data_6YVP # _model_server_result.job_id m1MtgHwCY9rOO61B3jxvlA _model_server_result.datetime_utc '2024-11-18 21:43:43' _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 6yvp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 6YVP # _exptl.entry_id 6YVP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" _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 103.034 _cell.angle_gamma 90 _cell.entry_id 6YVP _cell.length_a 71.649 _cell.length_b 36.531 _cell.length_c 86.887 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YVP _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1,2 B,D,F 2 1,3 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -19.595557 0 84.648478 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id DGP _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 P OP1 DGP doub 83 n n P OP2 DGP sing 84 n n P OP3 DGP sing 85 n n P O5' DGP sing 86 n n OP2 HOP2 DGP sing 87 n n OP3 HOP3 DGP sing 88 n n O5' C5' DGP sing 89 n n C5' C4' DGP sing 90 n n C5' H5' DGP sing 91 n n C5' "H5''" DGP sing 92 n n C4' O4' DGP sing 93 n n C4' C3' DGP sing 94 n n C4' H4' DGP sing 95 n n O4' C1' DGP sing 96 n n C3' O3' DGP sing 97 n n C3' C2' DGP sing 98 n n C3' H3' DGP sing 99 n n O3' HO3' DGP sing 100 n n C2' C1' DGP sing 101 n n C2' H2' DGP sing 102 n n C2' "H2''" DGP sing 103 n n C1' N9 DGP sing 104 n n C1' H1' DGP sing 105 n n N9 C8 DGP sing 106 n y N9 C4 DGP sing 107 n y C8 N7 DGP doub 108 n y C8 H8 DGP sing 109 n n N7 C5 DGP sing 110 n y C5 C6 DGP sing 111 n n C5 C4 DGP doub 112 n y C6 O6 DGP doub 113 n n C6 N1 DGP sing 114 n n N1 C2 DGP sing 115 n n N1 HN1 DGP sing 116 n n C2 N2 DGP sing 117 n n C2 N3 DGP doub 118 n n N2 HN21 DGP sing 119 n n N2 HN22 DGP sing 120 n n N3 C4 DGP sing 121 n n # _atom_sites.entry_id 6YVP _atom_sites.fract_transf_matrix[1][1] 0.013957 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003231 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027374 _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] 0.011814 _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 DGP AAA 1 201 201 DGP DGP . D 2 DGP BBB 1 201 201 DGP DGP . E 3 HOH AAA 1 301 2 HOH HOH . E 3 HOH AAA 2 302 27 HOH HOH . E 3 HOH AAA 3 303 9 HOH HOH . E 3 HOH AAA 4 304 98 HOH HOH . E 3 HOH AAA 5 305 118 HOH HOH . E 3 HOH AAA 6 306 5 HOH HOH . E 3 HOH AAA 7 307 1 HOH HOH . E 3 HOH AAA 8 308 8 HOH HOH . E 3 HOH AAA 9 309 58 HOH HOH . E 3 HOH AAA 10 310 23 HOH HOH . E 3 HOH AAA 11 311 6 HOH HOH . E 3 HOH AAA 12 312 4 HOH HOH . E 3 HOH AAA 13 313 24 HOH HOH . E 3 HOH AAA 14 314 65 HOH HOH . E 3 HOH AAA 15 315 7 HOH HOH . E 3 HOH AAA 16 316 66 HOH HOH . E 3 HOH AAA 17 317 57 HOH HOH . E 3 HOH AAA 18 318 103 HOH HOH . E 3 HOH AAA 19 319 19 HOH HOH . E 3 HOH AAA 20 320 111 HOH HOH . E 3 HOH AAA 21 321 84 HOH HOH . E 3 HOH AAA 22 322 20 HOH HOH . E 3 HOH AAA 23 323 94 HOH HOH . E 3 HOH AAA 24 324 99 HOH HOH . E 3 HOH AAA 25 325 100 HOH HOH . E 3 HOH AAA 26 326 97 HOH HOH . E 3 HOH AAA 27 327 92 HOH HOH . E 3 HOH AAA 28 328 95 HOH HOH . E 3 HOH AAA 29 329 59 HOH HOH . E 3 HOH AAA 30 330 112 HOH HOH . E 3 HOH AAA 31 331 90 HOH HOH . E 3 HOH AAA 32 332 88 HOH HOH . E 3 HOH AAA 33 333 63 HOH HOH . E 3 HOH AAA 34 334 87 HOH HOH . E 3 HOH AAA 35 335 18 HOH HOH . E 3 HOH AAA 36 336 104 HOH HOH . E 3 HOH AAA 37 337 60 HOH HOH . E 3 HOH AAA 38 338 22 HOH HOH . E 3 HOH AAA 39 339 106 HOH HOH . E 3 HOH AAA 40 340 93 HOH HOH . E 3 HOH AAA 41 341 101 HOH HOH . E 3 HOH AAA 42 342 105 HOH HOH . E 3 HOH AAA 43 343 89 HOH HOH . E 3 HOH AAA 44 344 21 HOH HOH . E 3 HOH AAA 45 345 62 HOH HOH . E 3 HOH AAA 46 346 68 HOH HOH . E 3 HOH AAA 47 347 86 HOH HOH . E 3 HOH AAA 48 348 64 HOH HOH . E 3 HOH AAA 49 349 96 HOH HOH . E 3 HOH AAA 50 350 91 HOH HOH . E 3 HOH AAA 51 351 61 HOH HOH . E 3 HOH AAA 52 352 56 HOH HOH . E 3 HOH AAA 53 353 67 HOH HOH . E 3 HOH AAA 54 354 107 HOH HOH . E 3 HOH AAA 55 355 117 HOH HOH . E 3 HOH AAA 56 356 36 HOH HOH . E 3 HOH AAA 57 357 83 HOH HOH . F 3 HOH BBB 1 301 14 HOH HOH . F 3 HOH BBB 2 302 71 HOH HOH . F 3 HOH BBB 3 303 12 HOH HOH . F 3 HOH BBB 4 304 52 HOH HOH . F 3 HOH BBB 5 305 13 HOH HOH . F 3 HOH BBB 6 306 48 HOH HOH . F 3 HOH BBB 7 307 79 HOH HOH . F 3 HOH BBB 8 308 82 HOH HOH . F 3 HOH BBB 9 309 16 HOH HOH . F 3 HOH BBB 10 310 109 HOH HOH . F 3 HOH BBB 11 311 10 HOH HOH . F 3 HOH BBB 12 312 114 HOH HOH . F 3 HOH BBB 13 313 43 HOH HOH . F 3 HOH BBB 14 314 11 HOH HOH . F 3 HOH BBB 15 315 17 HOH HOH . F 3 HOH BBB 16 316 15 HOH HOH . F 3 HOH BBB 17 317 28 HOH HOH . F 3 HOH BBB 18 318 33 HOH HOH . F 3 HOH BBB 19 319 41 HOH HOH . F 3 HOH BBB 20 320 32 HOH HOH . F 3 HOH BBB 21 321 47 HOH HOH . F 3 HOH BBB 22 322 69 HOH HOH . F 3 HOH BBB 23 323 73 HOH HOH . F 3 HOH BBB 24 324 49 HOH HOH . F 3 HOH BBB 25 325 51 HOH HOH . F 3 HOH BBB 26 326 116 HOH HOH . F 3 HOH BBB 27 327 26 HOH HOH . F 3 HOH BBB 28 328 115 HOH HOH . F 3 HOH BBB 29 329 76 HOH HOH . F 3 HOH BBB 30 330 72 HOH HOH . F 3 HOH BBB 31 331 70 HOH HOH . F 3 HOH BBB 32 332 75 HOH HOH . F 3 HOH BBB 33 333 53 HOH HOH . F 3 HOH BBB 34 334 46 HOH HOH . F 3 HOH BBB 35 335 45 HOH HOH . F 3 HOH BBB 36 336 113 HOH HOH . F 3 HOH BBB 37 337 77 HOH HOH . F 3 HOH BBB 38 338 29 HOH HOH . F 3 HOH BBB 39 339 34 HOH HOH . F 3 HOH BBB 40 340 42 HOH HOH . F 3 HOH BBB 41 341 39 HOH HOH . F 3 HOH BBB 42 342 44 HOH HOH . F 3 HOH BBB 43 343 55 HOH HOH . F 3 HOH BBB 44 344 78 HOH HOH . F 3 HOH BBB 45 345 102 HOH HOH . F 3 HOH BBB 46 346 50 HOH HOH . F 3 HOH BBB 47 347 37 HOH HOH . F 3 HOH BBB 48 348 81 HOH HOH . F 3 HOH BBB 49 349 25 HOH HOH . F 3 HOH BBB 50 350 85 HOH HOH . F 3 HOH BBB 51 351 38 HOH HOH . F 3 HOH BBB 52 352 80 HOH HOH . F 3 HOH BBB 53 353 54 HOH HOH . F 3 HOH BBB 54 354 40 HOH HOH . F 3 HOH BBB 55 355 74 HOH HOH . F 3 HOH BBB 56 356 110 HOH HOH . F 3 HOH BBB 57 357 3 HOH HOH . F 3 HOH BBB 58 358 108 HOH HOH . F 3 HOH BBB 59 359 30 HOH HOH . F 3 HOH BBB 60 360 35 HOH HOH . F 3 HOH BBB 61 361 31 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 P DGP . . . D 2 -5.064 6.694 32.427 1 44.2 ? P DGP 201 BBB 1 HETATM 2 O OP1 DGP . . . D 2 -4.955 7.983 31.648 1 41.72 ? OP1 DGP 201 BBB 1 HETATM 3 O OP2 DGP . . . D 2 -5.79 6.928 33.734 1 44.35 ? OP2 DGP 201 BBB 1 HETATM 4 O OP3 DGP . . . D 2 -5.576 5.474 31.667 1 41.33 ? OP3 DGP 201 BBB 1 HETATM 5 O O5' DGP . . . D 2 -3.539 6.357 32.848 1 42.65 ? O5' DGP 201 BBB 1 HETATM 6 C C5' DGP . . . D 2 -2.41 6.469 31.983 1 43.56 ? C5' DGP 201 BBB 1 HETATM 7 C C4' DGP . . . D 2 -1.182 6.841 32.808 1 44.44 ? C4' DGP 201 BBB 1 HETATM 8 O O4' DGP . . . D 2 -0.034 6.323 32.139 1 45.51 ? O4' DGP 201 BBB 1 HETATM 9 C C3' DGP . . . D 2 -0.955 8.35 32.969 1 45.16 ? C3' DGP 201 BBB 1 HETATM 10 O O3' DGP . . . D 2 -1.163 8.849 34.298 1 46.04 ? O3' DGP 201 BBB 1 HETATM 11 C C2' DGP . . . D 2 0.486 8.599 32.582 1 45.27 ? C2' DGP 201 BBB 1 HETATM 12 C C1' DGP . . . D 2 1.06 7.207 32.374 1 45.77 ? C1' DGP 201 BBB 1 HETATM 13 N N9 DGP . . . D 2 2.007 7.216 31.243 1 45.59 ? N9 DGP 201 BBB 1 HETATM 14 C C8 DGP . . . D 2 1.789 7.612 29.976 1 45.44 ? C8 DGP 201 BBB 1 HETATM 15 N N7 DGP . . . D 2 2.922 7.477 29.241 1 44.84 ? N7 DGP 201 BBB 1 HETATM 16 C C5 DGP . . . D 2 3.883 6.984 30.042 1 45.75 ? C5 DGP 201 BBB 1 HETATM 17 C C6 DGP . . . D 2 5.316 6.59 29.926 1 45.92 ? C6 DGP 201 BBB 1 HETATM 18 O O6 DGP . . . D 2 5.948 6.682 28.847 1 45.97 ? O6 DGP 201 BBB 1 HETATM 19 N N1 DGP . . . D 2 5.919 6.122 31.036 1 46.19 ? N1 DGP 201 BBB 1 HETATM 20 C C2 DGP . . . D 2 5.266 6 32.221 1 44.82 ? C2 DGP 201 BBB 1 HETATM 21 N N2 DGP . . . D 2 5.916 5.528 33.301 1 43.78 ? N2 DGP 201 BBB 1 HETATM 22 N N3 DGP . . . D 2 3.971 6.342 32.397 1 46.09 ? N3 DGP 201 BBB 1 HETATM 23 C C4 DGP . . . D 2 3.255 6.822 31.362 1 45.9 ? C4 DGP 201 BBB 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 23 #