data_2NZJ # _model_server_result.job_id zthMIk5SBKZl0-3WFFNpRQ _model_server_result.datetime_utc '2025-02-26 21:54:26' _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 2nzj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1003}' # _entry.id 2NZJ # _exptl.entry_id 2NZJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 2NZJ _cell.length_a 43.64 _cell.length_b 102.284 _cell.length_c 165.565 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NZJ _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 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,O 1 1 B,H,I,J,P 2 1 C,K,L,Q 3 1 D,M,N,R 4 1 A,E,F,G,O 5 1 C,K,L,Q 5 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_444 -x-1,y-1/2,-z-1/2 -1 0 0 0 1 0 0 0 -1 -43.64 -51.142 -82.7825 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 J N N ? 4 L N N ? 4 N 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 metalc ? metalc1 O O HOH . A HOH 1 1_555 E MG MG . A MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc2 O O HOH . A HOH 2 1_555 E MG MG . A MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc3 O O HOH . A HOH 3 1_555 E MG MG . A MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc4 O O HOH . A HOH 4 1_555 E MG MG . A MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc5 A OG1 THR 18 A THR 94 1_555 E MG MG . A MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc6 E MG MG . A MG 252 1_555 G O2B GDP . A GDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 P O HOH . B HOH 5 1_555 H MG MG . B MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc8 P O HOH . B HOH 6 1_555 H MG MG . B MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc9 P O HOH . B HOH 7 1_555 H MG MG . B MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc10 P O HOH . B HOH 8 1_555 H MG MG . B MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc11 B OG1 THR 18 B THR 94 1_555 H MG MG . B MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc12 H MG MG . B MG 252 1_555 J O3B GDP . B GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.146 ? metalc ? metalc13 H MG MG . B MG 252 1_555 J O2B GDP . B GDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc14 Q O HOH . C HOH 9 1_555 K MG MG . C MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc15 Q O HOH . C HOH 10 1_555 K MG MG . C MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc16 Q O HOH . C HOH 11 1_555 K MG MG . C MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc17 Q O HOH . C HOH 12 1_555 K MG MG . C MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc18 C OG1 THR 18 C THR 94 1_555 K MG MG . C MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc19 K MG MG . C MG 252 1_555 L O2B GDP . C GDP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc20 R O HOH . D HOH 13 1_555 M MG MG . D MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? metalc ? metalc21 R O HOH . D HOH 14 1_555 M MG MG . D MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? metalc ? metalc22 R O HOH . D HOH 15 1_555 M MG MG . D MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? metalc ? metalc23 R O HOH . D HOH 16 1_555 M MG MG . D MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc24 D OG1 THR 18 D THR 94 1_555 M MG MG . D MG 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc25 M MG MG . D MG 252 1_555 N O2B GDP . D GDP 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _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 2NZJ _atom_sites.fract_transf_matrix[1][1] 0.022915 _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] 0.009777 _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] 0.00604 _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 2 MG A 1 252 101 MG MG . F 3 CL A 1 253 106 CL CL . G 4 GDP A 1 1001 1001 GDP GDP . H 2 MG B 1 252 102 MG MG . I 3 CL B 1 253 105 CL CL . J 4 GDP B 1 1002 1002 GDP GDP . K 2 MG C 1 252 103 MG MG . L 4 GDP C 1 1003 1003 GDP GDP . M 2 MG D 1 252 104 MG MG . N 4 GDP D 1 1004 1004 GDP GDP . O 5 HOH A 1 1 1 HOH HOH . O 5 HOH A 2 2 2 HOH HOH . O 5 HOH A 3 3 3 HOH HOH . O 5 HOH A 4 4 4 HOH HOH . P 5 HOH B 1 5 5 HOH HOH . P 5 HOH B 2 6 6 HOH HOH . P 5 HOH B 3 7 7 HOH HOH . P 5 HOH B 4 8 8 HOH HOH . Q 5 HOH C 1 9 9 HOH HOH . Q 5 HOH C 2 10 10 HOH HOH . Q 5 HOH C 3 11 11 HOH HOH . Q 5 HOH C 4 12 12 HOH HOH . R 5 HOH D 1 13 13 HOH HOH . R 5 HOH D 2 14 14 HOH HOH . R 5 HOH D 3 15 15 HOH HOH . R 5 HOH D 4 16 16 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 . . . L 4 1.357 42.521 -61.364 1 40.97 ? PB GDP 1003 C 1 HETATM 2 O O1B GDP . . . L 4 0.517 42.736 -62.597 1 39.85 ? O1B GDP 1003 C 1 HETATM 3 O O2B GDP . . . L 4 0.864 41.331 -60.579 1 40.81 ? O2B GDP 1003 C 1 HETATM 4 O O3B GDP . . . L 4 2.778 42.306 -61.817 1 40.9 ? O3B GDP 1003 C 1 HETATM 5 O O3A GDP . . . L 4 1.29 43.82 -60.437 1 40.73 ? O3A GDP 1003 C 1 HETATM 6 P PA GDP . . . L 4 0.84 43.825 -58.885 1 42.49 ? PA GDP 1003 C 1 HETATM 7 O O1A GDP . . . L 4 1.719 42.967 -58 1 40.8 ? O1A GDP 1003 C 1 HETATM 8 O O2A GDP . . . L 4 -0.641 43.531 -58.682 1 41.51 ? O2A GDP 1003 C 1 HETATM 9 O O5' GDP . . . L 4 1.061 45.378 -58.567 1 42.65 ? O5' GDP 1003 C 1 HETATM 10 C C5' GDP . . . L 4 2.221 46.074 -59.013 1 43.52 ? C5' GDP 1003 C 1 HETATM 11 C C4' GDP . . . L 4 2.326 47.367 -58.21 1 44.09 ? C4' GDP 1003 C 1 HETATM 12 O O4' GDP . . . L 4 1.323 48.281 -58.668 1 42.86 ? O4' GDP 1003 C 1 HETATM 13 C C3' GDP . . . L 4 2.087 47.137 -56.723 1 43.29 ? C3' GDP 1003 C 1 HETATM 14 O O3' GDP . . . L 4 3.068 47.831 -55.94 1 44.98 ? O3' GDP 1003 C 1 HETATM 15 C C2' GDP . . . L 4 0.71 47.683 -56.467 1 42.44 ? C2' GDP 1003 C 1 HETATM 16 O O2' GDP . . . L 4 0.649 48.294 -55.177 1 43.32 ? O2' GDP 1003 C 1 HETATM 17 C C1' GDP . . . L 4 0.517 48.693 -57.58 1 41.84 ? C1' GDP 1003 C 1 HETATM 18 N N9 GDP . . . L 4 -0.851 48.811 -58.127 1 41.91 ? N9 GDP 1003 C 1 HETATM 19 C C8 GDP . . . L 4 -1.64 47.829 -58.58 1 41.79 ? C8 GDP 1003 C 1 HETATM 20 N N7 GDP . . . L 4 -2.814 48.327 -59.024 1 41.66 ? N7 GDP 1003 C 1 HETATM 21 C C5 GDP . . . L 4 -2.787 49.646 -58.858 1 41.76 ? C5 GDP 1003 C 1 HETATM 22 C C6 GDP . . . L 4 -3.697 50.776 -59.121 1 42 ? C6 GDP 1003 C 1 HETATM 23 O O6 GDP . . . L 4 -4.823 50.562 -59.638 1 42.06 ? O6 GDP 1003 C 1 HETATM 24 N N1 GDP . . . L 4 -3.266 52.012 -58.804 1 41.59 ? N1 GDP 1003 C 1 HETATM 25 C C2 GDP . . . L 4 -2.054 52.238 -58.256 1 41.65 ? C2 GDP 1003 C 1 HETATM 26 N N2 GDP . . . L 4 -1.648 53.492 -57.944 1 41.73 ? N2 GDP 1003 C 1 HETATM 27 N N3 GDP . . . L 4 -1.182 51.245 -57.998 1 41.02 ? N3 GDP 1003 C 1 HETATM 28 C C4 GDP . . . L 4 -1.487 49.963 -58.273 1 41.89 ? C4 GDP 1003 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #