17.442 1 51.03 ? C6 GDP 593 B 1 HETATM 23 O O6 GDP . . . G 3 80.449 30.506 17.406 1 48 ? O6 GDP 593 B 1 HETATM 24 N N1 GDP . . . G 3 78.19 30.651 17.535 1 49.05 ? N1 GDP 593 B 1 HETATM 25 C C2 GDP . . . G 3 77.057 31.48 17.576 1 50.69 ? C2 GDP 593 B 1 HETATM 26 N N2 GDP . . . G 3 75.85 30.947 17.666 1 49.52 ? N2 GDP 593 B 1 HETATM 27 N N3 GDP . . . G 3 77.192 32.804 17.518 1 51.82 ? N3 GDP 593 B 1 HETATM 28 C C4 GDP . . . G 3 78.412 33.369 17.436 1 48.36 ? C4 GDP 593 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #