data_6JOQ # _model_server_result.job_id H3-57Xk1LaH4XpHra529QQ _model_server_result.datetime_utc '2024-11-24 08:55:18' _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 6joq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6JOQ # _exptl.entry_id 6JOQ _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 "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 95.48 _cell.angle_gamma 90 _cell.entry_id 6JOQ _cell.length_a 134.36 _cell.length_b 55.388 _cell.length_c 50.774 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JOQ _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 2 _struct_asym.id B _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 89 A THR 69 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc2 A O ASP 92 A ASP 72 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc3 A OD1 ASP 92 A ASP 72 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc4 A O PHE 94 A PHE 74 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc5 A OD1 ASP 98 A ASP 78 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc6 A OD1 ASP 100 A ASP 80 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc7 A O GLU 162 A GLU 142 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc8 B O1G DGT . A DGT 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc9 B O1B DGT . A DGT 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc10 B O1A DGT . A DGT 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? # _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 6JOQ _atom_sites.fract_transf_matrix[1][1] 0.007443 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000714 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018054 _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] 0.019785 _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 DGT A 1 401 1 DGT DGT . C 3 MG A 1 402 1 MG MG . D 3 MG A 1 403 2 MG MG . E 4 HOH A 1 501 45 HOH HOH . E 4 HOH A 2 502 9 HOH HOH . E 4 HOH A 3 503 4 HOH HOH . E 4 HOH A 4 504 36 HOH HOH . E 4 HOH A 5 505 12 HOH HOH . E 4 HOH A 6 506 30 HOH HOH . E 4 HOH A 7 507 33 HOH HOH . E 4 HOH A 8 508 40 HOH HOH . E 4 HOH A 9 509 6 HOH HOH . E 4 HOH A 10 510 32 HOH HOH . E 4 HOH A 11 511 63 HOH HOH . E 4 HOH A 12 512 19 HOH HOH . E 4 HOH A 13 513 52 HOH HOH . E 4 HOH A 14 514 31 HOH HOH . E 4 HOH A 15 515 65 HOH HOH . E 4 HOH A 16 516 26 HOH HOH . E 4 HOH A 17 517 17 HOH HOH . E 4 HOH A 18 518 60 HOH HOH . E 4 HOH A 19 519 34 HOH HOH . E 4 HOH A 20 520 5 HOH HOH . E 4 HOH A 21 521 43 HOH HOH . E 4 HOH A 22 522 20 HOH HOH . E 4 HOH A 23 523 29 HOH HOH . E 4 HOH A 24 524 2 HOH HOH . E 4 HOH A 25 525 1 HOH HOH . E 4 HOH A 26 526 59 HOH HOH . E 4 HOH A 27 527 13 HOH HOH . E 4 HOH A 28 528 35 HOH HOH . E 4 HOH A 29 529 3 HOH HOH . E 4 HOH A 30 530 69 HOH HOH . E 4 HOH A 31 531 23 HOH HOH . E 4 HOH A 32 532 50 HOH HOH . E 4 HOH A 33 533 7 HOH HOH . E 4 HOH A 34 534 16 HOH HOH . E 4 HOH A 35 535 41 HOH HOH . E 4 HOH A 36 536 21 HOH HOH . E 4 HOH A 37 537 10 HOH HOH . E 4 HOH A 38 538 46 HOH HOH . E 4 HOH A 39 539 47 HOH HOH . E 4 HOH A 40 540 8 HOH HOH . E 4 HOH A 41 541 25 HOH HOH . E 4 HOH A 42 542 24 HOH HOH . E 4 HOH A 43 543 11 HOH HOH . E 4 HOH A 44 544 73 HOH HOH . E 4 HOH A 45 545 42 HOH HOH . E 4 HOH A 46 546 71 HOH HOH . E 4 HOH A 47 547 37 HOH HOH . E 4 HOH A 48 548 56 HOH HOH . E 4 HOH A 49 549 18 HOH HOH . E 4 HOH A 50 550 22 HOH HOH . E 4 HOH A 51 551 54 HOH HOH . E 4 HOH A 52 552 14 HOH HOH . E 4 HOH A 53 553 68 HOH HOH . E 4 HOH A 54 554 48 HOH HOH . E 4 HOH A 55 555 66 HOH HOH . E 4 HOH A 56 556 58 HOH HOH . E 4 HOH A 57 557 28 HOH HOH . E 4 HOH A 58 558 27 HOH HOH . E 4 HOH A 59 559 39 HOH HOH . E 4 HOH A 60 560 15 HOH HOH . E 4 HOH A 61 561 57 HOH HOH . E 4 HOH A 62 562 51 HOH HOH . E 4 HOH A 63 563 44 HOH HOH . E 4 HOH A 64 564 64 HOH HOH . E 4 HOH A 65 565 38 HOH HOH . E 4 HOH A 66 566 70 HOH HOH . E 4 HOH A 67 567 53 HOH HOH . E 4 HOH A 68 568 72 HOH HOH . E 4 HOH A 69 569 67 HOH HOH . E 4 HOH A 70 570 62 HOH HOH . E 4 HOH A 71 571 55 HOH HOH . E 4 HOH A 72 572 49 HOH HOH . E 4 HOH A 73 573 61 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 . . . B 2 -14.881 -3.136 28.329 1 41.68 ? PG DGT 401 A 1 HETATM 2 O O1G DGT . . . B 2 -16.08 -2.3 28.334 1 38.75 ? O1G DGT 401 A 1 HETATM 3 O O2G DGT . . . B 2 -14.49 -3.234 29.727 1 29.05 ? O2G DGT 401 A 1 HETATM 4 O O3G DGT . . . B 2 -13.871 -2.304 27.678 1 41.46 ? O3G DGT 401 A 1 HETATM 5 O O3B DGT . . . B 2 -15.091 -4.613 27.637 1 42.23 ? O3B DGT 401 A 1 HETATM 6 P PB DGT . . . B 2 -16.388 -4.915 26.682 1 35.4 ? PB DGT 401 A 1 HETATM 7 O O1B DGT . . . B 2 -17.626 -4.76 27.438 1 35.74 ? O1B DGT 401 A 1 HETATM 8 O O2B DGT . . . B 2 -16.441 -6.313 26.274 1 38.53 ? O2B DGT 401 A 1 HETATM 9 O O3A DGT . . . B 2 -16.311 -3.911 25.388 1 29.7 ? O3A DGT 401 A 1 HETATM 10 P PA DGT . . . B 2 -17.415 -2.746 25.045 1 33.14 ? PA DGT 401 A 1 HETATM 11 O O1A DGT . . . B 2 -18.133 -2.308 26.238 1 31.79 ? O1A DGT 401 A 1 HETATM 12 O O2A DGT . . . B 2 -16.768 -1.518 24.602 1 27.13 ? O2A DGT 401 A 1 HETATM 13 O O5' DGT . . . B 2 -18.458 -3.282 23.902 1 34.03 ? O5' DGT 401 A 1 HETATM 14 C C5' DGT . . . B 2 -19.484 -4.114 24.344 1 37.23 ? C5' DGT 401 A 1 HETATM 15 C C4' DGT . . . B 2 -19.477 -5.396 23.52 1 32.48 ? C4' DGT 401 A 1 HETATM 16 O O4' DGT . . . B 2 -19.825 -5.117 22.163 1 30.29 ? O4' DGT 401 A 1 HETATM 17 C C3' DGT . . . B 2 -18.13 -6.016 23.475 1 28.44 ? C3' DGT 401 A 1 HETATM 18 O O3' DGT . . . B 2 -17.987 -6.936 24.583 1 24.95 ? O3' DGT 401 A 1 HETATM 19 C C2' DGT . . . B 2 -18.028 -6.734 22.184 1 28.42 ? C2' DGT 401 A 1 HETATM 20 C C1' DGT . . . B 2 -19.377 -6.377 21.555 1 35.07 ? C1' DGT 401 A 1 HETATM 21 N N9 DGT . . . B 2 -19.435 -6.329 20.14 1 47.47 ? N9 DGT 401 A 1 HETATM 22 C C8 DGT . . . B 2 -20.472 -6.872 19.614 1 50.99 ? C8 DGT 401 A 1 HETATM 23 N N7 DGT . . . B 2 -20.384 -6.741 18.252 1 51.11 ? N7 DGT 401 A 1 HETATM 24 C C5 DGT . . . B 2 -19.068 -6.003 18.073 1 51.22 ? C5 DGT 401 A 1 HETATM 25 C C6 DGT . . . B 2 -18.276 -5.503 16.937 1 59.16 ? C6 DGT 401 A 1 HETATM 26 O O6 DGT . . . B 2 -18.736 -5.679 15.627 1 66.36 ? O6 DGT 401 A 1 HETATM 27 N N1 DGT . . . B 2 -17.089 -4.863 17.169 1 59.74 ? N1 DGT 401 A 1 HETATM 28 C C2 DGT . . . B 2 -16.635 -4.689 18.508 1 60.63 ? C2 DGT 401 A 1 HETATM 29 N N2 DGT . . . B 2 -15.371 -4.004 18.704 1 66.85 ? N2 DGT 401 A 1 HETATM 30 N N3 DGT . . . B 2 -17.32 -5.127 19.612 1 56.21 ? N3 DGT 401 A 1 HETATM 31 C C4 DGT . . . B 2 -18.537 -5.788 19.422 1 49.46 ? C4 DGT 401 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #