data_7TTE # _model_server_result.job_id ovCq58LrTa0y4bfqdHs7Wg _model_server_result.datetime_utc '2025-01-25 11:31:57' _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 7tte # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 7TTE # _exptl.entry_id 7TTE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 7TTE _cell.length_a 66.062 _cell.length_b 127.425 _cell.length_c 251.622 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TTE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 K O3G GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? metalc ? metalc2 K O2B GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 L MG MG . C MG 502 1_555 S O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc4 L MG MG . C MG 502 1_555 S O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc5 L MG MG . C MG 502 1_555 S O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc6 L MG MG . C MG 502 1_555 S O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? # _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 7TTE _atom_sites.fract_transf_matrix[1][1] 0.015137 _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] 0.007848 _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] 0.003974 _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 F 4 GTP A 1 501 501 GTP GTP . G 5 SO4 A 1 502 1 SO4 SO4 . H 6 GDP B 1 501 501 GDP GDP . I 7 JVR B 1 502 502 JVR Z35 . J 5 SO4 B 1 503 2 SO4 SO4 . K 4 GTP C 1 501 501 GTP GTP . L 8 MG C 1 502 502 MG MG . M 4 GTP D 1 501 501 GTP GTP . N 7 JVR D 1 502 502 JVR Z35 . O 5 SO4 D 1 503 3 SO4 SO4 . P 5 SO4 D 1 504 4 SO4 SO4 . Q 9 HOH A 1 601 6 HOH HOH . R 9 HOH B 1 601 12 HOH HOH . R 9 HOH B 2 602 7 HOH HOH . S 9 HOH C 1 601 1 HOH HOH . S 9 HOH C 2 602 2 HOH HOH . S 9 HOH C 3 603 4 HOH HOH . S 9 HOH C 4 604 3 HOH HOH . S 9 HOH C 5 605 8 HOH HOH . S 9 HOH C 6 606 10 HOH HOH . T 9 HOH D 1 601 11 HOH HOH . T 9 HOH D 2 602 5 HOH HOH . T 9 HOH D 3 603 9 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 . . . H 6 3.863 21.493 33.877 1 77.7 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 5.329 22.122 33.709 1 68.95 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 2.845 22.349 34.786 1 78.38 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 4.028 20.163 34.5 1 92.63 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 3.317 21.357 32.369 1 79.21 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 1.984 20.865 31.694 1 125.83 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 1.159 22.124 31.175 1 129.1 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 1.164 20.135 32.656 1 107.37 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 2.484 19.912 30.52 1 96.82 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 2.42 20.176 29.123 1 85.76 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 1.91 18.857 28.576 1 79.82 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 0.702 18.603 29.305 1 73.19 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 1.536 18.861 27.087 1 83.84 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 1.667 17.53 26.569 1 101.24 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 0.052 19.28 27.141 1 84.88 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 -0.653 18.827 25.987 1 88.21 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 -0.39 18.471 28.383 1 75.36 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 -1.547 18.992 29.107 1 67.13 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 -1.613 20.151 29.804 1 67.52 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 -2.801 20.264 30.327 1 71.01 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 -3.566 19.2 30.004 1 65.87 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 -4.889 18.787 30.306 1 72.97 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 -5.626 19.471 30.997 1 79.28 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 -5.324 17.607 29.795 1 71.1 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 -4.497 16.847 29.002 1 70.69 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 -4.95 15.658 28.487 1 76.55 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 -3.257 17.212 28.731 1 73.62 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 -2.762 18.366 29.215 1 72.38 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #