data_5G53 # _model_server_result.job_id V_ujEukLTy_2VZkYGMsQAQ _model_server_result.datetime_utc '2024-11-28 00:58:29' _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 5g53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":400}' # _entry.id 5G53 # _exptl.entry_id 5G53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 5G53 _cell.length_a 90.632 _cell.length_b 111.814 _cell.length_c 161.304 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5G53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,I 1 1 B,D,H 2 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 5 _struct_asym.id I _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 disulf ? disulf1 A SG CYS 71 A CYS 71 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 74 A CYS 74 1_555 A SG CYS 146 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 77 A CYS 77 1_555 A SG CYS 166 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 259 A CYS 259 1_555 A SG CYS 262 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 B SG CYS 71 B CYS 71 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 74 B CYS 74 1_555 B SG CYS 146 B CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 B SG CYS 77 B CYS 77 1_555 B SG CYS 166 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 259 B CYS 259 1_555 B SG CYS 262 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _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 5G53 _atom_sites.fract_transf_matrix[1][1] 0.011034 _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] 0.008943 _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] 0.006199 _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 E 3 NEC A 1 400 400 NEC NEC . F 4 SOG A 1 501 501 SOG SOG . G 4 SOG A 1 502 502 SOG SOG . H 3 NEC B 1 400 400 NEC NEC . I 5 GDP C 1 400 400 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 . . . I 5 -0.018 12.769 -17.176 1 70.97 ? PB GDP 400 C 1 HETATM 2 O O1B GDP . . . I 5 0.173 13.683 -15.993 1 71.24 ? O1B GDP 400 C 1 HETATM 3 O O2B GDP . . . I 5 0.01 11.331 -16.806 1 69.46 ? O2B GDP 400 C 1 HETATM 4 O O3B GDP . . . I 5 -1.141 13.167 -18.099 1 73.04 ? O3B GDP 400 C 1 HETATM 5 O O3A GDP . . . I 5 1.341 12.83 -18.048 1 69.12 ? O3A GDP 400 C 1 HETATM 6 P PA GDP . . . I 5 1.562 11.965 -19.396 1 65.42 ? PA GDP 400 C 1 HETATM 7 O O1A GDP . . . I 5 0.541 12.42 -20.415 1 68.82 ? O1A GDP 400 C 1 HETATM 8 O O2A GDP . . . I 5 1.647 10.49 -19.113 1 63.25 ? O2A GDP 400 C 1 HETATM 9 O O5' GDP . . . I 5 3.039 12.468 -19.798 1 63.76 ? O5' GDP 400 C 1 HETATM 10 C C5' GDP . . . I 5 3.268 13.782 -20.308 1 65.52 ? C5' GDP 400 C 1 HETATM 11 C C4' GDP . . . I 5 4.565 13.845 -21.106 1 67.2 ? C4' GDP 400 C 1 HETATM 12 O O4' GDP . . . I 5 5.623 13.428 -20.235 1 67.13 ? O4' GDP 400 C 1 HETATM 13 C C3' GDP . . . I 5 4.587 12.962 -22.365 1 68.27 ? C3' GDP 400 C 1 HETATM 14 O O3' GDP . . . I 5 4.501 13.727 -23.594 1 62.67 ? O3' GDP 400 C 1 HETATM 15 C C2' GDP . . . I 5 5.873 12.141 -22.227 1 69.44 ? C2' GDP 400 C 1 HETATM 16 O O2' GDP . . . I 5 6.739 12.315 -23.361 1 71.09 ? O2' GDP 400 C 1 HETATM 17 C C1' GDP . . . I 5 6.549 12.575 -20.913 1 68.43 ? C1' GDP 400 C 1 HETATM 18 N N9 GDP . . . I 5 6.898 11.435 -20.012 1 67.35 ? N9 GDP 400 C 1 HETATM 19 C C8 GDP . . . I 5 6.036 10.786 -19.215 1 66.26 ? C8 GDP 400 C 1 HETATM 20 N N7 GDP . . . I 5 6.642 9.795 -18.513 1 65.5 ? N7 GDP 400 C 1 HETATM 21 C C5 GDP . . . I 5 7.934 9.793 -18.857 1 69.08 ? C5 GDP 400 C 1 HETATM 22 C C6 GDP . . . I 5 9.14 8.999 -18.489 1 72.08 ? C6 GDP 400 C 1 HETATM 23 O O6 GDP . . . I 5 9.057 8.064 -17.659 1 72.86 ? O6 GDP 400 C 1 HETATM 24 N N1 GDP . . . I 5 10.314 9.321 -19.078 1 73.85 ? N1 GDP 400 C 1 HETATM 25 C C2 GDP . . . I 5 10.411 10.334 -19.982 1 73.48 ? C2 GDP 400 C 1 HETATM 26 N N2 GDP . . . I 5 11.607 10.623 -20.55 1 72.03 ? N2 GDP 400 C 1 HETATM 27 N N3 GDP . . . I 5 9.339 11.095 -20.36 1 73.43 ? N3 GDP 400 C 1 HETATM 28 C C4 GDP . . . I 5 8.1 10.879 -19.844 1 70 ? C4 GDP 400 C 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 215 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #