data_5HUQ # _model_server_result.job_id sC6vFTFREdBdiXYqfe7paw _model_server_result.datetime_utc '2025-02-23 06:34:10' _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 5huq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5HUQ # _exptl.entry_id 5HUQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 396.353 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium _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 90 _cell.angle_gamma 90 _cell.entry_id 5HUQ _cell.length_a 111.277 _cell.length_b 111.277 _cell.length_c 306.181 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HUQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N 1 1 B,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 3 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 P 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 covale ? covale1 A NZ LYS 184 A LYS 184 1_555 C C7 4EY . A 4EY 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale2 B NZ LYS 184 B LYS 184 1_555 P C7 4EY . B 4EY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 B NE2 HIS 200 B HIS 200 1_555 O NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 O NI NI . B NI 501 1_555 P S2 4EY . B 4EY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc3 O NI NI . B NI 501 1_555 P S7 4EY . B 4EY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? # _chem_comp.formula 'C12 H15 N O8 P S2 1' _chem_comp.formula_weight 396.353 _chem_comp.id 4EY _chem_comp.mon_nstd_flag . _chem_comp.name 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Dithiodinicotinic acid mononucleotide' # 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 O4R C4R 4EY sing 1 n n O4R C1R 4EY sing 2 n n O3R C3R 4EY sing 3 n n C4R C3R 4EY sing 4 n n C4R C5R 4EY sing 5 n n C1R N1 4EY sing 6 n n C1R C2R 4EY sing 7 n n O2 C1 4EY doub 8 n n C3R C2R 4EY sing 9 n n C6 N1 4EY doub 10 n y C6 C5 4EY sing 11 n y C5R O5R 4EY sing 12 n n N1 C2 4EY sing 13 n y O2R C2R 4EY sing 14 n n C1 C5 4EY sing 15 n n C1 S2 4EY sing 16 n n C5 C4 4EY doub 17 n y C2 C3 4EY doub 18 n y O5R P 4EY sing 19 n n C4 C3 4EY sing 20 n y C3 C7 4EY sing 21 n n C7 S7 4EY doub 22 n n P O3P 4EY doub 23 n n P O1P 4EY sing 24 n n P O2P 4EY sing 25 n n C2 H1 4EY sing 26 n n C4 H2 4EY sing 27 n n C6 H3 4EY sing 28 n n O2P H4 4EY sing 29 n n O1P H5 4EY sing 30 n n C5R H6 4EY sing 31 n n C5R H7 4EY sing 32 n n C4R H8 4EY sing 33 n n C3R H9 4EY sing 34 n n O3R H10 4EY sing 35 n n C2R H11 4EY sing 36 n n O2R H12 4EY sing 37 n n C1R H13 4EY sing 38 n n C7 H14 4EY sing 39 n n S2 H15 4EY sing 40 n n # _atom_sites.entry_id 5HUQ _atom_sites.fract_transf_matrix[1][1] 0.008987 _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] 0.008987 _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] 0.003266 _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 4EY A 1 501 700 4EY NAR . D 3 SO4 A 1 502 800 SO4 SO4 . E 3 SO4 A 1 503 801 SO4 SO4 . F 3 SO4 A 1 504 802 SO4 SO4 . G 3 SO4 A 1 505 803 SO4 SO4 . H 3 SO4 A 1 506 804 SO4 SO4 . I 3 SO4 A 1 507 805 SO4 SO4 . J 3 SO4 A 1 508 806 SO4 SO4 . K 3 SO4 A 1 509 807 SO4 SO4 . L 3 SO4 A 1 510 808 SO4 SO4 . M 3 SO4 A 1 511 809 SO4 SO4 . N 3 SO4 A 1 512 810 SO4 SO4 . O 4 NI B 1 501 600 NI NI . P 2 4EY B 1 502 700 4EY NAR . Q 3 SO4 B 1 503 800 SO4 SO4 . R 3 SO4 B 1 504 801 SO4 SO4 . S 3 SO4 B 1 505 802 SO4 SO4 . T 3 SO4 B 1 506 803 SO4 SO4 . U 3 SO4 B 1 507 804 SO4 SO4 . V 3 SO4 B 1 508 805 SO4 SO4 . W 3 SO4 B 1 509 806 SO4 SO4 . X 3 SO4 B 1 510 807 SO4 SO4 . Y 3 SO4 B 1 511 808 SO4 SO4 . Z 3 SO4 B 1 512 809 SO4 SO4 . AA 3 SO4 B 1 513 810 SO4 SO4 . BA 3 SO4 B 1 514 811 SO4 SO4 . # 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 C2 4EY . . . C 2 -64.391 18.04 -12.458 1 58.52 ? C2 4EY 501 A 1 HETATM 2 C C3 4EY . . . C 2 -64.298 19.271 -11.825 1 59.16 ? C3 4EY 501 A 1 HETATM 3 C C1 4EY . . . C 2 -60.859 20.182 -12.981 1 71.69 ? C1 4EY 501 A 1 HETATM 4 C C4 4EY . . . C 2 -63.129 19.986 -11.961 1 62.88 ? C4 4EY 501 A 1 HETATM 5 C C5 4EY . . . C 2 -62.12 19.44 -12.755 1 68.71 ? C5 4EY 501 A 1 HETATM 6 C C6 4EY . . . C 2 -62.283 18.216 -13.369 1 65.56 ? C6 4EY 501 A 1 HETATM 7 O O2 4EY . . . C 2 -59.943 19.751 -13.67 1 61.67 ? O2 4EY 501 A 1 HETATM 8 O O2P 4EY . . . C 2 -66.326 15.911 -9.684 1 46.99 ? O2P 4EY 501 A 1 HETATM 9 P P 4EY . . . C 2 -66.974 14.974 -10.639 1 54.19 ? P 4EY 501 A 1 HETATM 10 O O3P 4EY . . . C 2 -68.461 15.279 -10.79 1 53.02 ? O3P 4EY 501 A 1 HETATM 11 O O1P 4EY . . . C 2 -66.517 13.493 -10.698 1 45.74 ? O1P 4EY 501 A 1 HETATM 12 O O5R 4EY . . . C 2 -66.329 15.615 -11.961 1 56.9 ? O5R 4EY 501 A 1 HETATM 13 C C5R 4EY . . . C 2 -66.799 15.38 -13.292 1 55.79 ? C5R 4EY 501 A 1 HETATM 14 C C4R 4EY . . . C 2 -65.605 15.086 -14.187 1 54.34 ? C4R 4EY 501 A 1 HETATM 15 O O4R 4EY . . . C 2 -64.873 16.276 -14.5 1 56.86 ? O4R 4EY 501 A 1 HETATM 16 C C3R 4EY . . . C 2 -64.616 14.154 -13.511 1 55.57 ? C3R 4EY 501 A 1 HETATM 17 O O3R 4EY . . . C 2 -64.141 13.214 -14.481 1 53.94 ? O3R 4EY 501 A 1 HETATM 18 C C2R 4EY . . . C 2 -63.524 15.076 -12.97 1 58.51 ? C2R 4EY 501 A 1 HETATM 19 O O2R 4EY . . . C 2 -62.174 14.593 -12.987 1 61.47 ? O2R 4EY 501 A 1 HETATM 20 C C1R 4EY . . . C 2 -63.577 16.266 -13.879 1 57.41 ? C1R 4EY 501 A 1 HETATM 21 N N1 4EY . . . C 2 -63.41 17.541 -13.198 1 58.71 ? N1 4EY 501 A 1 HETATM 22 C C7 4EY . . . C 2 -65.43 19.762 -10.961 1 58.86 ? C7 4EY 501 A 1 HETATM 23 S S7 4EY . . . C 2 -65.344 21.191 -10.391 1 60.23 ? S7 4EY 501 A 1 HETATM 24 S S2 4EY . . . C 2 -60.825 21.589 -12.314 1 101.31 ? S2 4EY 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #