data_8VGB # _model_server_result.job_id 9BPKzN30QDrMalIdLv6LLA _model_server_result.datetime_utc '2024-11-23 12:53:08' _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 8vgb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8VGB # _exptl.entry_id 8VGB _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 89.91 _cell.angle_gamma 90 _cell.entry_id 8VGB _cell.length_a 68.393 _cell.length_b 68.419 _cell.length_c 167.977 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VGB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F 1 1 B,G,H 2 1 C,I,J 3 1 D,K,L 4 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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 E O2B GDP . A GDP 500 1_555 F MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc2 E O3B GDP . A GDP 500 1_555 F MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 B OG SER 56 B SER 53 1_555 H MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc4 G O1B GDP . B GDP 401 1_555 H MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc5 G O2B GDP . B GDP 401 1_555 H MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc6 I O1B GDP . C GDP 401 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc7 I O2B GDP . C GDP 401 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc8 I O3B GDP . C GDP 401 1_555 J MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc9 D OG SER 56 D SER 53 1_555 L MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc10 K O1B GDP . D GDP 401 1_555 L MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc11 K O2B GDP . D GDP 401 1_555 L MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc12 K O3B GDP . D GDP 401 1_555 L MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? # _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 8VGB _atom_sites.fract_transf_matrix[1][1] 0.014621 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000023 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014616 _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] 0.005953 _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 E 2 GDP A 1 500 500 GDP GDP . F 3 MG A 1 501 501 MG MG . G 2 GDP B 1 401 500 GDP GDP . H 3 MG B 1 402 502 MG MG . I 2 GDP C 1 401 500 GDP GDP . J 3 MG C 1 402 503 MG MG . K 2 GDP D 1 401 500 GDP GDP . L 3 MG D 1 402 504 MG MG . # 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 . . . I 2 -98.942 -218.892 30.008 1 104.31 ? PB GDP 401 C 1 HETATM 2 O O1B GDP . . . I 2 -100.172 -219.019 29.14 1 84.3 ? O1B GDP 401 C 1 HETATM 3 O O2B GDP . . . I 2 -99.268 -219.259 31.434 1 87.89 ? O2B GDP 401 C 1 HETATM 4 O O3B GDP . . . I 2 -98.438 -217.47 29.953 1 82.26 ? O3B GDP 401 C 1 HETATM 5 O O3A GDP . . . I 2 -97.799 -219.874 29.451 1 90.62 ? O3A GDP 401 C 1 HETATM 6 P PA GDP . . . I 2 -97.503 -219.888 27.873 1 111.62 ? PA GDP 401 C 1 HETATM 7 O O1A GDP . . . I 2 -98.397 -220.897 27.194 1 76.31 ? O1A GDP 401 C 1 HETATM 8 O O2A GDP . . . I 2 -97.711 -218.518 27.273 1 94.97 ? O2A GDP 401 C 1 HETATM 9 O O5' GDP . . . I 2 -95.957 -220.312 27.781 1 78.15 ? O5' GDP 401 C 1 HETATM 10 C C5' GDP . . . I 2 -95.012 -219.287 27.493 1 81.59 ? C5' GDP 401 C 1 HETATM 11 C C4' GDP . . . I 2 -93.766 -219.868 26.846 1 84.07 ? C4' GDP 401 C 1 HETATM 12 O O4' GDP . . . I 2 -93.32 -221.035 27.537 1 84.01 ? O4' GDP 401 C 1 HETATM 13 C C3' GDP . . . I 2 -94.021 -220.298 25.413 1 86.76 ? C3' GDP 401 C 1 HETATM 14 O O3' GDP . . . I 2 -93.706 -219.235 24.511 1 89.65 ? O3' GDP 401 C 1 HETATM 15 C C2' GDP . . . I 2 -93.089 -221.472 25.211 1 84.75 ? C2' GDP 401 C 1 HETATM 16 O O2' GDP . . . I 2 -91.916 -221.035 24.523 1 97.95 ? O2' GDP 401 C 1 HETATM 17 C C1' GDP . . . I 2 -92.714 -221.938 26.609 1 80.25 ? C1' GDP 401 C 1 HETATM 18 N N9 GDP . . . I 2 -93.248 -223.304 26.809 1 78.64 ? N9 GDP 401 C 1 HETATM 19 C C8 GDP . . . I 2 -94.544 -223.614 26.984 1 78.14 ? C8 GDP 401 C 1 HETATM 20 N N7 GDP . . . I 2 -94.699 -224.95 27.138 1 77.32 ? N7 GDP 401 C 1 HETATM 21 C C5 GDP . . . I 2 -93.484 -225.522 27.061 1 79.68 ? C5 GDP 401 C 1 HETATM 22 C C6 GDP . . . I 2 -92.933 -226.896 27.141 1 83.37 ? C6 GDP 401 C 1 HETATM 23 O O6 GDP . . . I 2 -93.669 -227.885 27.325 1 88.47 ? O6 GDP 401 C 1 HETATM 24 N N1 GDP . . . I 2 -91.611 -227.052 27.012 1 82.74 ? N1 GDP 401 C 1 HETATM 25 C C2 GDP . . . I 2 -90.782 -226.012 26.814 1 77.45 ? C2 GDP 401 C 1 HETATM 26 N N2 GDP . . . I 2 -89.457 -226.259 26.693 1 70.57 ? N2 GDP 401 C 1 HETATM 27 N N3 GDP . . . I 2 -91.216 -224.728 26.73 1 77.11 ? N3 GDP 401 C 1 HETATM 28 C C4 GDP . . . I 2 -92.53 -224.428 26.844 1 78.71 ? C4 GDP 401 C 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #