data_4B8Z # _model_server_result.job_id 0tCxo0kaXuhicsD3s0FoCg _model_server_result.datetime_utc '2024-11-27 20:25:54' _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 4b8z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":901}' # _entry.id 4B8Z # _exptl.entry_id 4B8Z _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 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 120 _cell.entry_id 4B8Z _cell.length_a 91.447 _cell.length_b 91.447 _cell.length_c 429.13 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4B8Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # 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 monomeric 1 author_and_software_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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,M 1 1 B,G,H,N 2 1 C,I,J,O 3 1 D,K,L,P 4 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 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _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 4B8Z _atom_sites.fract_transf_matrix[1][1] 0.010935 _atom_sites.fract_transf_matrix[1][2] 0.006313 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012627 _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] 0.00233 _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 NAP A 1 900 900 NAP NAP . F 3 GDP A 1 901 901 GDP GDP . G 2 NAP B 1 900 900 NAP NAP . H 3 GDP B 1 901 901 GDP GDP . I 2 NAP C 1 900 900 NAP NAP . J 3 GDP C 1 901 901 GDP GDP . K 2 NAP D 1 900 900 NAP NAP . L 3 GDP D 1 901 901 GDP GDP . M 4 HOH A 1 2001 2001 HOH HOH . M 4 HOH A 2 2002 2002 HOH HOH . M 4 HOH A 3 2003 2003 HOH HOH . N 4 HOH B 1 2001 2001 HOH HOH . N 4 HOH B 2 2002 2002 HOH HOH . N 4 HOH B 3 2003 2003 HOH HOH . N 4 HOH B 4 2004 2004 HOH HOH . N 4 HOH B 5 2005 2005 HOH HOH . N 4 HOH B 6 2006 2006 HOH HOH . N 4 HOH B 7 2007 2007 HOH HOH . O 4 HOH C 1 2001 2001 HOH HOH . O 4 HOH C 2 2002 2002 HOH HOH . O 4 HOH C 3 2003 2003 HOH HOH . O 4 HOH C 4 2004 2004 HOH HOH . O 4 HOH C 5 2005 2005 HOH HOH . P 4 HOH D 1 2001 2001 HOH HOH . P 4 HOH D 2 2002 2002 HOH HOH . P 4 HOH D 3 2003 2003 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 . . . J 3 3.715 24.182 2.975 1 67.77 ? PB GDP 901 C 1 HETATM 2 O O1B GDP . . . J 3 2.566 23.974 1.963 1 66.79 ? O1B GDP 901 C 1 HETATM 3 O O2B GDP . . . J 3 4.979 23.495 2.419 1 69.4 ? O2B GDP 901 C 1 HETATM 4 O O3B GDP . . . J 3 3.386 23.761 4.346 1 69.24 ? O3B GDP 901 C 1 HETATM 5 O O3A GDP . . . J 3 4.117 25.712 3.102 1 65.92 ? O3A GDP 901 C 1 HETATM 6 P PA GDP . . . J 3 3.586 27.03 3.801 1 65.74 ? PA GDP 901 C 1 HETATM 7 O O1A GDP . . . J 3 4.061 27.015 5.202 1 66.71 ? O1A GDP 901 C 1 HETATM 8 O O2A GDP . . . J 3 4.052 28.233 2.987 1 66.93 ? O2A GDP 901 C 1 HETATM 9 O O5' GDP . . . J 3 2.007 26.904 3.764 1 66.78 ? O5' GDP 901 C 1 HETATM 10 C C5' GDP . . . J 3 1.271 27.064 2.533 1 67.59 ? C5' GDP 901 C 1 HETATM 11 C C4' GDP . . . J 3 -0.206 26.845 2.765 1 68.13 ? C4' GDP 901 C 1 HETATM 12 O O4' GDP . . . J 3 -0.72 27.842 3.679 1 69.7 ? O4' GDP 901 C 1 HETATM 13 C C3' GDP . . . J 3 -1.079 26.951 1.516 1 69.6 ? C3' GDP 901 C 1 HETATM 14 O O3' GDP . . . J 3 -2.193 26.071 1.626 1 69.77 ? O3' GDP 901 C 1 HETATM 15 C C2' GDP . . . J 3 -1.492 28.425 1.53 1 70.2 ? C2' GDP 901 C 1 HETATM 16 O O2' GDP . . . J 3 -2.657 28.694 0.758 1 69.51 ? O2' GDP 901 C 1 HETATM 17 C C1' GDP . . . J 3 -1.706 28.629 3.029 1 70.86 ? C1' GDP 901 C 1 HETATM 18 N N9 GDP . . . J 3 -1.577 30.021 3.484 1 70.96 ? N9 GDP 901 C 1 HETATM 19 C C8 GDP . . . J 3 -2.582 30.799 3.993 1 72.75 ? C8 GDP 901 C 1 HETATM 20 N N7 GDP . . . J 3 -2.188 31.987 4.388 1 73.47 ? N7 GDP 901 C 1 HETATM 21 C C5 GDP . . . J 3 -0.827 31.991 4.131 1 72.59 ? C5 GDP 901 C 1 HETATM 22 C C6 GDP . . . J 3 0.17 32.972 4.392 1 73.01 ? C6 GDP 901 C 1 HETATM 23 O O6 GDP . . . J 3 0.005 34.056 4.949 1 75.43 ? O6 GDP 901 C 1 HETATM 24 N N1 GDP . . . J 3 1.432 32.559 3.999 1 71.42 ? N1 GDP 901 C 1 HETATM 25 C C2 GDP . . . J 3 1.725 31.344 3.432 1 69.45 ? C2 GDP 901 C 1 HETATM 26 N N2 GDP . . . J 3 3.002 31.106 3.132 1 69.14 ? N2 GDP 901 C 1 HETATM 27 N N3 GDP . . . J 3 0.809 30.408 3.189 1 68.68 ? N3 GDP 901 C 1 HETATM 28 C C4 GDP . . . J 3 -0.436 30.788 3.561 1 70.84 ? C4 GDP 901 C 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #