data_6RP0 # _model_server_result.job_id sj9Bkk1pcymUQEBd4SIZPg _model_server_result.datetime_utc '2024-11-18 14:54:18' _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 6rp0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6RP0 # _exptl.entry_id 6RP0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 200.241 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one _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 90 _cell.angle_gamma 90 _cell.entry_id 6RP0 _cell.length_a 92.18 _cell.length_b 92.18 _cell.length_c 139.726 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RP0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 4 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 245 A CYS 245 1_555 A SG CYS 265 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 B O3' DT 6 B DT 6 1_555 B P 3DR 7 B 3DR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale2 B O3' 3DR 7 B 3DR 7 1_555 B P DT 8 B DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? hydrog WATSON-CRICK hydrog1 B N3 DT 2 B DT 2 1_555 C N1 DA 14 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 2 B DT 2 1_555 C N6 DA 14 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DC 3 B DC 3 1_555 C N1 DG 13 C DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 DC 3 B DC 3 1_555 C O6 DG 13 C DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 DC 3 B DC 3 1_555 C N2 DG 13 C DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 4 B DT 4 1_555 C N1 DA 12 C DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 4 B DT 4 1_555 C N6 DA 12 C DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 5 B DT 5 1_555 C N1 DA 11 C DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 5 B DT 5 1_555 C N6 DA 11 C DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DT 6 B DT 6 1_555 C N1 DA 10 C DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 DT 6 B DT 6 1_555 C N6 DA 10 C DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DT 8 B DT 8 1_555 C N1 DA 8 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O4 DT 8 B DT 8 1_555 C N6 DA 8 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 9 B DT 9 1_555 C N1 DA 7 C DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 9 B DT 9 1_555 C N6 DA 7 C DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 10 B DT 10 1_555 C N1 DA 6 C DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 10 B DT 10 1_555 C N6 DA 6 C DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 11 B DC 11 1_555 C N1 DG 5 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 11 B DC 11 1_555 C O6 DG 5 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 11 B DC 11 1_555 C N2 DG 5 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DT 12 B DT 12 1_555 C N1 DA 4 C DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O4 DT 12 B DT 12 1_555 C N6 DA 4 C DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 13 B DC 13 1_555 C N1 DG 3 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 13 B DC 13 1_555 C O6 DG 3 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 13 B DC 13 1_555 C N2 DG 3 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N1 DG 14 B DG 14 1_555 C N3 DC 2 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N2 DG 14 B DG 14 1_555 C O2 DC 2 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O6 DG 14 B DG 14 1_555 C N4 DC 2 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog29 C N6 DA 10 C DA 24 1_555 D O4 DT 8 F DT 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog30 C N7 DA 10 C DA 24 1_555 D N3 DT 8 F DT 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog31 C N6 DA 11 C DA 25 1_555 D O4 DT 9 F DT 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog32 C N7 DA 11 C DA 25 1_555 D N3 DT 9 F DT 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog33 C N6 DA 12 C DA 26 1_555 D O4 DT 10 F DT 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog HOOGSTEEN hydrog34 C N7 DA 12 C DA 26 1_555 D N3 DT 10 F DT 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog35 C O6 DG 13 C DG 27 1_555 D N4 DC 11 F DC 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog36 C N7 DA 14 C DA 28 1_555 D N3 DT 12 F DT 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C5 H4 N4 O S2' _chem_comp.formula_weight 200.241 _chem_comp.id 5JL _chem_comp.mon_nstd_flag . _chem_comp.name 2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one _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 O6 C6 5JL doub 24 n n N7 C5 5JL sing 25 n n N7 C8 5JL sing 26 n n C6 C5 5JL sing 27 n n C6 N1 5JL sing 28 n n S8 C8 5JL doub 29 n n C5 C4 5JL doub 30 n n C8 N9 5JL sing 31 n n N1 C2 5JL sing 32 n n C4 N9 5JL sing 33 n n C4 N3 5JL sing 34 n n C2 N3 5JL sing 35 n n C2 S2 5JL doub 36 n n N1 H1 5JL sing 37 n n N3 H2 5JL sing 38 n n N7 H3 5JL sing 39 n n N9 H4 5JL sing 40 n n # _atom_sites.entry_id 6RP0 _atom_sites.fract_transf_matrix[1][1] 0.010848 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010848 _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] 0.007157 _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 4 5JL A 1 301 1 5JL 5JL . F 5 GOL A 1 302 1 GOL GOL . G 6 HOH A 1 401 125 HOH HOH . G 6 HOH A 2 402 11 HOH HOH . G 6 HOH A 3 403 35 HOH HOH . G 6 HOH A 4 404 89 HOH HOH . G 6 HOH A 5 405 84 HOH HOH . G 6 HOH A 6 406 105 HOH HOH . G 6 HOH A 7 407 81 HOH HOH . G 6 HOH A 8 408 40 HOH HOH . G 6 HOH A 9 409 100 HOH HOH . G 6 HOH A 10 410 62 HOH HOH . G 6 HOH A 11 411 47 HOH HOH . G 6 HOH A 12 412 21 HOH HOH . G 6 HOH A 13 413 104 HOH HOH . G 6 HOH A 14 414 1 HOH HOH . G 6 HOH A 15 415 6 HOH HOH . G 6 HOH A 16 416 14 HOH HOH . G 6 HOH A 17 417 3 HOH HOH . G 6 HOH A 18 418 122 HOH HOH . G 6 HOH A 19 419 4 HOH HOH . G 6 HOH A 20 420 69 HOH HOH . G 6 HOH A 21 421 88 HOH HOH . G 6 HOH A 22 422 9 HOH HOH . G 6 HOH A 23 423 13 HOH HOH . G 6 HOH A 24 424 33 HOH HOH . G 6 HOH A 25 425 38 HOH HOH . G 6 HOH A 26 426 7 HOH HOH . G 6 HOH A 27 427 17 HOH HOH . G 6 HOH A 28 428 75 HOH HOH . G 6 HOH A 29 429 110 HOH HOH . G 6 HOH A 30 430 2 HOH HOH . G 6 HOH A 31 431 16 HOH HOH . G 6 HOH A 32 432 80 HOH HOH . G 6 HOH A 33 433 93 HOH HOH . G 6 HOH A 34 434 86 HOH HOH . G 6 HOH A 35 435 32 HOH HOH . G 6 HOH A 36 436 15 HOH HOH . G 6 HOH A 37 437 46 HOH HOH . G 6 HOH A 38 438 24 HOH HOH . G 6 HOH A 39 439 82 HOH HOH . G 6 HOH A 40 440 30 HOH HOH . G 6 HOH A 41 441 41 HOH HOH . G 6 HOH A 42 442 10 HOH HOH . G 6 HOH A 43 443 52 HOH HOH . G 6 HOH A 44 444 96 HOH HOH . G 6 HOH A 45 445 8 HOH HOH . G 6 HOH A 46 446 106 HOH HOH . G 6 HOH A 47 447 68 HOH HOH . G 6 HOH A 48 448 63 HOH HOH . G 6 HOH A 49 449 22 HOH HOH . G 6 HOH A 50 450 27 HOH HOH . G 6 HOH A 51 451 92 HOH HOH . G 6 HOH A 52 452 19 HOH HOH . G 6 HOH A 53 453 64 HOH HOH . G 6 HOH A 54 454 70 HOH HOH . G 6 HOH A 55 455 39 HOH HOH . G 6 HOH A 56 456 66 HOH HOH . G 6 HOH A 57 457 71 HOH HOH . G 6 HOH A 58 458 20 HOH HOH . G 6 HOH A 59 459 44 HOH HOH . G 6 HOH A 60 460 29 HOH HOH . G 6 HOH A 61 461 54 HOH HOH . G 6 HOH A 62 462 49 HOH HOH . G 6 HOH A 63 463 112 HOH HOH . G 6 HOH A 64 464 23 HOH HOH . G 6 HOH A 65 465 50 HOH HOH . G 6 HOH A 66 466 114 HOH HOH . G 6 HOH A 67 467 51 HOH HOH . G 6 HOH A 68 468 72 HOH HOH . G 6 HOH A 69 469 53 HOH HOH . G 6 HOH A 70 470 43 HOH HOH . G 6 HOH A 71 471 113 HOH HOH . G 6 HOH A 72 472 60 HOH HOH . G 6 HOH A 73 473 65 HOH HOH . G 6 HOH A 74 474 79 HOH HOH . G 6 HOH A 75 475 90 HOH HOH . G 6 HOH A 76 476 77 HOH HOH . G 6 HOH A 77 477 95 HOH HOH . G 6 HOH A 78 478 111 HOH HOH . G 6 HOH A 79 479 36 HOH HOH . G 6 HOH A 80 480 42 HOH HOH . G 6 HOH A 81 481 97 HOH HOH . G 6 HOH A 82 482 34 HOH HOH . G 6 HOH A 83 483 121 HOH HOH . G 6 HOH A 84 484 25 HOH HOH . G 6 HOH A 85 485 12 HOH HOH . G 6 HOH A 86 486 73 HOH HOH . G 6 HOH A 87 487 28 HOH HOH . G 6 HOH A 88 488 108 HOH HOH . G 6 HOH A 89 489 119 HOH HOH . G 6 HOH A 90 490 99 HOH HOH . G 6 HOH A 91 491 87 HOH HOH . G 6 HOH A 92 492 107 HOH HOH . G 6 HOH A 93 493 120 HOH HOH . G 6 HOH A 94 494 58 HOH HOH . G 6 HOH A 95 495 124 HOH HOH . G 6 HOH A 96 496 123 HOH HOH . G 6 HOH A 97 497 61 HOH HOH . G 6 HOH A 98 498 116 HOH HOH . G 6 HOH A 99 499 117 HOH HOH . G 6 HOH A 100 500 101 HOH HOH . G 6 HOH A 101 501 76 HOH HOH . G 6 HOH A 102 502 115 HOH HOH . G 6 HOH A 103 503 45 HOH HOH . G 6 HOH A 104 504 48 HOH HOH . G 6 HOH A 105 505 91 HOH HOH . G 6 HOH A 106 506 59 HOH HOH . G 6 HOH A 107 507 74 HOH HOH . G 6 HOH A 108 508 67 HOH HOH . G 6 HOH A 109 509 83 HOH HOH . G 6 HOH A 110 510 103 HOH HOH . G 6 HOH A 111 511 109 HOH HOH . H 6 HOH B 1 101 18 HOH HOH . H 6 HOH B 2 102 31 HOH HOH . H 6 HOH B 3 103 26 HOH HOH . H 6 HOH B 4 104 5 HOH HOH . H 6 HOH B 5 105 57 HOH HOH . H 6 HOH B 6 106 56 HOH HOH . H 6 HOH B 7 107 98 HOH HOH . H 6 HOH B 8 108 126 HOH HOH . H 6 HOH B 9 109 55 HOH HOH . I 6 HOH C 1 101 118 HOH HOH . I 6 HOH C 2 102 94 HOH HOH . I 6 HOH C 3 103 37 HOH HOH . I 6 HOH C 4 104 85 HOH HOH . J 6 HOH F 1 201 102 HOH HOH . J 6 HOH F 2 202 78 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 C C4 5JL . . . E 4 -1.967 23.785 -21.46 1 38.45 ? C4 5JL 301 A 1 HETATM 2 C C5 5JL . . . E 4 -2.857 22.728 -21.44 1 38.04 ? C5 5JL 301 A 1 HETATM 3 C C6 5JL . . . E 4 -4.066 22.874 -22.077 1 39.16 ? C6 5JL 301 A 1 HETATM 4 C C8 5JL . . . E 4 -1.112 22.213 -20.41 1 39.58 ? C8 5JL 301 A 1 HETATM 5 N N1 5JL . . . E 4 -4.327 24.051 -22.696 1 40.98 ? N1 5JL 301 A 1 HETATM 6 N N3 5JL . . . E 4 -2.234 24.941 -22.085 1 40.96 ? N3 5JL 301 A 1 HETATM 7 O O6 5JL . . . E 4 -4.874 21.91 -22.06 1 38.92 ? O6 5JL 301 A 1 HETATM 8 N N7 5JL . . . E 4 -2.299 21.713 -20.762 1 31.86 ? N7 5JL 301 A 1 HETATM 9 S S8 5JL . . . E 4 0.026 21.236 -19.495 1 32.57 ? S8 5JL 301 A 1 HETATM 10 N N9 5JL . . . E 4 -0.842 23.475 -20.798 1 38.83 ? N9 5JL 301 A 1 HETATM 11 C C2 5JL . . . E 4 -3.426 25.067 -22.699 1 45.54 ? C2 5JL 301 A 1 HETATM 12 S S2 5JL . . . E 4 -3.774 26.559 -23.488 1 46.96 ? S2 5JL 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 12 #