data_4QJ3 # _model_server_result.job_id dGqbDuIMEjtPimpwBZyRbA _model_server_result.datetime_utc '2024-11-01 07:27:04' _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 4qj3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 4QJ3 # _exptl.entry_id 4QJ3 _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.39 _cell.angle_gamma 90 _cell.entry_id 4QJ3 _cell.length_a 200.623 _cell.length_b 88.761 _cell.length_c 92.232 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QJ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 A OG SER 73 A SER 53 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 A OG1 THR 206 A THR 186 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc3 C O2B GDP . A GDP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc4 E MG MG . A MG 402 1_555 G O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc5 B OD1 ASN 334 B ASN 333 1_555 F CA CA . B CA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc6 B OE2 GLU 363 B GLU 362 1_555 F CA CA . B CA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc7 B OD2 ASP 365 B ASP 364 1_555 F CA CA . B CA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc8 B OD1 ASP 365 B ASP 364 1_555 F CA CA . B CA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc9 B OE1 GLU 414 B GLU 413 1_555 F CA CA . B CA 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 4QJ3 _atom_sites.fract_transf_matrix[1][1] 0.004984 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001004 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011266 _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] 0.01106 _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 C 3 GDP A 1 400 400 GDP GDP . D 4 ALF A 1 401 401 ALF ALF . E 5 MG A 1 402 402 MG MG . F 6 CA B 1 900 900 CA CA . G 7 HOH A 1 501 1 HOH HOH . G 7 HOH A 2 502 2 HOH HOH . G 7 HOH A 3 503 3 HOH HOH . G 7 HOH A 4 504 4 HOH HOH . G 7 HOH A 5 505 6 HOH HOH . G 7 HOH A 6 506 8 HOH HOH . G 7 HOH A 7 507 13 HOH HOH . G 7 HOH A 8 508 24 HOH HOH . G 7 HOH A 9 509 26 HOH HOH . G 7 HOH A 10 510 35 HOH HOH . G 7 HOH A 11 511 36 HOH HOH . G 7 HOH A 12 512 58 HOH HOH . G 7 HOH A 13 513 149 HOH HOH . H 7 HOH B 1 1001 19 HOH HOH . H 7 HOH B 2 1002 22 HOH HOH . H 7 HOH B 3 1003 70 HOH HOH . H 7 HOH B 4 1004 73 HOH HOH . H 7 HOH B 5 1005 75 HOH HOH . H 7 HOH B 6 1006 85 HOH HOH . H 7 HOH B 7 1007 96 HOH HOH . H 7 HOH B 8 1008 102 HOH HOH . H 7 HOH B 9 1009 111 HOH HOH . H 7 HOH B 10 1010 116 HOH HOH . H 7 HOH B 11 1011 122 HOH HOH . H 7 HOH B 12 1012 125 HOH HOH . H 7 HOH B 13 1013 131 HOH HOH . H 7 HOH B 14 1014 135 HOH HOH . H 7 HOH B 15 1015 138 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 . . . C 3 14.26 -1.939 44.529 1 29.87 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . C 3 14.868 -2.486 45.798 1 29.94 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . C 3 14.323 -0.437 44.422 1 30.85 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . C 3 14.682 -2.679 43.279 1 29.96 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . C 3 12.699 -2.298 44.716 1 29.38 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . C 3 11.49 -1.267 44.46 1 29.53 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . C 3 11.566 -0.127 45.44 1 30.02 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . C 3 11.437 -0.956 42.983 1 30.05 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . C 3 10.209 -2.149 44.87 1 29.47 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . C 3 9.953 -3.413 44.259 1 29.76 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . C 3 8.452 -3.685 44.17 1 30.04 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . C 3 7.953 -4.137 45.432 1 30.21 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . C 3 7.638 -2.453 43.811 1 30.57 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . C 3 6.56 -2.824 42.949 1 30.81 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . C 3 7.108 -1.947 45.135 1 30.87 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . C 3 5.853 -1.277 45.001 1 31.14 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . C 3 6.989 -3.218 45.958 1 30.85 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . C 3 7.256 -3.011 47.402 1 31.77 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . C 3 8.31 -2.371 47.948 1 32.33 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . C 3 8.235 -2.393 49.303 1 32.75 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . C 3 7.123 -3.062 49.635 1 33.07 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . C 3 6.445 -3.449 50.89 1 34.04 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . C 3 6.936 -3.131 51.99 1 35.18 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . C 3 5.299 -4.143 50.815 1 34.23 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . C 3 4.757 -4.492 49.63 1 33.85 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . C 3 3.599 -5.193 49.616 1 34.14 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . C 3 5.324 -4.168 48.437 1 33.28 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . C 3 6.483 -3.469 48.381 1 32.54 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #