data_4RH1 # _model_server_result.job_id 8XJmt_l3JB3DyrqIo6sAfA _model_server_result.datetime_utc '2024-11-20 13:40:27' _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 4rh1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":409}' # _entry.id 4RH1 # _exptl.entry_id 4RH1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.457 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione _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 4RH1 _cell.length_a 53.44 _cell.length_b 58.56 _cell.length_c 130.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RH1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H,I,J,K _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 5 _struct_asym.id J _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 SG CYS 117 A CYS 90 1_555 B FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc2 A SG CYS 121 A CYS 94 1_555 B FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc3 A SG CYS 124 A CYS 97 1_555 B FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc4 B FE2 SF4 . A SF4 401 1_555 C O EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc5 B FE2 SF4 . A SF4 401 1_555 C N EEM . A EEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? # _chem_comp.formula 'C20 H28 N4 O10' _chem_comp.formula_weight 484.457 _chem_comp.id 0TT _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione _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 C1 CI 0TT sing 1 n n O6 CL 0TT doub 2 n n CI CL 0TT sing 3 n n CI CH 0TT sing 4 n n CI CJ 0TT sing 5 n n CL N4 0TT sing 6 n n CH CF 0TT sing 7 n n CJ N3 0TT sing 8 n n N4 CK 0TT sing 9 n n CF CE 0TT doub 10 n n CF CG 0TT sing 11 n n O4 CG 0TT doub 12 n n CE N1 0TT sing 13 n n CG N2 0TT sing 14 n n N3 CK 0TT sing 15 n n N3 C2 0TT sing 16 n n CK O5 0TT doub 17 n n CM CD 0TT sing 18 n n CM CA 0TT sing 19 n n N1 CD 0TT sing 20 n n N1 CB 0TT sing 21 n n N2 CB 0TT sing 22 n n C2 O7 0TT sing 23 n n C2 C3 0TT sing 24 n n CD OB 0TT sing 25 n n CA O1 0TT sing 26 n n CA C9 0TT sing 27 n n CB O3 0TT doub 28 n n O7 C5 0TT sing 29 n n C3 C4 0TT sing 30 n n OB C9 0TT sing 31 n n C9 C8 0TT sing 32 n n C8 OA 0TT sing 33 n n C5 C4 0TT sing 34 n n C5 C6 0TT sing 35 n n C4 O9 0TT sing 36 n n O8 C6 0TT sing 37 n n O8 H1 0TT sing 38 n n C6 H2 0TT sing 39 n n C6 H3 0TT sing 40 n n C5 H4 0TT sing 41 n n C4 H5 0TT sing 42 n n O9 H6 0TT sing 43 n n C3 H7 0TT sing 44 n n C3 H8 0TT sing 45 n n C2 H9 0TT sing 46 n n CJ H10 0TT sing 47 n n CJ H11 0TT sing 48 n n N4 H12 0TT sing 49 n n C1 H13 0TT sing 50 n n C1 H14 0TT sing 51 n n C1 H15 0TT sing 52 n n CH H16 0TT sing 53 n n CH H17 0TT sing 54 n n CE H18 0TT sing 55 n n N2 H19 0TT sing 56 n n CD H20 0TT sing 57 n n CM H21 0TT sing 58 n n CM H22 0TT sing 59 n n CA H23 0TT sing 60 n n O1 H24 0TT sing 61 n n C9 H25 0TT sing 62 n n C8 H26 0TT sing 63 n n C8 H27 0TT sing 64 n n OA H28 0TT sing 65 n n # _atom_sites.entry_id 4RH1 _atom_sites.fract_transf_matrix[1][1] 0.018713 _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] 0.017077 _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] 0.007636 _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 SF4 A 1 401 1 SF4 SF4 . C 3 EEM A 1 402 1 EEM EEM . D 4 SO4 A 1 403 1 SO4 SO4 . E 4 SO4 A 1 404 3 SO4 SO4 . F 4 SO4 A 1 405 4 SO4 SO4 . G 4 SO4 A 1 406 5 SO4 SO4 . H 4 SO4 A 1 407 7 SO4 SO4 . I 4 SO4 A 1 408 9 SO4 SO4 . J 5 0TT A 1 409 1 0TT SP . K 6 HOH A 1 501 3 HOH HOH . K 6 HOH A 2 502 6 HOH HOH . K 6 HOH A 3 503 7 HOH HOH . K 6 HOH A 4 504 10 HOH HOH . K 6 HOH A 5 505 12 HOH HOH . K 6 HOH A 6 506 15 HOH HOH . K 6 HOH A 7 507 18 HOH HOH . K 6 HOH A 8 508 26 HOH HOH . K 6 HOH A 9 509 29 HOH HOH . K 6 HOH A 10 510 32 HOH HOH . K 6 HOH A 11 511 37 HOH HOH . K 6 HOH A 12 512 39 HOH HOH . K 6 HOH A 13 513 42 HOH HOH . K 6 HOH A 14 514 43 HOH HOH . K 6 HOH A 15 515 44 HOH HOH . K 6 HOH A 16 516 45 HOH HOH . K 6 HOH A 17 517 47 HOH HOH . K 6 HOH A 18 518 48 HOH HOH . K 6 HOH A 19 519 49 HOH HOH . K 6 HOH A 20 520 51 HOH HOH . K 6 HOH A 21 521 52 HOH HOH . K 6 HOH A 22 522 53 HOH HOH . K 6 HOH A 23 523 55 HOH HOH . K 6 HOH A 24 524 56 HOH HOH . K 6 HOH A 25 525 58 HOH HOH . K 6 HOH A 26 526 63 HOH HOH . K 6 HOH A 27 527 64 HOH HOH . K 6 HOH A 28 528 65 HOH HOH . K 6 HOH A 29 529 66 HOH HOH . K 6 HOH A 30 530 67 HOH HOH . K 6 HOH A 31 531 68 HOH HOH . K 6 HOH A 32 532 69 HOH HOH . K 6 HOH A 33 533 70 HOH HOH . K 6 HOH A 34 534 71 HOH HOH . K 6 HOH A 35 535 73 HOH HOH . K 6 HOH A 36 536 74 HOH HOH . K 6 HOH A 37 537 75 HOH HOH . K 6 HOH A 38 538 76 HOH HOH . K 6 HOH A 39 539 77 HOH HOH . K 6 HOH A 40 540 78 HOH HOH . K 6 HOH A 41 541 79 HOH HOH . K 6 HOH A 42 542 80 HOH HOH . K 6 HOH A 43 543 81 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 O O8 0TT . . . J 5 -19.396 -3.82 26.164 1 36.35 ? O8 0TT 409 A 1 HETATM 2 C C6 0TT . . . J 5 -20.015 -2.63 26.661 1 37.9 ? C6 0TT 409 A 1 HETATM 3 C C5 0TT . . . J 5 -21.293 -2.281 25.931 1 38.85 ? C5 0TT 409 A 1 HETATM 4 O O7 0TT . . . J 5 -21.013 -2.161 24.52 1 39.47 ? O7 0TT 409 A 1 HETATM 5 C C4 0TT . . . J 5 -22.431 -3.308 26.021 1 39.19 ? C4 0TT 409 A 1 HETATM 6 O O9 0TT . . . J 5 -23.668 -2.586 25.911 1 41.2 ? O9 0TT 409 A 1 HETATM 7 C C3 0TT . . . J 5 -22.142 -4.181 24.843 1 39.32 ? C3 0TT 409 A 1 HETATM 8 C C2 0TT . . . J 5 -21.796 -3.121 23.786 1 39.24 ? C2 0TT 409 A 1 HETATM 9 N N3 0TT . . . J 5 -21.069 -3.554 22.591 1 39.54 ? N3 0TT 409 A 1 HETATM 10 C CJ 0TT . . . J 5 -21.574 -3.181 21.263 1 39.36 ? CJ 0TT 409 A 1 HETATM 11 C CK 0TT . . . J 5 -19.838 -4.177 22.722 1 39.98 ? CK 0TT 409 A 1 HETATM 12 O O5 0TT . . . J 5 -19.37 -4.623 23.772 1 39.09 ? O5 0TT 409 A 1 HETATM 13 N N4 0TT . . . J 5 -19.15 -4.431 21.528 1 39.56 ? N4 0TT 409 A 1 HETATM 14 C CL 0TT . . . J 5 -19.278 -3.714 20.36 1 40.59 ? CL 0TT 409 A 1 HETATM 15 O O6 0TT . . . J 5 -18.534 -3.939 19.415 1 43.05 ? O6 0TT 409 A 1 HETATM 16 C CI 0TT . . . J 5 -20.475 -2.749 20.28 1 39.55 ? CI 0TT 409 A 1 HETATM 17 C C1 0TT . . . J 5 -21.045 -2.822 18.844 1 38.76 ? C1 0TT 409 A 1 HETATM 18 C CH 0TT . . . J 5 -20.069 -1.25 20.506 1 40 ? CH 0TT 409 A 1 HETATM 19 C CF 0TT . . . J 5 -19.729 -0.697 21.867 1 40.73 ? CF 0TT 409 A 1 HETATM 20 C CE 0TT . . . J 5 -20.539 0.167 22.526 1 41.53 ? CE 0TT 409 A 1 HETATM 21 C CG 0TT . . . J 5 -18.464 -1.053 22.506 1 40.91 ? CG 0TT 409 A 1 HETATM 22 O O4 0TT . . . J 5 -17.647 -1.813 22.029 1 42.46 ? O4 0TT 409 A 1 HETATM 23 N N2 0TT . . . J 5 -18.212 -0.492 23.745 1 40.91 ? N2 0TT 409 A 1 HETATM 24 C CB 0TT . . . J 5 -19.033 0.374 24.421 1 41 ? CB 0TT 409 A 1 HETATM 25 O O3 0TT . . . J 5 -18.72 0.821 25.525 1 39.01 ? O3 0TT 409 A 1 HETATM 26 N N1 0TT . . . J 5 -20.215 0.705 23.78 1 42.09 ? N1 0TT 409 A 1 HETATM 27 C CD 0TT . . . J 5 -21.109 1.62 24.505 1 44.07 ? CD 0TT 409 A 1 HETATM 28 O OB 0TT . . . J 5 -22.166 0.766 24.914 1 45.16 ? OB 0TT 409 A 1 HETATM 29 C CM 0TT . . . J 5 -21.721 2.766 23.75 1 45.06 ? CM 0TT 409 A 1 HETATM 30 C CA 0TT . . . J 5 -23.219 2.481 23.891 1 46.04 ? CA 0TT 409 A 1 HETATM 31 O O1 0TT . . . J 5 -23.937 3.688 23.967 1 47.95 ? O1 0TT 409 A 1 HETATM 32 C C9 0TT . . . J 5 -23.286 1.598 25.139 1 46.7 ? C9 0TT 409 A 1 HETATM 33 C C8 0TT . . . J 5 -24.487 0.719 25.349 1 47.7 ? C8 0TT 409 A 1 HETATM 34 O OA 0TT . . . J 5 -24.519 0.335 26.742 1 47.62 ? OA 0TT 409 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 34 #