data_6EG8 # _model_server_result.job_id pDNZLdfzTkTWXgkKDmyMtw _model_server_result.datetime_utc '2024-11-27 15:06:56' _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 6eg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 6EG8 # _exptl.entry_id 6EG8 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.18 _cell.angle_gamma 90 _cell.entry_id 6EG8 _cell.length_a 100.86 _cell.length_b 100.81 _cell.length_c 179.33 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EG8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 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,C,I,M,N,U,W,Z 1 1 B,G,L,S,T,V,CA 2 1 D,E,K,Q,R,X,BA 3 1 F,H,J,O,P,Y,AA 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 ? 4 M N N ? 4 O N N ? 4 Q N N ? 4 S 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 I OG SER 55 I SER 54 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc2 I OG1 THR 191 I THR 204 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc3 M O3B GDP . I GDP 401 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc4 N MG MG . I MG 402 1_555 Z O HOH . I HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc5 N MG MG . I MG 402 1_555 Z O HOH . I HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc6 J OG SER 55 J SER 54 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc7 J OG1 THR 191 J THR 204 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc8 O O3B GDP . J GDP 401 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc9 P MG MG . J MG 402 1_555 AA O HOH . J HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc10 P MG MG . J MG 402 1_555 AA O HOH . J HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc11 P MG MG . J MG 402 1_555 AA O HOH . J HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc12 K OG SER 55 K SER 54 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc13 K OG1 THR 191 K THR 204 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc14 Q O1B GDP . K GDP 401 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc15 R MG MG . K MG 402 1_555 BA O HOH . K HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc16 L OG SER 55 L SER 54 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc17 L OG1 THR 191 L THR 204 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc18 S O3B GDP . L GDP 401 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc19 T MG MG . L MG 402 1_555 CA O HOH . L HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc20 T MG MG . L MG 402 1_555 CA O HOH . L HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? # _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 6EG8 _atom_sites.fract_transf_matrix[1][1] 0.009915 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002876 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00992 _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] 0.005806 _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 M 4 GDP I 1 401 401 GDP GDP . N 5 MG I 1 402 1 MG MG . O 4 GDP J 1 401 401 GDP GDP . P 5 MG J 1 402 2 MG MG . Q 4 GDP K 1 401 401 GDP GDP . R 5 MG K 1 402 3 MG MG . S 4 GDP L 1 401 401 GDP GDP . T 5 MG L 1 402 4 MG MG . U 6 HOH A 1 401 54 HOH HOH . U 6 HOH A 2 402 60 HOH HOH . U 6 HOH A 3 403 55 HOH HOH . U 6 HOH A 4 404 61 HOH HOH . U 6 HOH A 5 405 59 HOH HOH . U 6 HOH A 6 406 28 HOH HOH . U 6 HOH A 7 407 57 HOH HOH . U 6 HOH A 8 408 29 HOH HOH . V 6 HOH B 1 401 48 HOH HOH . V 6 HOH B 2 402 1 HOH HOH . V 6 HOH B 3 403 41 HOH HOH . V 6 HOH B 4 404 42 HOH HOH . V 6 HOH B 5 405 43 HOH HOH . V 6 HOH B 6 406 37 HOH HOH . V 6 HOH B 7 407 45 HOH HOH . V 6 HOH B 8 408 47 HOH HOH . V 6 HOH B 9 409 30 HOH HOH . V 6 HOH B 10 410 31 HOH HOH . V 6 HOH B 11 411 46 HOH HOH . W 6 HOH C 1 101 63 HOH HOH . X 6 HOH D 1 401 64 HOH HOH . X 6 HOH D 2 402 65 HOH HOH . X 6 HOH D 3 403 18 HOH HOH . X 6 HOH D 4 404 68 HOH HOH . X 6 HOH D 5 405 27 HOH HOH . X 6 HOH D 6 406 67 HOH HOH . X 6 HOH D 7 407 70 HOH HOH . Y 6 HOH F 1 401 77 HOH HOH . Y 6 HOH F 2 402 76 HOH HOH . Y 6 HOH F 3 403 124 HOH HOH . Y 6 HOH F 4 404 74 HOH HOH . Y 6 HOH F 5 405 75 HOH HOH . Y 6 HOH F 6 406 80 HOH HOH . Y 6 HOH F 7 407 73 HOH HOH . Y 6 HOH F 8 408 33 HOH HOH . Z 6 HOH I 1 501 82 HOH HOH . Z 6 HOH I 2 502 83 HOH HOH . Z 6 HOH I 3 503 3 HOH HOH . Z 6 HOH I 4 504 122 HOH HOH . Z 6 HOH I 5 505 7 HOH HOH . Z 6 HOH I 6 506 123 HOH HOH . Z 6 HOH I 7 507 90 HOH HOH . Z 6 HOH I 8 508 9 HOH HOH . Z 6 HOH I 9 509 128 HOH HOH . Z 6 HOH I 10 510 6 HOH HOH . Z 6 HOH I 11 511 8 HOH HOH . Z 6 HOH I 12 512 88 HOH HOH . Z 6 HOH I 13 513 84 HOH HOH . Z 6 HOH I 14 514 32 HOH HOH . Z 6 HOH I 15 515 71 HOH HOH . AA 6 HOH J 1 501 119 HOH HOH . AA 6 HOH J 2 502 96 HOH HOH . AA 6 HOH J 3 503 93 HOH HOH . AA 6 HOH J 4 504 95 HOH HOH . AA 6 HOH J 5 505 13 HOH HOH . AA 6 HOH J 6 506 91 HOH HOH . AA 6 HOH J 7 507 11 HOH HOH . AA 6 HOH J 8 508 15 HOH HOH . AA 6 HOH J 9 509 35 HOH HOH . AA 6 HOH J 10 510 14 HOH HOH . AA 6 HOH J 11 511 92 HOH HOH . AA 6 HOH J 12 512 98 HOH HOH . AA 6 HOH J 13 513 121 HOH HOH . AA 6 HOH J 14 514 12 HOH HOH . AA 6 HOH J 15 515 10 HOH HOH . AA 6 HOH J 16 516 94 HOH HOH . BA 6 HOH K 1 501 104 HOH HOH . BA 6 HOH K 2 502 117 HOH HOH . BA 6 HOH K 3 503 16 HOH HOH . BA 6 HOH K 4 504 105 HOH HOH . BA 6 HOH K 5 505 116 HOH HOH . BA 6 HOH K 6 506 34 HOH HOH . BA 6 HOH K 7 507 20 HOH HOH . BA 6 HOH K 8 508 103 HOH HOH . BA 6 HOH K 9 509 106 HOH HOH . BA 6 HOH K 10 510 17 HOH HOH . BA 6 HOH K 11 511 101 HOH HOH . CA 6 HOH L 1 501 24 HOH HOH . CA 6 HOH L 2 502 126 HOH HOH . CA 6 HOH L 3 503 109 HOH HOH . CA 6 HOH L 4 504 23 HOH HOH . CA 6 HOH L 5 505 108 HOH HOH . CA 6 HOH L 6 506 127 HOH HOH . CA 6 HOH L 7 507 107 HOH HOH . CA 6 HOH L 8 508 21 HOH HOH . CA 6 HOH L 9 509 110 HOH HOH . CA 6 HOH L 10 510 26 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 . . . O 4 44.287 -23.565 2.158 1 28.7 ? PB GDP 401 J 1 HETATM 2 O O1B GDP . . . O 4 43.302 -24.501 1.503 1 29.18 ? O1B GDP 401 J 1 HETATM 3 O O2B GDP . . . O 4 43.848 -22.143 1.902 1 29.22 -1 O2B GDP 401 J 1 HETATM 4 O O3B GDP . . . O 4 45.668 -23.791 1.589 1 28.67 ? O3B GDP 401 J 1 HETATM 5 O O3A GDP . . . O 4 44.293 -23.835 3.744 1 28.58 ? O3A GDP 401 J 1 HETATM 6 P PA GDP . . . O 4 45.599 -24.397 4.499 1 25.75 ? PA GDP 401 J 1 HETATM 7 O O1A GDP . . . O 4 45.884 -25.829 4.113 1 26.15 -1 O1A GDP 401 J 1 HETATM 8 O O2A GDP . . . O 4 46.801 -23.521 4.236 1 24.77 ? O2A GDP 401 J 1 HETATM 9 O O5' GDP . . . O 4 45.16 -24.298 6.041 1 25.18 ? O5' GDP 401 J 1 HETATM 10 C C5' GDP . . . O 4 45.537 -23.151 6.794 1 27.08 ? C5' GDP 401 J 1 HETATM 11 C C4' GDP . . . O 4 45.523 -23.483 8.276 1 29.57 ? C4' GDP 401 J 1 HETATM 12 O O4' GDP . . . O 4 44.383 -24.285 8.591 1 29.1 ? O4' GDP 401 J 1 HETATM 13 C C3' GDP . . . O 4 46.755 -24.283 8.663 1 31.81 ? C3' GDP 401 J 1 HETATM 14 O O3' GDP . . . O 4 47.571 -23.518 9.554 1 34.09 ? O3' GDP 401 J 1 HETATM 15 C C2' GDP . . . O 4 46.231 -25.513 9.373 1 32.97 ? C2' GDP 401 J 1 HETATM 16 O O2' GDP . . . O 4 46.875 -25.68 10.635 1 38.64 ? O2' GDP 401 J 1 HETATM 17 C C1' GDP . . . O 4 44.754 -25.238 9.587 1 28.75 ? C1' GDP 401 J 1 HETATM 18 N N9 GDP . . . O 4 43.977 -26.496 9.478 1 24.99 ? N9 GDP 401 J 1 HETATM 19 C C8 GDP . . . O 4 43.726 -27.199 8.357 1 22.78 ? C8 GDP 401 J 1 HETATM 20 N N7 GDP . . . O 4 42.979 -28.3 8.633 1 21.77 ? N7 GDP 401 J 1 HETATM 21 C C5 GDP . . . O 4 42.741 -28.307 9.959 1 22.25 ? C5 GDP 401 J 1 HETATM 22 C C6 GDP . . . O 4 42.02 -29.178 10.917 1 23.55 ? C6 GDP 401 J 1 HETATM 23 O O6 GDP . . . O 4 41.431 -30.211 10.531 1 22.68 ? O6 GDP 401 J 1 HETATM 24 N N1 GDP . . . O 4 42.017 -28.825 12.209 1 24.68 ? N1 GDP 401 J 1 HETATM 25 C C2 GDP . . . O 4 42.641 -27.718 12.657 1 21.57 ? C2 GDP 401 J 1 HETATM 26 N N2 GDP . . . O 4 42.59 -27.432 13.98 1 19.3 ? N2 GDP 401 J 1 HETATM 27 N N3 GDP . . . O 4 43.32 -26.876 11.837 1 21.56 ? N3 GDP 401 J 1 HETATM 28 C C4 GDP . . . O 4 43.402 -27.116 10.508 1 23.29 ? C4 GDP 401 J 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 102 _model_server_stats.query_time_ms 547 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 28 #