data_7W5R # _model_server_result.job_id JIAIe-mJtPOkeupt3VFtqg _model_server_result.datetime_utc '2025-08-01 03:57:47' _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 7w5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1002}' # _entry.id 7W5R # _exptl.entry_id 7W5R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 119.986 _cell.angle_beta 90.061 _cell.angle_gamma 90.015 _cell.entry_id 7W5R _cell.length_a 40.556 _cell.length_b 82.513 _cell.length_c 82.573 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W5R _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 ? 4 J N N ? 4 L N N ? 4 N N N ? 4 P N N ? 4 R N N ? 4 T 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 covale ? covale1 B NZ LYS 117 E LYS 117 1_555 L O3' GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale2 D N SER 17 I SER 17 1_555 N O1B GDP . I GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale3 F NZ LYS 117 Q LYS 117 1_555 R O3' GDP . Q GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? metalc ? metalc1 I MG MG . A MG 1001 1_555 J O1B GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 I MG MG . A MG 1001 1_555 J O2B GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc3 I MG MG . A MG 1001 1_555 J O3A GDP . A GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc4 B OG SER 17 E SER 17 1_555 K MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc5 K MG MG . E MG 1001 1_555 L O3B GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc6 K MG MG . E MG 1001 1_555 L O2B GDP . E GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc7 D OG SER 17 I SER 17 1_555 M MG MG . I MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc8 M MG MG . I MG 1001 1_555 N O2B GDP . I GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc9 E OG SER 17 M SER 17 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc10 E OD1 ASP 57 M ASP 57 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc11 E OD2 ASP 57 M ASP 57 1_555 O MG MG . M MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc12 O MG MG . M MG 1001 1_555 P O3B GDP . M GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc13 F OG SER 17 Q SER 17 1_555 Q MG MG . Q MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc14 Q MG MG . Q MG 1001 1_555 R O2B GDP . Q GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc15 G OG SER 17 U SER 17 1_555 S MG MG . U MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc16 S MG MG . U MG 1001 1_555 T O2B GDP . U GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? # _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 7W5R _atom_sites.fract_transf_matrix[1][1] 0.024657 _atom_sites.fract_transf_matrix[1][2] 0.000006 _atom_sites.fract_transf_matrix[1][3] 0.000034 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012119 _atom_sites.fract_transf_matrix[2][3] 0.006993 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013982 _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 I 3 MG A 1 1001 1001 MG MG . J 4 GDP A 1 1002 1002 GDP GDP . K 3 MG E 1 1001 1001 MG MG . L 4 GDP E 1 1002 1002 GDP GDP . M 3 MG I 1 1001 1001 MG MG . N 4 GDP I 1 1002 1002 GDP GDP . O 3 MG M 1 1001 1001 MG MG . P 4 GDP M 1 1002 1002 GDP GDP . Q 3 MG Q 1 1001 1001 MG MG . R 4 GDP Q 1 1002 1002 GDP GDP . S 3 MG U 1 1001 1001 MG MG . T 4 GDP U 1 1002 1002 GDP GDP . # 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 . . . P 4 7.865 -49.734 13.177 1 90.23 ? PB GDP 1002 M 1 HETATM 2 O O1B GDP . . . P 4 7.728 -51.212 12.929 1 86.31 ? O1B GDP 1002 M 1 HETATM 3 O O2B GDP . . . P 4 9.315 -49.406 13.443 1 95.01 ? O2B GDP 1002 M 1 HETATM 4 O O3B GDP . . . P 4 7.011 -49.317 14.343 1 90.39 ? O3B GDP 1002 M 1 HETATM 5 O O3A GDP . . . P 4 7.348 -48.938 11.887 1 86.14 ? O3A GDP 1002 M 1 HETATM 6 P PA GDP . . . P 4 7.378 -47.336 11.92 1 85.24 ? PA GDP 1002 M 1 HETATM 7 O O1A GDP . . . P 4 8.806 -46.871 11.769 1 90.19 ? O1A GDP 1002 M 1 HETATM 8 O O2A GDP . . . P 4 6.755 -46.783 13.179 1 82.58 ? O2A GDP 1002 M 1 HETATM 9 O O5' GDP . . . P 4 6.515 -46.955 10.625 1 86.05 ? O5' GDP 1002 M 1 HETATM 10 C C5' GDP . . . P 4 7.243 -46.723 9.43 1 93.19 ? C5' GDP 1002 M 1 HETATM 11 C C4' GDP . . . P 4 6.328 -46.155 8.364 1 100.72 ? C4' GDP 1002 M 1 HETATM 12 O O4' GDP . . . P 4 7.164 -45.703 7.303 1 106.76 ? O4' GDP 1002 M 1 HETATM 13 C C3' GDP . . . P 4 5.388 -47.208 7.8 1 104.1 ? C3' GDP 1002 M 1 HETATM 14 O O3' GDP . . . P 4 4.031 -46.852 8.093 1 103.79 ? O3' GDP 1002 M 1 HETATM 15 C C2' GDP . . . P 4 5.619 -47.212 6.301 1 108.68 ? C2' GDP 1002 M 1 HETATM 16 O O2' GDP . . . P 4 4.394 -46.887 5.636 1 110.73 ? O2' GDP 1002 M 1 HETATM 17 C C1' GDP . . . P 4 6.665 -46.135 6.037 1 107.12 ? C1' GDP 1002 M 1 HETATM 18 N N9 GDP . . . P 4 7.8 -46.611 5.195 1 103.78 ? N9 GDP 1002 M 1 HETATM 19 C C8 GDP . . . P 4 8.981 -47.08 5.647 1 100.68 ? C8 GDP 1002 M 1 HETATM 20 N N7 GDP . . . P 4 9.804 -47.419 4.62 1 98.79 ? N7 GDP 1002 M 1 HETATM 21 C C5 GDP . . . P 4 9.146 -47.16 3.475 1 99.82 ? C5 GDP 1002 M 1 HETATM 22 C C6 GDP . . . P 4 9.434 -47.285 2.027 1 97.04 ? C6 GDP 1002 M 1 HETATM 23 O O6 GDP . . . P 4 10.532 -47.731 1.627 1 95.29 ? O6 GDP 1002 M 1 HETATM 24 N N1 GDP . . . P 4 8.483 -46.905 1.164 1 94.51 ? N1 GDP 1002 M 1 HETATM 25 C C2 GDP . . . P 4 7.294 -46.422 1.573 1 93.24 ? C2 GDP 1002 M 1 HETATM 26 N N2 GDP . . . P 4 6.381 -46.058 0.645 1 89.66 ? N2 GDP 1002 M 1 HETATM 27 N N3 GDP . . . P 4 6.963 -46.281 2.881 1 97.68 ? N3 GDP 1002 M 1 HETATM 28 C C4 GDP . . . P 4 7.831 -46.626 3.859 1 101.28 ? C4 GDP 1002 M 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #