data_6ZXB # _model_server_result.job_id 24jsJ-p-vNKcy5q-xYfh2g _model_server_result.datetime_utc '2024-11-15 03:49:26' _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 6zxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 6ZXB # _exptl.entry_id 6ZXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" _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 108.77 _cell.angle_gamma 90 _cell.entry_id 6ZXB _cell.length_a 136.676 _cell.length_b 39.344 _cell.length_c 146.222 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZXB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _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 # 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 L 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 A OE2 GLU 7 A GLU 12 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 A OD1 ASP 8 A ASP 13 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc3 A OD2 ASP 51 A ASP 56 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc4 A OD2 ASP 169 A ASP 174 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc5 A OD1 ASP 169 A ASP 174 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc6 A O ILE 170 A ILE 175 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc7 A OE2 GLU 212 A GLU 217 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc8 A OE1 GLU 212 A GLU 217 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc9 A OE2 GLU 212 A GLU 217 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc10 A OE2 GLU 213 A GLU 218 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 C O2G GH3 . A GH3 301 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc12 C O2B GH3 . A GH3 301 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc13 E MG MG . A MG 303 1_555 R O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc14 E MG MG . A MG 303 1_555 R O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc15 B OE2 GLU 7 B GLU 12 1_555 M MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc16 B OD1 ASP 8 B ASP 13 1_555 M MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc17 B OD2 ASP 51 B ASP 56 1_555 M MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc18 B OD2 ASP 169 B ASP 174 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc19 B OD1 ASP 169 B ASP 174 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc20 B O ILE 170 B ILE 175 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc21 B OE2 GLU 212 B GLU 217 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc22 B OE1 GLU 212 B GLU 217 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc23 B OE1 GLU 213 B GLU 218 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc24 L O1A GH3 . B GH3 301 1_555 N MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc25 L O2G GH3 . B GH3 301 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc26 L O2B GH3 . B GH3 301 1_555 O MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id GH3 _chem_comp.mon_nstd_flag n _chem_comp.name "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G GH3 doub 92 n n PG O2G GH3 sing 93 n n PG O3G GH3 sing 94 n n PG O3B GH3 sing 95 n n O2G HOG2 GH3 sing 96 n n O3G HOG3 GH3 sing 97 n n O3B PB GH3 sing 98 n n PB O1B GH3 doub 99 n n PB O2B GH3 sing 100 n n PB O3A GH3 sing 101 n n O2B HOB2 GH3 sing 102 n n O3A PA GH3 sing 103 n n PA O1A GH3 doub 104 n n PA O2A GH3 sing 105 n n PA O5' GH3 sing 106 n n O2A HOA2 GH3 sing 107 n n O5' C5' GH3 sing 108 n n C5' C4' GH3 sing 109 n n C5' H5' GH3 sing 110 n n C5' "H5''" GH3 sing 111 n n C4' O4' GH3 sing 112 n n C4' C3' GH3 sing 113 n n C4' H4' GH3 sing 114 n n O4' C1' GH3 sing 115 n n C3' C2' GH3 sing 116 n n C3' "H3'2" GH3 sing 117 n n C3' H3' GH3 sing 118 n n C2' O2' GH3 sing 119 n n C2' C1' GH3 sing 120 n n C2' H2' GH3 sing 121 n n O2' HO2' GH3 sing 122 n n C1' N9 GH3 sing 123 n n C1' H1' GH3 sing 124 n n N9 C8 GH3 sing 125 n y N9 C4 GH3 sing 126 n y C8 N7 GH3 doub 127 n y C8 H8 GH3 sing 128 n n N7 C5 GH3 sing 129 n y C5 C6 GH3 sing 130 n n C5 C4 GH3 doub 131 n y C6 O6 GH3 doub 132 n n C6 N1 GH3 sing 133 n n N1 C2 GH3 sing 134 n n N1 HN1 GH3 sing 135 n n C2 N2 GH3 sing 136 n n C2 N3 GH3 doub 137 n n N2 HN21 GH3 sing 138 n n N2 HN22 GH3 sing 139 n n N3 C4 GH3 sing 140 n n # _atom_sites.entry_id 6ZXB _atom_sites.fract_transf_matrix[1][1] 0.007317 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002487 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025417 _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] 0.007223 _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 GH3 A 1 301 301 GH3 GH3 . D 3 MG A 1 302 401 MG MG . E 3 MG A 1 303 402 MG MG . F 3 MG A 1 304 403 MG MG . G 4 SO4 A 1 305 501 SO4 SO4 . H 4 SO4 A 1 306 502 SO4 SO4 . I 4 SO4 A 1 307 503 SO4 SO4 . J 4 SO4 A 1 308 504 SO4 SO4 . K 5 EDO A 1 309 601 EDO EDO . L 2 GH3 B 1 301 301 GH3 GH3 . M 3 MG B 1 302 401 MG MG . N 3 MG B 1 303 402 MG MG . O 3 MG B 1 304 403 MG MG . P 4 SO4 B 1 305 501 SO4 SO4 . Q 5 EDO B 1 306 601 EDO EDO . R 6 HOH A 1 401 33 HOH HOH . R 6 HOH A 2 402 36 HOH HOH . R 6 HOH A 3 403 30 HOH HOH . R 6 HOH A 4 404 6 HOH HOH . R 6 HOH A 5 405 15 HOH HOH . R 6 HOH A 6 406 5 HOH HOH . R 6 HOH A 7 407 40 HOH HOH . R 6 HOH A 8 408 44 HOH HOH . R 6 HOH A 9 409 35 HOH HOH . R 6 HOH A 10 410 45 HOH HOH . R 6 HOH A 11 411 39 HOH HOH . R 6 HOH A 12 412 10 HOH HOH . R 6 HOH A 13 413 59 HOH HOH . R 6 HOH A 14 414 3 HOH HOH . R 6 HOH A 15 415 13 HOH HOH . R 6 HOH A 16 416 47 HOH HOH . R 6 HOH A 17 417 31 HOH HOH . R 6 HOH A 18 418 38 HOH HOH . R 6 HOH A 19 419 23 HOH HOH . R 6 HOH A 20 420 42 HOH HOH . R 6 HOH A 21 421 41 HOH HOH . R 6 HOH A 22 422 37 HOH HOH . R 6 HOH A 23 423 32 HOH HOH . R 6 HOH A 24 424 8 HOH HOH . R 6 HOH A 25 425 43 HOH HOH . R 6 HOH A 26 426 18 HOH HOH . R 6 HOH A 27 427 46 HOH HOH . R 6 HOH A 28 428 34 HOH HOH . S 6 HOH B 1 401 14 HOH HOH . S 6 HOH B 2 402 17 HOH HOH . S 6 HOH B 3 403 50 HOH HOH . S 6 HOH B 4 404 52 HOH HOH . S 6 HOH B 5 405 1 HOH HOH . S 6 HOH B 6 406 58 HOH HOH . S 6 HOH B 7 407 55 HOH HOH . S 6 HOH B 8 408 48 HOH HOH . S 6 HOH B 9 409 2 HOH HOH . S 6 HOH B 10 410 9 HOH HOH . S 6 HOH B 11 411 16 HOH HOH . S 6 HOH B 12 412 20 HOH HOH . S 6 HOH B 13 413 7 HOH HOH . S 6 HOH B 14 414 51 HOH HOH . S 6 HOH B 15 415 56 HOH HOH . S 6 HOH B 16 416 53 HOH HOH . S 6 HOH B 17 417 57 HOH HOH . S 6 HOH B 18 418 54 HOH HOH . S 6 HOH B 19 419 60 HOH HOH . S 6 HOH B 20 420 61 HOH HOH . S 6 HOH B 21 421 25 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 PG GH3 . . . L 2 -13.85 0.149 46.234 1 52.1 ? PG GH3 301 B 1 HETATM 2 O O1G GH3 . . . L 2 -14.216 -1.297 46.025 1 52.11 ? O1G GH3 301 B 1 HETATM 3 O O2G GH3 . . . L 2 -12.402 0.328 46.68 1 48.63 ? O2G GH3 301 B 1 HETATM 4 O O3G GH3 . . . L 2 -14.764 0.884 47.123 1 53.71 ? O3G GH3 301 B 1 HETATM 5 O O3B GH3 . . . L 2 -13.987 0.923 44.78 1 55.07 ? O3B GH3 301 B 1 HETATM 6 P PB GH3 . . . L 2 -12.919 1.822 43.972 1 56.79 ? PB GH3 301 B 1 HETATM 7 O O1B GH3 . . . L 2 -13.523 2.565 42.84 1 60.4 ? O1B GH3 301 B 1 HETATM 8 O O2B GH3 . . . L 2 -12.147 2.621 45.019 1 52.47 ? O2B GH3 301 B 1 HETATM 9 O O3A GH3 . . . L 2 -12.057 0.604 43.404 1 65.24 ? O3A GH3 301 B 1 HETATM 10 P PA GH3 . . . L 2 -10.98 0.643 42.223 1 86.13 ? PA GH3 301 B 1 HETATM 11 O O1A GH3 . . . L 2 -9.905 -0.369 42.519 1 85.04 ? O1A GH3 301 B 1 HETATM 12 O O2A GH3 . . . L 2 -11.774 0.614 40.947 1 82.26 ? O2A GH3 301 B 1 HETATM 13 O O5' GH3 . . . L 2 -10.311 2.103 42.345 1 77.53 ? O5' GH3 301 B 1 HETATM 14 C C5' GH3 . . . L 2 -9.347 2.396 41.286 1 74.63 ? C5' GH3 301 B 1 HETATM 15 C C4' GH3 . . . L 2 -9.685 3.684 40.57 1 69.62 ? C4' GH3 301 B 1 HETATM 16 O O4' GH3 . . . L 2 -8.603 4.617 40.852 1 67.35 ? O4' GH3 301 B 1 HETATM 17 C C3' GH3 . . . L 2 -9.77 3.611 39.033 1 67.56 ? C3' GH3 301 B 1 HETATM 18 C C2' GH3 . . . L 2 -8.349 4.026 38.626 1 67.37 ? C2' GH3 301 B 1 HETATM 19 O O2' GH3 . . . L 2 -8.233 4.498 37.302 1 71 ? O2' GH3 301 B 1 HETATM 20 C C1' GH3 . . . L 2 -8.112 5.141 39.642 1 63.04 ? C1' GH3 301 B 1 HETATM 21 N N9 GH3 . . . L 2 -6.726 5.562 39.822 1 55.87 ? N9 GH3 301 B 1 HETATM 22 C C8 GH3 . . . L 2 -5.609 4.756 39.874 1 54.37 ? C8 GH3 301 B 1 HETATM 23 N N7 GH3 . . . L 2 -4.489 5.419 40.01 1 50.26 ? N7 GH3 301 B 1 HETATM 24 C C5 GH3 . . . L 2 -4.887 6.75 40.02 1 50.34 ? C5 GH3 301 B 1 HETATM 25 C C6 GH3 . . . L 2 -4.115 7.932 40.134 1 49.95 ? C6 GH3 301 B 1 HETATM 26 O O6 GH3 . . . L 2 -2.893 8.04 40.23 1 47.91 ? O6 GH3 301 B 1 HETATM 27 N N1 GH3 . . . L 2 -4.898 9.083 40.08 1 49.72 ? N1 GH3 301 B 1 HETATM 28 C C2 GH3 . . . L 2 -6.253 9.102 39.936 1 49.88 ? C2 GH3 301 B 1 HETATM 29 N N2 GH3 . . . L 2 -6.818 10.318 39.936 1 50.2 ? N2 GH3 301 B 1 HETATM 30 N N3 GH3 . . . L 2 -6.997 7.997 39.855 1 51.29 ? N3 GH3 301 B 1 HETATM 31 C C4 GH3 . . . L 2 -6.254 6.859 39.894 1 52.37 ? C4 GH3 301 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #