data_6K9A # _model_server_result.job_id jw-i8R2WKFj0oDOgqkmr2A _model_server_result.datetime_utc '2024-11-28 10:24:38' _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 6k9a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 6K9A # _exptl.entry_id 6K9A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 92.96 _cell.angle_gamma 90 _cell.entry_id 6K9A _cell.length_a 119.114 _cell.length_b 58.007 _cell.length_c 47.135 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6K9A _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 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,E _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 3 _struct_asym.id D _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 O THR 70 A THR 69 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc2 A O ASP 73 A ASP 72 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? metalc ? metalc3 A OD1 ASP 73 A ASP 72 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc4 A O PHE 75 A PHE 74 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc5 A OD1 ASP 79 A ASP 78 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc6 A OD2 ASP 79 A ASP 78 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc7 A OD1 ASP 81 A ASP 80 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc8 A O GLU 143 A GLU 142 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc9 B CA CA . A CA 401 1_555 D O1A DGT . A DGT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc10 B CA CA . A CA 401 1_555 D O2G DGT . A DGT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc11 B CA CA . A CA 401 1_555 D O2B DGT . A DGT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 B CA CA . A CA 401 1_555 E O HOH . A HOH 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc13 C CA CA . A CA 402 1_555 E O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id DGT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G DGT sing 83 n n PG O2G DGT sing 84 n n O1G HO1G DGT sing 85 n n O2G HO2G DGT sing 86 n n O3G PG DGT doub 87 n n O3B PG DGT sing 88 n n PB O3B DGT sing 89 n n PB O1B DGT sing 90 n n PB O3A DGT sing 91 n n O1B HO1B DGT sing 92 n n O2B PB DGT doub 93 n n PA O3A DGT sing 94 n n PA O1A DGT sing 95 n n O1A HO1A DGT sing 96 n n O2A PA DGT doub 97 n n O5' PA DGT sing 98 n n O5' C5' DGT sing 99 n n C5' H5' DGT sing 100 n n C5' "H5'A" DGT sing 101 n n C4' C5' DGT sing 102 n n C4' H4' DGT sing 103 n n O4' C4' DGT sing 104 n n C3' C4' DGT sing 105 n n C3' O3' DGT sing 106 n n C3' H3' DGT sing 107 n n O3' HO3' DGT sing 108 n n C2' C3' DGT sing 109 n n C2' C1' DGT sing 110 n n C2' H2' DGT sing 111 n n C2' "H2'A" DGT sing 112 n n C1' O4' DGT sing 113 n n C1' H1' DGT sing 114 n n N9 C1' DGT sing 115 n n N9 C4 DGT sing 116 n y C8 N9 DGT sing 117 n y C8 H8 DGT sing 118 n n N7 C8 DGT doub 119 n y N7 C5 DGT sing 120 n y C5 C6 DGT sing 121 n n C5 C4 DGT doub 122 n y C6 N1 DGT sing 123 n n O6 C6 DGT doub 124 n n N1 C2 DGT sing 125 n n C2 N3 DGT doub 126 n n C2 N2 DGT sing 127 n n N2 HN2 DGT sing 128 n n N2 HN2A DGT sing 129 n n C4 N3 DGT sing 130 n n N1 H16 DGT sing 131 n n # _atom_sites.entry_id 6K9A _atom_sites.fract_transf_matrix[1][1] 0.008395 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000434 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017239 _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] 0.021244 _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 CA A 1 401 1 CA CA . C 2 CA A 1 402 2 CA CA . D 3 DGT A 1 403 1 DGT GTP . E 4 HOH A 1 501 44 HOH HOH . E 4 HOH A 2 502 43 HOH HOH . E 4 HOH A 3 503 33 HOH HOH . E 4 HOH A 4 504 47 HOH HOH . E 4 HOH A 5 505 68 HOH HOH . E 4 HOH A 6 506 24 HOH HOH . E 4 HOH A 7 507 42 HOH HOH . E 4 HOH A 8 508 35 HOH HOH . E 4 HOH A 9 509 46 HOH HOH . E 4 HOH A 10 510 41 HOH HOH . E 4 HOH A 11 511 15 HOH HOH . E 4 HOH A 12 512 61 HOH HOH . E 4 HOH A 13 513 28 HOH HOH . E 4 HOH A 14 514 27 HOH HOH . E 4 HOH A 15 515 69 HOH HOH . E 4 HOH A 16 516 20 HOH HOH . E 4 HOH A 17 517 5 HOH HOH . E 4 HOH A 18 518 65 HOH HOH . E 4 HOH A 19 519 59 HOH HOH . E 4 HOH A 20 520 3 HOH HOH . E 4 HOH A 21 521 34 HOH HOH . E 4 HOH A 22 522 56 HOH HOH . E 4 HOH A 23 523 6 HOH HOH . E 4 HOH A 24 524 26 HOH HOH . E 4 HOH A 25 525 22 HOH HOH . E 4 HOH A 26 526 10 HOH HOH . E 4 HOH A 27 527 67 HOH HOH . E 4 HOH A 28 528 32 HOH HOH . E 4 HOH A 29 529 14 HOH HOH . E 4 HOH A 30 530 9 HOH HOH . E 4 HOH A 31 531 60 HOH HOH . E 4 HOH A 32 532 57 HOH HOH . E 4 HOH A 33 533 52 HOH HOH . E 4 HOH A 34 534 63 HOH HOH . E 4 HOH A 35 535 12 HOH HOH . E 4 HOH A 36 536 31 HOH HOH . E 4 HOH A 37 537 54 HOH HOH . E 4 HOH A 38 538 13 HOH HOH . E 4 HOH A 39 539 49 HOH HOH . E 4 HOH A 40 540 30 HOH HOH . E 4 HOH A 41 541 53 HOH HOH . E 4 HOH A 42 542 48 HOH HOH . E 4 HOH A 43 543 4 HOH HOH . E 4 HOH A 44 544 37 HOH HOH . E 4 HOH A 45 545 16 HOH HOH . E 4 HOH A 46 546 8 HOH HOH . E 4 HOH A 47 547 11 HOH HOH . E 4 HOH A 48 548 17 HOH HOH . E 4 HOH A 49 549 23 HOH HOH . E 4 HOH A 50 550 29 HOH HOH . E 4 HOH A 51 551 64 HOH HOH . E 4 HOH A 52 552 18 HOH HOH . E 4 HOH A 53 553 55 HOH HOH . E 4 HOH A 54 554 62 HOH HOH . E 4 HOH A 55 555 70 HOH HOH . E 4 HOH A 56 556 51 HOH HOH . E 4 HOH A 57 557 45 HOH HOH . E 4 HOH A 58 558 66 HOH HOH . E 4 HOH A 59 559 36 HOH HOH . E 4 HOH A 60 560 58 HOH HOH . E 4 HOH A 61 561 50 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 DGT . . . D 3 -9.888 8.23 24.376 1 28.35 ? PG DGT 403 A 1 HETATM 2 O O1G DGT . . . D 3 -8.828 8.951 23.576 1 24.75 ? O1G DGT 403 A 1 HETATM 3 O O2G DGT . . . D 3 -11.182 9.003 24.33 1 38.21 ? O2G DGT 403 A 1 HETATM 4 O O3G DGT . . . D 3 -9.435 8.103 25.809 1 17.26 ? O3G DGT 403 A 1 HETATM 5 O O3B DGT . . . D 3 -10.099 6.755 23.76 1 28.02 ? O3B DGT 403 A 1 HETATM 6 P PB DGT . . . D 3 -11.403 6.299 22.924 1 19.26 ? PB DGT 403 A 1 HETATM 7 O O1B DGT . . . D 3 -11.244 4.826 22.637 1 18.64 ? O1B DGT 403 A 1 HETATM 8 O O2B DGT . . . D 3 -12.678 6.533 23.694 1 16.56 ? O2B DGT 403 A 1 HETATM 9 O O3A DGT . . . D 3 -11.351 7.119 21.532 1 16.49 ? O3A DGT 403 A 1 HETATM 10 P PA DGT . . . D 3 -12.461 8.187 21.039 1 18.27 ? PA DGT 403 A 1 HETATM 11 O O1A DGT . . . D 3 -13.206 8.798 22.199 1 16.7 ? O1A DGT 403 A 1 HETATM 12 O O2A DGT . . . D 3 -11.795 9.272 20.229 1 20.97 ? O2A DGT 403 A 1 HETATM 13 O O5' DGT . . . D 3 -13.488 7.371 20.102 1 18.23 ? O5' DGT 403 A 1 HETATM 14 C C5' DGT . . . D 3 -14.51 6.555 20.631 1 18.24 ? C5' DGT 403 A 1 HETATM 15 C C4' DGT . . . D 3 -14.468 5.198 19.941 1 16.38 ? C4' DGT 403 A 1 HETATM 16 O O4' DGT . . . D 3 -14.55 5.363 18.54 1 16.49 ? O4' DGT 403 A 1 HETATM 17 C C3' DGT . . . D 3 -13.163 4.47 20.193 1 16.24 ? C3' DGT 403 A 1 HETATM 18 O O3' DGT . . . D 3 -13.271 3.601 21.295 1 20.51 ? O3' DGT 403 A 1 HETATM 19 C C2' DGT . . . D 3 -12.916 3.696 18.914 1 16.25 ? C2' DGT 403 A 1 HETATM 20 C C1' DGT . . . D 3 -13.753 4.409 17.862 1 16.44 ? C1' DGT 403 A 1 HETATM 21 N N9 DGT . . . D 3 -12.84 5.089 16.926 1 16.57 ? N9 DGT 403 A 1 HETATM 22 C C8 DGT . . . D 3 -11.905 6.03 17.27 1 18.34 ? C8 DGT 403 A 1 HETATM 23 N N7 DGT . . . D 3 -11.255 6.426 16.153 1 19.77 ? N7 DGT 403 A 1 HETATM 24 C C5 DGT . . . D 3 -11.762 5.753 15.098 1 18.96 ? C5 DGT 403 A 1 HETATM 25 C C6 DGT . . . D 3 -11.459 5.782 13.744 1 24.75 ? C6 DGT 403 A 1 HETATM 26 O O6 DGT . . . D 3 -10.577 6.529 13.326 1 29.07 ? O6 DGT 403 A 1 HETATM 27 N N1 DGT . . . D 3 -12.152 4.97 12.871 1 23.68 ? N1 DGT 403 A 1 HETATM 28 C C2 DGT . . . D 3 -13.14 4.136 13.352 1 20.09 ? C2 DGT 403 A 1 HETATM 29 N N2 DGT . . . D 3 -13.808 3.352 12.513 1 22.08 ? N2 DGT 403 A 1 HETATM 30 N N3 DGT . . . D 3 -13.436 4.113 14.701 1 19.38 ? N3 DGT 403 A 1 HETATM 31 C C4 DGT . . . D 3 -12.76 4.908 15.566 1 17.6 ? C4 DGT 403 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 806 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #