data_7XQX # _model_server_result.job_id iIe7oj7oGO8XjCFzpgacnQ _model_server_result.datetime_utc '2025-03-13 21:49:11' _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 7xqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 7XQX # _exptl.entry_id 7XQX _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 7XQX _cell.length_a 105.386 _cell.length_b 157.49 _cell.length_c 180.668 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 ? 9 K N N ? 9 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 covale ? covale1 B N SER 296 B SER 296 1_555 N O2S MES . B MES 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.309 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc11 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc12 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc13 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc14 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc15 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc16 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc17 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc18 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc19 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc20 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? # _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 7XQX _atom_sites.fract_transf_matrix[1][1] 0.009489 _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] 0.00635 _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] 0.005535 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 9 GDP B 1 501 499 GDP GDP . L 6 MG B 1 502 500 MG MG . M 10 MES B 1 503 502 MES MES . N 10 MES B 1 504 503 MES MES . O 11 GXI B 1 505 601 GXI LLL . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 503 CA CA . S 9 GDP D 1 501 598 GDP GDP . T 11 GXI D 1 502 601 GXI LLL . # 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 . . . K 9 19.007 49.48 16.176 1 38.77 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 18.543 50.503 15.156 1 32.4 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 19.312 50.066 17.556 1 42.99 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 20.202 48.702 15.674 1 38.3 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 17.797 48.445 16.354 1 39.61 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 16.398 48.839 17.041 1 33.55 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 15.358 48.752 15.931 1 43.49 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 16.441 50.179 17.742 1 40.39 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 16.23 47.688 18.171 1 37.76 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 15.005 46.951 18.332 1 44.75 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 14.463 46.995 19.762 1 33.08 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 14.061 48.327 20.002 1 29.13 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 13.229 46.147 19.949 1 31.27 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 13.127 45.762 21.319 1 31.26 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 12.136 47.125 19.606 1 34.41 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 10.872 46.868 20.231 1 43.44 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 12.664 48.394 20.18 1 28.04 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 12.208 49.547 19.408 1 33.25 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 12.456 49.823 18.113 1 37.02 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 11.899 51.008 17.754 1 40.04 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 11.304 51.501 18.855 1 32.2 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 10.535 52.706 19.208 1 39.26 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 10.307 53.592 18.366 1 43.98 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 10.078 52.835 20.455 1 39.1 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 10.307 51.928 21.405 1 35.8 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 9.809 52.183 22.619 1 27.14 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 11.014 50.789 21.182 1 37.7 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 11.514 50.538 19.945 1 35.89 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 28 #