data_4KLZ # _model_server_result.job_id WnVE3P5F8gUvyMTbcgmkMQ _model_server_result.datetime_utc '2025-03-04 14:45:36' _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 4klz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4KLZ # _exptl.entry_id 4KLZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 95.9 _cell.angle_gamma 90 _cell.entry_id 4KLZ _cell.length_a 40.278 _cell.length_b 37.048 _cell.length_c 40.736 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KLZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 19 A SER 35 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 B O2B GDP . A GDP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc3 C MG MG . A MG 502 1_555 D O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? # _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 4KLZ _atom_sites.fract_transf_matrix[1][1] 0.024827 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002565 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026992 _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] 0.024679 _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 B 2 GDP A 1 501 501 GDP GDP . C 3 MG A 1 502 502 MG MG . D 4 HOH A 1 601 4 HOH HOH . D 4 HOH A 2 602 5 HOH HOH . D 4 HOH A 3 603 6 HOH HOH . D 4 HOH A 4 604 7 HOH HOH . D 4 HOH A 5 605 8 HOH HOH . D 4 HOH A 6 606 9 HOH HOH . D 4 HOH A 7 607 10 HOH HOH . D 4 HOH A 8 608 11 HOH HOH . D 4 HOH A 9 609 12 HOH HOH . D 4 HOH A 10 610 13 HOH HOH . D 4 HOH A 11 611 14 HOH HOH . D 4 HOH A 12 612 15 HOH HOH . D 4 HOH A 13 613 16 HOH HOH . D 4 HOH A 14 614 17 HOH HOH . D 4 HOH A 15 615 18 HOH HOH . D 4 HOH A 16 616 19 HOH HOH . D 4 HOH A 17 617 20 HOH HOH . D 4 HOH A 18 618 21 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 . . . B 2 14.951 6.199 1.479 1 10.98 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 14.929 5.969 2.947 1 10.32 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 13.671 5.516 1.145 1 12.09 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 15.044 7.621 1.105 1 8.48 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 16.28 5.567 0.852 1 5.94 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 16.386 4.427 -0.291 1 11.91 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 15.788 4.921 -1.576 1 9.21 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 15.826 3.033 0.084 1 8.95 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 17.917 4.182 -0.652 1 10.64 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 18.619 5.451 -0.788 1 13.53 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 20.059 5.417 -1.308 1 10.73 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 20.885 4.658 -0.426 1 7.78 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 20.199 4.91 -2.717 1 12.5 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 21.362 5.632 -3.246 1 15.8 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 20.381 3.449 -2.297 1 15.16 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 21.052 2.748 -3.274 1 17.74 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 21.27 3.526 -1.054 1 11.4 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 21.066 2.432 -0.07 1 11.95 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 19.942 2.002 0.578 1 9.54 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 20.226 0.928 1.328 1 8.01 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 21.555 0.742 1.219 1 9.05 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 22.59 -0.123 1.819 1 8.28 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 22.233 -0.992 2.594 1 11.61 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 23.868 -0.006 1.482 1 9.31 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 24.295 0.851 0.605 1 4.76 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 25.562 0.878 0.378 1 9.23 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 23.494 1.732 -0.012 1 12.39 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 22.117 1.726 0.299 1 11.43 ? 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 2 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #