data_5HUQ # _model_server_result.job_id -AZbHtY9ysHfgWiWRHtezA _model_server_result.datetime_utc '2025-02-23 06:08:44' _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":"P","auth_seq_id":502}' # _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 . . . P 2 -42.655 20.001 -35.488 1 61.51 ? C2 4EY 502 B 1 HETATM 2 C C3 4EY . . . P 2 -41.55 19.451 -34.85 1 64.85 ? C3 4EY 502 B 1 HETATM 3 C C1 4EY . . . P 2 -42.81 19.329 -31.37 1 65.63 ? C1 4EY 502 B 1 HETATM 4 C C4 4EY . . . P 2 -41.634 19.25 -33.485 1 65.59 ? C4 4EY 502 B 1 HETATM 5 C C5 4EY . . . P 2 -42.798 19.6 -32.811 1 61.71 ? C5 4EY 502 B 1 HETATM 6 C C6 4EY . . . P 2 -43.863 20.136 -33.477 1 58.87 ? C6 4EY 502 B 1 HETATM 7 O O2 4EY . . . P 2 -43.555 19.901 -30.566 1 72.29 ? O2 4EY 502 B 1 HETATM 8 O O2P 4EY . . . P 2 -43.07 22.763 -40.034 1 46.17 ? O2P 4EY 502 B 1 HETATM 9 P P 4EY . . . P 2 -42.428 21.442 -39.603 1 49.73 ? P 4EY 502 B 1 HETATM 10 O O3P 4EY . . . P 2 -41.676 20.696 -40.664 1 50.85 ? O3P 4EY 502 B 1 HETATM 11 O O1P 4EY . . . P 2 -41.603 21.476 -38.339 1 50.6 ? O1P 4EY 502 B 1 HETATM 12 O O5R 4EY . . . P 2 -43.729 20.491 -39.482 1 48.17 ? O5R 4EY 502 B 1 HETATM 13 C C5R 4EY . . . P 2 -44.101 19.525 -38.513 1 46.42 ? C5R 4EY 502 B 1 HETATM 14 C C4R 4EY . . . P 2 -45.312 20.062 -37.732 1 49.11 ? C4R 4EY 502 B 1 HETATM 15 O O4R 4EY . . . P 2 -45.265 19.685 -36.364 1 50.56 ? O4R 4EY 502 B 1 HETATM 16 C C3R 4EY . . . P 2 -45.492 21.574 -37.651 1 47.59 ? C3R 4EY 502 B 1 HETATM 17 O O3R 4EY . . . P 2 -46.892 21.794 -37.452 1 45.91 ? O3R 4EY 502 B 1 HETATM 18 C C2R 4EY . . . P 2 -44.726 22.037 -36.434 1 48.18 ? C2R 4EY 502 B 1 HETATM 19 O O2R 4EY . . . P 2 -45.302 23.145 -35.706 1 45.61 ? O2R 4EY 502 B 1 HETATM 20 C C1R 4EY . . . P 2 -44.897 20.828 -35.558 1 53.03 ? C1R 4EY 502 B 1 HETATM 21 N N1 4EY . . . P 2 -43.751 20.33 -34.808 1 58.99 ? N1 4EY 502 B 1 HETATM 22 C C7 4EY . . . P 2 -40.296 19.101 -35.602 1 59.67 ? C7 4EY 502 B 1 HETATM 23 S S7 4EY . . . P 2 -39.143 18.427 -34.82 1 58.5 ? S7 4EY 502 B 1 HETATM 24 S S2 4EY . . . P 2 -41.742 18.223 -31.053 1 57.1 ? S2 4EY 502 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #