data_4G5Q # _model_server_result.job_id E-ZzTbwL9jY9sNJfbIwHHg _model_server_result.datetime_utc '2024-11-29 04:11:47' _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 4g5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 4G5Q # _exptl.entry_id 4G5Q _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 4 _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 4G5Q _cell.length_a 207.376 _cell.length_b 207.376 _cell.length_c 236.661 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 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,I,J,K,L,M,HA,LA 1 1 B,F,N,O,P,Q,R,S,T,IA,MA 2 1 C,G,U,V,W,X,Y,Z,JA,NA 3 1 D,H,AA,BA,CA,DA,EA,FA,GA,KA 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 ? 3 I N N ? 3 N N N ? 3 U N N ? 3 AA N 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 103 n n PB O2B GDP sing 104 n n PB O3B GDP sing 105 n n PB O3A GDP sing 106 n n O2B HOB2 GDP sing 107 n n O3B HOB3 GDP sing 108 n n O3A PA GDP sing 109 n n PA O1A GDP doub 110 n n PA O2A GDP sing 111 n n PA O5' GDP sing 112 n n O2A HOA2 GDP sing 113 n n O5' C5' GDP sing 114 n n C5' C4' GDP sing 115 n n C5' H5' GDP sing 116 n n C5' "H5''" GDP sing 117 n n C4' O4' GDP sing 118 n n C4' C3' GDP sing 119 n n C4' H4' GDP sing 120 n n O4' C1' GDP sing 121 n n C3' O3' GDP sing 122 n n C3' C2' GDP sing 123 n n C3' H3' GDP sing 124 n n O3' HO3' GDP sing 125 n n C2' O2' GDP sing 126 n n C2' C1' GDP sing 127 n n C2' H2' GDP sing 128 n n O2' HO2' GDP sing 129 n n C1' N9 GDP sing 130 n n C1' H1' GDP sing 131 n n N9 C8 GDP sing 132 n y N9 C4 GDP sing 133 n y C8 N7 GDP doub 134 n y C8 H8 GDP sing 135 n n N7 C5 GDP sing 136 n y C5 C6 GDP sing 137 n n C5 C4 GDP doub 138 n y C6 O6 GDP doub 139 n n C6 N1 GDP sing 140 n n N1 C2 GDP sing 141 n n N1 HN1 GDP sing 142 n n C2 N2 GDP sing 143 n n C2 N3 GDP doub 144 n n N2 HN21 GDP sing 145 n n N2 HN22 GDP sing 146 n n N3 C4 GDP sing 147 n n # _atom_sites.entry_id 4G5Q _atom_sites.fract_transf_matrix[1][1] 0.004822 _atom_sites.fract_transf_matrix[1][2] 0.002784 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005568 _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] 0.004225 _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 GDP A 1 401 1 GDP GDP . J 4 SO4 A 1 402 3 SO4 SO4 . K 4 SO4 A 1 403 5 SO4 SO4 . L 4 SO4 A 1 404 7 SO4 SO4 . M 4 SO4 A 1 405 16 SO4 SO4 . N 3 GDP B 1 401 1 GDP GDP . O 5 CIT B 1 402 1 CIT CIT . P 5 CIT B 1 403 1 CIT CIT . Q 4 SO4 B 1 404 1 SO4 SO4 . R 4 SO4 B 1 405 4 SO4 SO4 . S 4 SO4 B 1 406 8 SO4 SO4 . T 4 SO4 B 1 407 18 SO4 SO4 . U 3 GDP C 1 401 1 GDP GDP . V 5 CIT C 1 402 1 CIT CIT . W 4 SO4 C 1 403 2 SO4 SO4 . X 4 SO4 C 1 404 6 SO4 SO4 . Y 4 SO4 C 1 405 11 SO4 SO4 . Z 4 SO4 C 1 406 13 SO4 SO4 . AA 3 GDP D 1 401 1 GDP GDP . BA 5 CIT D 1 402 1 CIT CIT . CA 4 SO4 D 1 403 9 SO4 SO4 . DA 4 SO4 D 1 404 10 SO4 SO4 . EA 4 SO4 D 1 405 15 SO4 SO4 . FA 4 SO4 D 1 406 17 SO4 SO4 . GA 4 SO4 D 1 407 19 SO4 SO4 . HA 6 HOH A 1 501 1 HOH HOH . HA 6 HOH A 2 502 14 HOH HOH . HA 6 HOH A 3 503 15 HOH HOH . HA 6 HOH A 4 504 22 HOH HOH . HA 6 HOH A 5 505 31 HOH HOH . HA 6 HOH A 6 506 32 HOH HOH . HA 6 HOH A 7 507 35 HOH HOH . IA 6 HOH B 1 501 4 HOH HOH . IA 6 HOH B 2 502 9 HOH HOH . IA 6 HOH B 3 503 11 HOH HOH . IA 6 HOH B 4 504 13 HOH HOH . IA 6 HOH B 5 505 24 HOH HOH . IA 6 HOH B 6 506 26 HOH HOH . IA 6 HOH B 7 507 27 HOH HOH . IA 6 HOH B 8 508 33 HOH HOH . JA 6 HOH C 1 501 2 HOH HOH . JA 6 HOH C 2 502 17 HOH HOH . JA 6 HOH C 3 503 21 HOH HOH . JA 6 HOH C 4 504 23 HOH HOH . JA 6 HOH C 5 505 25 HOH HOH . JA 6 HOH C 6 506 28 HOH HOH . JA 6 HOH C 7 507 29 HOH HOH . JA 6 HOH C 8 508 30 HOH HOH . JA 6 HOH C 9 509 34 HOH HOH . KA 6 HOH D 1 501 5 HOH HOH . KA 6 HOH D 2 502 6 HOH HOH . KA 6 HOH D 3 503 7 HOH HOH . KA 6 HOH D 4 504 12 HOH HOH . KA 6 HOH D 5 505 19 HOH HOH . KA 6 HOH D 6 506 20 HOH HOH . KA 6 HOH D 7 507 36 HOH HOH . LA 6 HOH E 1 701 18 HOH HOH . MA 6 HOH F 1 701 10 HOH HOH . NA 6 HOH G 1 701 3 HOH HOH . NA 6 HOH G 2 702 16 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 . . . N 3 82.395 -18.774 53.693 1 40.71 ? PB GDP 401 B 1 HETATM 2 O O1B GDP . . . N 3 82.754 -17.536 52.899 1 38.46 ? O1B GDP 401 B 1 HETATM 3 O O2B GDP . . . N 3 83.298 -19.971 53.436 1 39.51 ? O2B GDP 401 B 1 HETATM 4 O O3B GDP . . . N 3 82.237 -18.558 55.178 1 40.52 ? O3B GDP 401 B 1 HETATM 5 O O3A GDP . . . N 3 80.938 -19.134 53.091 1 37.88 ? O3A GDP 401 B 1 HETATM 6 P PA GDP . . . N 3 79.627 -18.773 53.932 1 37.74 ? PA GDP 401 B 1 HETATM 7 O O1A GDP . . . N 3 79.727 -17.313 54.23 1 39.26 ? O1A GDP 401 B 1 HETATM 8 O O2A GDP . . . N 3 79.494 -19.736 55.084 1 41.29 ? O2A GDP 401 B 1 HETATM 9 O O5' GDP . . . N 3 78.382 -19.014 52.943 1 40.15 ? O5' GDP 401 B 1 HETATM 10 C C5' GDP . . . N 3 78.385 -18.401 51.646 1 42.69 ? C5' GDP 401 B 1 HETATM 11 C C4' GDP . . . N 3 76.965 -18.08 51.18 1 41.78 ? C4' GDP 401 B 1 HETATM 12 O O4' GDP . . . N 3 76.288 -19.218 50.636 1 42.81 ? O4' GDP 401 B 1 HETATM 13 C C3' GDP . . . N 3 76.088 -17.642 52.317 1 42.85 ? C3' GDP 401 B 1 HETATM 14 O O3' GDP . . . N 3 75.1 -16.793 51.725 1 42.77 ? O3' GDP 401 B 1 HETATM 15 C C2' GDP . . . N 3 75.445 -18.923 52.82 1 43.45 ? C2' GDP 401 B 1 HETATM 16 O O2' GDP . . . N 3 74.169 -18.64 53.384 1 45.01 ? O2' GDP 401 B 1 HETATM 17 C C1' GDP . . . N 3 75.256 -19.699 51.535 1 46.42 ? C1' GDP 401 B 1 HETATM 18 N N9 GDP . . . N 3 75.412 -21.18 51.601 1 48.14 ? N9 GDP 401 B 1 HETATM 19 C C8 GDP . . . N 3 76.433 -21.869 52.15 1 47.95 ? C8 GDP 401 B 1 HETATM 20 N N7 GDP . . . N 3 76.297 -23.199 51.979 1 44.23 ? N7 GDP 401 B 1 HETATM 21 C C5 GDP . . . N 3 75.173 -23.376 51.282 1 46.62 ? C5 GDP 401 B 1 HETATM 22 C C6 GDP . . . N 3 74.448 -24.545 50.746 1 47.38 ? C6 GDP 401 B 1 HETATM 23 O O6 GDP . . . N 3 74.936 -25.684 50.949 1 48.11 ? O6 GDP 401 B 1 HETATM 24 N N1 GDP . . . N 3 73.298 -24.33 50.068 1 45.98 ? N1 GDP 401 B 1 HETATM 25 C C2 GDP . . . N 3 72.815 -23.079 49.864 1 47.25 ? C2 GDP 401 B 1 HETATM 26 N N2 GDP . . . N 3 71.666 -22.885 49.166 1 44.52 ? N2 GDP 401 B 1 HETATM 27 N N3 GDP . . . N 3 73.444 -21.966 50.335 1 47.66 ? N3 GDP 401 B 1 HETATM 28 C C4 GDP . . . N 3 74.598 -22.053 51.028 1 46.74 ? C4 GDP 401 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 411 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #