data_6EVX # _model_server_result.job_id m1UXwqJRmWmAmO6G5ymtQg _model_server_result.datetime_utc '2025-03-04 16:05:54' _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 6evx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 6EVX # _exptl.entry_id 6EVX _exptl.method 'ELECTRON MICROSCOPY' # _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 6 _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 6EVX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details 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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 M N N ? 3 R N N ? 3 S N N ? 3 U N N ? 3 V N N ? 3 X 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 B OE2 GLU 71 A GLU 71 1_555 O MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc2 N O2B GTP . A GTP 501 1_555 O MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc3 H OE2 GLU 71 E GLU 71 1_555 AA MG MG . E MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc4 Z O2B GTP . E GTP 502 1_555 AA MG MG . E MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc5 I OE2 GLU 71 J GLU 71 1_555 CA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc6 BA O2B GTP . J GTP 501 1_555 CA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc7 J OE2 GLU 71 C GLU 71 1_555 FA MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? metalc ? metalc8 EA O2B GTP . C GTP 502 1_555 FA MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc9 K OE2 GLU 71 L GLU 71 1_555 HA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc10 GA O2B GTP . L GTP 501 1_555 HA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? metalc ? metalc11 L OE2 GLU 71 K GLU 71 1_555 JA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc12 IA O2B GTP . K GTP 501 1_555 JA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? # _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 6EVX _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 GDP F 1 501 430 GDP GDP . N 4 GTP A 1 501 442 GTP GTP . O 5 MG A 1 502 443 MG MG . P 6 PO4 A 1 503 431 PO4 PO4 . Q 6 PO4 G 1 501 430 PO4 PO4 . R 3 GDP G 1 502 431 GDP GDP . S 3 GDP D 1 501 430 GDP GDP . T 6 PO4 I 1 501 430 PO4 PO4 . U 3 GDP I 1 502 431 GDP GDP . V 3 GDP B 1 501 430 GDP GDP . W 6 PO4 H 1 501 430 PO4 PO4 . X 3 GDP H 1 502 431 GDP GDP . Y 6 PO4 E 1 501 431 PO4 PO4 . Z 4 GTP E 1 502 442 GTP GTP . AA 5 MG E 1 503 443 MG MG . BA 4 GTP J 1 501 442 GTP GTP . CA 5 MG J 1 502 443 MG MG . DA 6 PO4 C 1 501 431 PO4 PO4 . EA 4 GTP C 1 502 442 GTP GTP . FA 5 MG C 1 503 443 MG MG . GA 4 GTP L 1 501 442 GTP GTP . HA 5 MG L 1 502 443 MG MG . IA 4 GTP K 1 501 442 GTP GTP . JA 5 MG K 1 502 443 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 . . . M 3 44.446 149.203 119.17 1 99.72 ? PB GDP 501 F 1 HETATM 2 O O1B GDP . . . M 3 43.783 149.22 117.847 1 99.72 ? O1B GDP 501 F 1 HETATM 3 O O2B GDP . . . M 3 43.77 150.125 120.173 1 99.72 ? O2B GDP 501 F 1 HETATM 4 O O3B GDP . . . M 3 45.921 149.581 119.109 1 99.72 ? O3B GDP 501 F 1 HETATM 5 O O3A GDP . . . M 3 44.414 147.742 119.8 1 99.72 ? O3A GDP 501 F 1 HETATM 6 P PA GDP . . . M 3 45.238 146.434 119.426 1 99.72 ? PA GDP 501 F 1 HETATM 7 O O1A GDP . . . M 3 46.368 146.858 118.507 1 99.72 ? O1A GDP 501 F 1 HETATM 8 O O2A GDP . . . M 3 45.798 145.822 120.647 1 99.72 ? O2A GDP 501 F 1 HETATM 9 O O5' GDP . . . M 3 44.295 145.462 118.614 1 99.72 ? O5' GDP 501 F 1 HETATM 10 C C5' GDP . . . M 3 44.039 144.086 118.953 1 99.72 ? C5' GDP 501 F 1 HETATM 11 C C4' GDP . . . M 3 44.125 143.247 117.705 1 99.72 ? C4' GDP 501 F 1 HETATM 12 O O4' GDP . . . M 3 45.458 143.334 117.151 1 99.72 ? O4' GDP 501 F 1 HETATM 13 C C3' GDP . . . M 3 43.84 141.756 117.909 1 99.72 ? C3' GDP 501 F 1 HETATM 14 O O3' GDP . . . M 3 42.997 141.246 116.884 1 99.72 ? O3' GDP 501 F 1 HETATM 15 C C2' GDP . . . M 3 45.234 141.127 117.866 1 99.72 ? C2' GDP 501 F 1 HETATM 16 O O2' GDP . . . M 3 45.195 139.79 117.383 1 99.72 ? O2' GDP 501 F 1 HETATM 17 C C1' GDP . . . M 3 45.916 142.032 116.853 1 99.72 ? C1' GDP 501 F 1 HETATM 18 N N9 GDP . . . M 3 47.383 142.019 116.928 1 99.72 ? N9 GDP 501 F 1 HETATM 19 C C8 GDP . . . M 3 48.181 142.664 117.834 1 99.72 ? C8 GDP 501 F 1 HETATM 20 N N7 GDP . . . M 3 49.462 142.508 117.598 1 99.72 ? N7 GDP 501 F 1 HETATM 21 C C5 GDP . . . M 3 49.506 141.709 116.468 1 99.72 ? C5 GDP 501 F 1 HETATM 22 C C6 GDP . . . M 3 50.606 141.226 115.708 1 99.72 ? C6 GDP 501 F 1 HETATM 23 O O6 GDP . . . M 3 51.799 141.41 115.934 1 99.72 ? O6 GDP 501 F 1 HETATM 24 N N1 GDP . . . M 3 50.205 140.476 114.622 1 99.72 ? N1 GDP 501 F 1 HETATM 25 C C2 GDP . . . M 3 48.907 140.202 114.294 1 99.72 ? C2 GDP 501 F 1 HETATM 26 N N2 GDP . . . M 3 48.699 139.447 113.216 1 99.72 ? N2 GDP 501 F 1 HETATM 27 N N3 GDP . . . M 3 47.868 140.648 114.995 1 99.72 ? N3 GDP 501 F 1 HETATM 28 C C4 GDP . . . M 3 48.234 141.392 116.053 1 99.72 ? C4 GDP 501 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #