data_7KZO # _model_server_result.job_id ntOVhPpVhz5-8JpqusEflw _model_server_result.datetime_utc '2024-11-22 17:48:17' _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 7kzo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":502}' # _entry.id 7KZO # _exptl.entry_id 7KZO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _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 7KZO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KZO _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 ? _pdbx_struct_assembly.oligomeric_details eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA _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 ? _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 ? 9 W N N ? 9 Z N N ? 9 CA N N ? 9 FA N N ? 9 GA N N ? 9 JA N N ? 9 MA N N ? 9 PA 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 U O1G GTP . A1 GTP 501 1_555 V MG MG . A1 MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc2 U O2G GTP . A1 GTP 501 1_555 V MG MG . A1 MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc3 U O1B GTP . A1 GTP 501 1_555 V MG MG . A1 MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc4 U O2B GTP . A1 GTP 501 1_555 V MG MG . A1 MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc5 B OG1 THR 145 A2 THR 145 1_555 X MG MG . A2 MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc6 X MG MG . A2 MG 501 1_555 Y O3A GTP . A3 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc7 X MG MG . A2 MG 501 1_555 Y O2G GTP . A3 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc8 D OG1 THR 145 A4 THR 145 1_555 AA MG MG . A4 MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc9 AA MG MG . A4 MG 501 1_555 BA O2B GTP . A5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc10 AA MG MG . A4 MG 501 1_555 BA O3A GTP . A5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? metalc ? metalc11 AA MG MG . A4 MG 501 1_555 BA O2G GTP . A5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc12 DA MG MG . A6 MG 501 1_555 EA O1G GTP . A7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc13 DA MG MG . A6 MG 501 1_555 EA O2G GTP . A7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc14 DA MG MG . A6 MG 501 1_555 EA O1B GTP . A7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? metalc ? metalc15 DA MG MG . A6 MG 501 1_555 EA O2B GTP . A7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc16 DA MG MG . A6 MG 501 1_555 EA O3A GTP . A7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc17 HA O2G GTP . B2 GTP 501 1_555 IA MG MG . B3 MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc18 HA O1B GTP . B2 GTP 501 1_555 IA MG MG . B3 MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc19 K OE1 GLU 71 B4 GLU 71 1_555 KA MG MG . B4 MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc20 KA MG MG . B4 MG 501 1_555 LA O3A GTP . B5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc21 KA MG MG . B4 MG 501 1_555 LA O1G GTP . B5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc22 KA MG MG . B4 MG 501 1_555 LA O2G GTP . B5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc23 KA MG MG . B4 MG 501 1_555 LA O3B GTP . B5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc24 KA MG MG . B4 MG 501 1_555 LA O1B GTP . B5 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc25 NA MG MG . B6 MG 501 1_555 OA O1B GTP . B7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc26 NA MG MG . B6 MG 501 1_555 OA O1G GTP . B7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc27 NA MG MG . B6 MG 501 1_555 OA O3A GTP . B7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.737 ? metalc ? metalc28 NA MG MG . B6 MG 501 1_555 OA O3B GTP . B7 GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? # _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 7KZO _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 U 7 GTP A1 1 501 501 GTP GTP . V 8 MG A1 1 502 502 MG MG . W 9 GDP A1 1 503 503 GDP GDP . X 8 MG A2 1 501 501 MG MG . Y 7 GTP A3 1 501 501 GTP GTP . Z 9 GDP A3 1 502 502 GDP GDP . AA 8 MG A4 1 501 501 MG MG . BA 7 GTP A5 1 501 501 GTP GTP . CA 9 GDP A5 1 502 502 GDP GDP . DA 8 MG A6 1 501 501 MG MG . EA 7 GTP A7 1 501 501 GTP GTP . FA 9 GDP A7 1 502 502 GDP GDP . GA 9 GDP B1 1 501 501 GDP GDP . HA 7 GTP B2 1 501 501 GTP GTP . IA 8 MG B3 1 501 501 MG MG . JA 9 GDP B3 1 502 502 GDP GDP . KA 8 MG B4 1 501 501 MG MG . LA 7 GTP B5 1 501 501 GTP GTP . MA 9 GDP B5 1 502 502 GDP GDP . NA 8 MG B6 1 501 501 MG MG . OA 7 GTP B7 1 501 501 GTP GTP . PA 9 GDP B7 1 502 502 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 . . . CA 9 193.637 175.572 258.105 1 38.6 ? PB GDP 502 A5 1 HETATM 2 O O1B GDP . . . CA 9 192.826 176.707 257.537 1 38.6 ? O1B GDP 502 A5 1 HETATM 3 O O2B GDP . . . CA 9 195.041 175.646 257.573 1 38.6 ? O2B GDP 502 A5 1 HETATM 4 O O3B GDP . . . CA 9 193.645 175.667 259.609 1 38.6 ? O3B GDP 502 A5 1 HETATM 5 O O3A GDP . . . CA 9 192.985 174.201 257.611 1 38.6 ? O3A GDP 502 A5 1 HETATM 6 P PA GDP . . . CA 9 193.057 172.86 258.484 1 38.6 ? PA GDP 502 A5 1 HETATM 7 O O1A GDP . . . CA 9 194.348 172.127 258.226 1 38.6 ? O1A GDP 502 A5 1 HETATM 8 O O2A GDP . . . CA 9 192.855 173.122 259.956 1 38.6 ? O2A GDP 502 A5 1 HETATM 9 O O5' GDP . . . CA 9 191.792 172.099 257.864 1 38.6 ? O5' GDP 502 A5 1 HETATM 10 C C5' GDP . . . CA 9 191.278 170.877 258.369 1 38.6 ? C5' GDP 502 A5 1 HETATM 11 C C4' GDP . . . CA 9 191.237 169.967 257.156 1 38.6 ? C4' GDP 502 A5 1 HETATM 12 O O4' GDP . . . CA 9 192.514 169.965 256.526 1 38.6 ? O4' GDP 502 A5 1 HETATM 13 C C3' GDP . . . CA 9 190.937 168.535 257.532 1 38.6 ? C3' GDP 502 A5 1 HETATM 14 O O3' GDP . . . CA 9 189.634 168.19 257.058 1 38.6 ? O3' GDP 502 A5 1 HETATM 15 C C2' GDP . . . CA 9 191.984 167.706 256.822 1 38.6 ? C2' GDP 502 A5 1 HETATM 16 O O2' GDP . . . CA 9 191.35 166.721 256.008 1 38.6 ? O2' GDP 502 A5 1 HETATM 17 C C1' GDP . . . CA 9 192.756 168.683 255.955 1 38.6 ? C1' GDP 502 A5 1 HETATM 18 N N9 GDP . . . CA 9 194.194 168.336 255.959 1 38.6 ? N9 GDP 502 A5 1 HETATM 19 C C8 GDP . . . CA 9 195.113 168.715 256.862 1 38.6 ? C8 GDP 502 A5 1 HETATM 20 N N7 GDP . . . CA 9 196.339 168.235 256.535 1 38.6 ? N7 GDP 502 A5 1 HETATM 21 C C5 GDP . . . CA 9 196.216 167.568 255.376 1 38.6 ? C5 GDP 502 A5 1 HETATM 22 C C6 GDP . . . CA 9 197.117 166.828 254.469 1 38.6 ? C6 GDP 502 A5 1 HETATM 23 O O6 GDP . . . CA 9 198.333 166.716 254.726 1 38.6 ? O6 GDP 502 A5 1 HETATM 24 N N1 GDP . . . CA 9 196.593 166.283 253.365 1 38.6 ? N1 GDP 502 A5 1 HETATM 25 C C2 GDP . . . CA 9 195.29 166.39 253.063 1 38.6 ? C2 GDP 502 A5 1 HETATM 26 N N2 GDP . . . CA 9 194.842 165.808 251.927 1 38.6 ? N2 GDP 502 A5 1 HETATM 27 N N3 GDP . . . CA 9 194.405 167.055 253.848 1 38.6 ? N3 GDP 502 A5 1 HETATM 28 C C4 GDP . . . CA 9 194.804 167.651 254.994 1 38.6 ? C4 GDP 502 A5 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #