data_2IF0 # _model_server_result.job_id ln70RUVTP28y-P7imRtnJg _model_server_result.datetime_utc '2024-11-22 14:59:23' _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 2if0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2IF0 # _exptl.entry_id 2IF0 _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 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 2IF0 _cell.length_a 54.96 _cell.length_b 64.755 _cell.length_c 153.327 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IF0 _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA,PQS dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 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 ? 3 D N N ? 3 F 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 disulf ? disulf1 A SG CYS 125 A CYS 123 1_555 A SG CYS 190 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 B SG CYS 125 B CYS 123 1_555 B SG CYS 190 B CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 A OG1 THR 25 A THR 23 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc2 D O1B GDP . A GDP 501 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc3 D O2B GDP . A GDP 501 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? metalc ? metalc4 B OG1 THR 25 B THR 23 1_555 E MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc5 E MG MG . B MG 502 1_555 F O3B GDP . B GDP 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? # _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 2IF0 _atom_sites.fract_transf_matrix[1][1] 0.018195 _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] 0.015443 _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] 0.006522 _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 2 MG A 1 602 602 MG MG . D 3 GDP A 1 501 501 GDP GDP . E 2 MG B 1 502 502 MG MG . F 3 GDP B 1 1501 501 GDP GDP . G 4 HOH A 1 603 1 HOH HOH . G 4 HOH A 2 604 2 HOH HOH . G 4 HOH A 3 605 3 HOH HOH . G 4 HOH A 4 606 4 HOH HOH . G 4 HOH A 5 607 5 HOH HOH . G 4 HOH A 6 608 6 HOH HOH . G 4 HOH A 7 609 7 HOH HOH . G 4 HOH A 8 610 8 HOH HOH . G 4 HOH A 9 611 12 HOH HOH . G 4 HOH A 10 612 13 HOH HOH . H 4 HOH B 1 1502 9 HOH HOH . H 4 HOH B 2 1503 10 HOH HOH . H 4 HOH B 3 1504 11 HOH HOH . H 4 HOH B 4 1505 14 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 . . . D 3 8.078 32.096 -24.23 1 23.57 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . D 3 8.395 32.067 -25.707 1 22.01 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . D 3 6.889 31.229 -23.908 1 22.89 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . D 3 9.31 31.638 -23.492 1 23.3 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . D 3 7.684 33.565 -23.706 1 25.34 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . D 3 7.61 34.861 -24.654 1 26.65 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . D 3 8.859 35.013 -25.483 1 26.72 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . D 3 6.367 34.835 -25.508 1 25.64 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . D 3 7.545 36.041 -23.581 1 29 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . D 3 6.494 36.063 -22.612 1 32.1 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . D 3 6.197 37.522 -22.292 1 34.73 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . D 3 7.304 38.104 -21.587 1 35.07 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . D 3 6.008 38.308 -23.589 1 35.15 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . D 3 4.833 39.113 -23.481 1 35.19 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . D 3 7.247 39.169 -23.72 1 34.99 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . D 3 6.96 40.465 -24.245 1 34.82 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . D 3 7.779 39.253 -22.298 1 35.08 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . D 3 9.255 39.267 -22.311 1 35.05 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . D 3 10.06 38.385 -22.925 1 35.23 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . D 3 11.362 38.711 -22.73 1 35.31 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . D 3 11.399 39.823 -21.978 1 34.98 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . D 3 12.448 40.697 -21.404 1 35.21 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . D 3 13.661 40.451 -21.592 1 35.29 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . D 3 12.055 41.759 -20.682 1 35.17 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . D 3 10.756 42.048 -20.466 1 35.33 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . D 3 10.432 43.132 -19.72 1 35.3 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . D 3 9.747 41.287 -20.963 1 35.25 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . D 3 10.004 40.186 -21.708 1 35.05 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #