data_2B92 # _model_server_result.job_id p0jaee2jbq5ngyrOC498Fg _model_server_result.datetime_utc '2024-11-22 15:39:29' _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 2b92 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","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 . . . D 3 67.805 15.151 10.759 1 48.03 ? PB GDP 593 A 1 HETATM 2 O O1B GDP . . . D 3 67.463 16.397 10.226 1 51.87 ? O1B GDP 593 A 1 HETATM 3 O O2B GDP . . . D 3 66.739 14.267 10.9 1 56.75 ? O2B GDP 593 A 1 HETATM 4 O O3B GDP . . . D 3 68.85 14.428 10.065 1 46.72 ? O3B GDP 593 A 1 HETATM 5 O O3A GDP . . . D 3 68.386 15.322 12.275 1 53.66 ? O3A GDP 593 A 1 HETATM 6 P PA GDP . . . D 3 67.728 14.458 13.522 1 55.1 ? PA GDP 593 A 1 HETATM 7 O O1A GDP . . . D 3 66.296 14.8 13.771 1 59.14 ? O1A GDP 593 A 1 HETATM 8 O O2A GDP . . . D 3 67.952 12.888 13.141 1 52.32 ? O2A GDP 593 A 1 HETATM 9 O O5' GDP . . . D 3 68.659 14.746 14.796 1 51.83 ? O5' GDP 593 A 1 HETATM 10 C C5' GDP . . . D 3 70.038 14.538 14.708 1 47.11 ? C5' GDP 593 A 1 HETATM 11 C C4' GDP . . . D 3 70.72 14.931 16.031 1 51.71 ? C4' GDP 593 A 1 HETATM 12 O O4' GDP . . . D 3 70.466 16.407 16.328 1 54.4 ? O4' GDP 593 A 1 HETATM 13 C C3' GDP . . . D 3 70.103 14.165 17.205 1 51.32 ? C3' GDP 593 A 1 HETATM 14 O O3' GDP . . . D 3 71.122 13.885 18.18 1 51.44 ? O3' GDP 593 A 1 HETATM 15 C C2' GDP . . . D 3 69.107 15.135 17.781 1 48.51 ? C2' GDP 593 A 1 HETATM 16 O O2' GDP . . . D 3 68.882 14.826 19.174 1 53.64 ? O2' GDP 593 A 1 HETATM 17 C C1' GDP . . . D 3 69.823 16.449 17.671 1 49.64 ? C1' GDP 593 A 1 HETATM 18 N N9 GDP . . . D 3 68.871 17.608 17.676 1 48.71 ? N9 GDP 593 A 1 HETATM 19 C C8 GDP . . . D 3 67.53 17.55 17.567 1 48.6 ? C8 GDP 593 A 1 HETATM 20 N N7 GDP . . . D 3 67.049 18.811 17.56 1 51.59 ? N7 GDP 593 A 1 HETATM 21 C C5 GDP . . . D 3 68.079 19.64 17.624 1 50.32 ? C5 GDP 593 A 1 HETATM 22 C C6 GDP . . . D 3 68.168 21.022 17.654 1 49.99 ? C6 GDP 593 A 1 HETATM 23 O O6 GDP . . . D 3 67.147 21.716 17.603 1 47.67 ? O6 GDP 593 A 1 HETATM 24 N N1 GDP . . . D 3 69.401 21.617 17.736 1 47.48 ? N1 GDP 593 A 1 HETATM 25 C C2 GDP . . . D 3 70.539 20.819 17.793 1 49.22 ? C2 GDP 593 A 1 HETATM 26 N N2 GDP . . . D 3 71.737 21.386 17.87 1 48.5 ? N2 GDP 593 A 1 HETATM 27 N N3 GDP . . . D 3 70.431 19.471 17.766 1 47.49 ? N3 GDP 593 A 1 HETATM 28 C C4 GDP . . . D 3 69.224 18.88 17.69 1 49.31 ? C4 GDP 593 A 1 # _model_server_stats.io_time_ms 112 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #