data_6C1W # _model_server_result.job_id 9k7z2i94u26mgNWrJgCbYw _model_server_result.datetime_utc '2025-02-24 00:44:11' _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 6c1w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6C1W # _exptl.entry_id 6C1W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.424 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid' _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 6C1W _cell.length_a 69.365 _cell.length_b 157.897 _cell.length_c 158.988 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C1W _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_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,D,E,F,G,H,I,AA 1 1 B,J,K,L,M,N,O,P,Q,R,S,BA 2 1 C,T,U,V,W,X,Y,Z,CA 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id D _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 covale ? covale1 A NZ LYS 184 A LYS 184 1_555 D C7 ENJ . A ENJ 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale2 B NZ LYS 184 B LYS 184 1_555 J C7 4EY . B 4EY 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale3 C NZ LYS 184 C LYS 184 1_555 T C7 4EY . C 4EY 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? metalc ? metalc1 A NE2 HIS 200 A HIS 200 1_555 E NI NI . A NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc2 D S2 ENJ . A ENJ 501 1_555 E NI NI . A NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc3 D S7 ENJ . A ENJ 501 1_555 E NI NI . A NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc4 B NE2 HIS 200 B HIS 200 1_555 K NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc5 J S7 4EY . B 4EY 501 1_555 K NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 J S2 4EY . B 4EY 501 1_555 K NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc7 C NE2 HIS 200 C HIS 200 1_555 U NI NI . C NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc8 T S7 4EY . C 4EY 501 1_555 U NI NI . C NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc9 T S2 4EY . C 4EY 501 1_555 U NI NI . C NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? # _chem_comp.formula 'C12 H16 N O11 P S3' _chem_comp.formula_weight 477.424 _chem_comp.id ENJ _chem_comp.mon_nstd_flag . _chem_comp.name '(4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid' _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 O1 S ENJ doub 123 n n O2R C2R ENJ sing 124 n n O S ENJ doub 125 n n S O21 ENJ sing 126 n n S C4 ENJ sing 127 n n O2 C1 ENJ doub 128 n n O3R C3R ENJ sing 129 n n C2R C1R ENJ sing 130 n n C2R C3R ENJ sing 131 n n C1R N1 ENJ sing 132 n n C1R O4R ENJ sing 133 n n C1 C5 ENJ sing 134 n n C1 S2 ENJ sing 135 n n C6 N1 ENJ sing 136 n n C6 C5 ENJ doub 137 n n N1 C2 ENJ sing 138 n n C3R C4R ENJ sing 139 n n C5 C4 ENJ sing 140 n n C4 C3 ENJ sing 141 n n O3P P ENJ doub 142 n n C2 C3 ENJ doub 143 n n O4R C4R ENJ sing 144 n n C3 C7 ENJ sing 145 n n C4R C5R ENJ sing 146 n n O2P P ENJ sing 147 n n P O5R ENJ sing 148 n n P O1P ENJ sing 149 n n O5R C5R ENJ sing 150 n n C7 S7 ENJ doub 151 n n C7 H1 ENJ sing 152 n n C6 H2 ENJ sing 153 n n C4 H3 ENJ sing 154 n n C2 H4 ENJ sing 155 n n C1R H5 ENJ sing 156 n n C2R H6 ENJ sing 157 n n C3R H7 ENJ sing 158 n n C4R H8 ENJ sing 159 n n C5R H9 ENJ sing 160 n n C5R H10 ENJ sing 161 n n O1P H11 ENJ sing 162 n n O2P H12 ENJ sing 163 n n O2R H13 ENJ sing 164 n n O3R H14 ENJ sing 165 n n S2 H15 ENJ sing 166 n n O21 H16 ENJ sing 167 n n # _atom_sites.entry_id 6C1W _atom_sites.fract_transf_matrix[1][1] 0.014416 _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] 0.006333 _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] 0.00629 _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 D 2 ENJ A 1 501 502 ENJ 4ES . E 3 NI A 1 502 603 NI NI . F 4 SO4 A 1 503 804 SO4 SO4 . G 4 SO4 A 1 504 805 SO4 SO4 . H 4 SO4 A 1 505 806 SO4 SO4 . I 4 SO4 A 1 506 807 SO4 SO4 . J 5 4EY B 1 501 503 4EY 4EY . K 3 NI B 1 502 601 NI NI . L 4 SO4 B 1 503 802 SO4 SO4 . M 4 SO4 B 1 504 808 SO4 SO4 . N 4 SO4 B 1 505 809 SO4 SO4 . O 4 SO4 B 1 506 810 SO4 SO4 . P 4 SO4 B 1 507 811 SO4 SO4 . Q 4 SO4 B 1 508 812 SO4 SO4 . R 4 SO4 B 1 509 817 SO4 SO4 . S 4 SO4 B 1 510 819 SO4 SO4 . T 5 4EY C 1 501 504 4EY 4EY . U 3 NI C 1 502 602 NI NI . V 6 SO3 C 1 503 702 SO3 SO3 . W 4 SO4 C 1 504 813 SO4 SO4 . X 4 SO4 C 1 505 814 SO4 SO4 . Y 4 SO4 C 1 506 815 SO4 SO4 . Z 4 SO4 C 1 507 816 SO4 SO4 . AA 7 HOH A 1 601 89 HOH HOH . AA 7 HOH A 2 602 98 HOH HOH . AA 7 HOH A 3 603 73 HOH HOH . AA 7 HOH A 4 604 46 HOH HOH . AA 7 HOH A 5 605 50 HOH HOH . AA 7 HOH A 6 606 115 HOH HOH . AA 7 HOH A 7 607 101 HOH HOH . AA 7 HOH A 8 608 51 HOH HOH . AA 7 HOH A 9 609 81 HOH HOH . AA 7 HOH A 10 610 39 HOH HOH . AA 7 HOH A 11 611 62 HOH HOH . AA 7 HOH A 12 612 65 HOH HOH . AA 7 HOH A 13 613 7 HOH HOH . AA 7 HOH A 14 614 20 HOH HOH . AA 7 HOH A 15 615 25 HOH HOH . AA 7 HOH A 16 616 118 HOH HOH . AA 7 HOH A 17 617 67 HOH HOH . AA 7 HOH A 18 618 12 HOH HOH . AA 7 HOH A 19 619 43 HOH HOH . AA 7 HOH A 20 620 5 HOH HOH . AA 7 HOH A 21 621 58 HOH HOH . AA 7 HOH A 22 622 111 HOH HOH . AA 7 HOH A 23 623 31 HOH HOH . AA 7 HOH A 24 624 76 HOH HOH . AA 7 HOH A 25 625 17 HOH HOH . AA 7 HOH A 26 626 71 HOH HOH . AA 7 HOH A 27 627 3 HOH HOH . AA 7 HOH A 28 628 14 HOH HOH . AA 7 HOH A 29 629 120 HOH HOH . AA 7 HOH A 30 630 37 HOH HOH . AA 7 HOH A 31 631 45 HOH HOH . AA 7 HOH A 32 632 80 HOH HOH . AA 7 HOH A 33 633 102 HOH HOH . AA 7 HOH A 34 634 97 HOH HOH . AA 7 HOH A 35 635 28 HOH HOH . AA 7 HOH A 36 636 10 HOH HOH . AA 7 HOH A 37 637 30 HOH HOH . AA 7 HOH A 38 638 42 HOH HOH . AA 7 HOH A 39 639 91 HOH HOH . AA 7 HOH A 40 640 100 HOH HOH . AA 7 HOH A 41 641 82 HOH HOH . AA 7 HOH A 42 642 96 HOH HOH . AA 7 HOH A 43 643 99 HOH HOH . AA 7 HOH A 44 644 108 HOH HOH . BA 7 HOH B 1 601 6 HOH HOH . BA 7 HOH B 2 602 88 HOH HOH . BA 7 HOH B 3 603 54 HOH HOH . BA 7 HOH B 4 604 4 HOH HOH . BA 7 HOH B 5 605 11 HOH HOH . BA 7 HOH B 6 606 55 HOH HOH . BA 7 HOH B 7 607 64 HOH HOH . BA 7 HOH B 8 608 93 HOH HOH . BA 7 HOH B 9 609 38 HOH HOH . BA 7 HOH B 10 610 9 HOH HOH . BA 7 HOH B 11 611 8 HOH HOH . BA 7 HOH B 12 612 29 HOH HOH . BA 7 HOH B 13 613 13 HOH HOH . BA 7 HOH B 14 614 105 HOH HOH . BA 7 HOH B 15 615 48 HOH HOH . BA 7 HOH B 16 616 63 HOH HOH . BA 7 HOH B 17 617 84 HOH HOH . BA 7 HOH B 18 618 117 HOH HOH . BA 7 HOH B 19 619 32 HOH HOH . BA 7 HOH B 20 620 119 HOH HOH . BA 7 HOH B 21 621 77 HOH HOH . BA 7 HOH B 22 622 22 HOH HOH . BA 7 HOH B 23 623 15 HOH HOH . BA 7 HOH B 24 624 56 HOH HOH . BA 7 HOH B 25 625 66 HOH HOH . BA 7 HOH B 26 626 21 HOH HOH . BA 7 HOH B 27 627 110 HOH HOH . BA 7 HOH B 28 628 109 HOH HOH . BA 7 HOH B 29 629 70 HOH HOH . BA 7 HOH B 30 630 95 HOH HOH . BA 7 HOH B 31 631 92 HOH HOH . BA 7 HOH B 32 632 78 HOH HOH . BA 7 HOH B 33 633 61 HOH HOH . CA 7 HOH C 1 601 112 HOH HOH . CA 7 HOH C 2 602 47 HOH HOH . CA 7 HOH C 3 603 1 HOH HOH . CA 7 HOH C 4 604 79 HOH HOH . CA 7 HOH C 5 605 114 HOH HOH . CA 7 HOH C 6 606 24 HOH HOH . CA 7 HOH C 7 607 104 HOH HOH . CA 7 HOH C 8 608 113 HOH HOH . CA 7 HOH C 9 609 35 HOH HOH . CA 7 HOH C 10 610 68 HOH HOH . CA 7 HOH C 11 611 23 HOH HOH . CA 7 HOH C 12 612 36 HOH HOH . CA 7 HOH C 13 613 27 HOH HOH . CA 7 HOH C 14 614 74 HOH HOH . CA 7 HOH C 15 615 26 HOH HOH . CA 7 HOH C 16 616 49 HOH HOH . CA 7 HOH C 17 617 103 HOH HOH . CA 7 HOH C 18 618 16 HOH HOH . CA 7 HOH C 19 619 83 HOH HOH . CA 7 HOH C 20 620 85 HOH HOH . CA 7 HOH C 21 621 33 HOH HOH . CA 7 HOH C 22 622 87 HOH HOH . CA 7 HOH C 23 623 59 HOH HOH . CA 7 HOH C 24 624 94 HOH HOH . CA 7 HOH C 25 625 86 HOH HOH . CA 7 HOH C 26 626 34 HOH HOH . CA 7 HOH C 27 627 75 HOH HOH . CA 7 HOH C 28 628 52 HOH HOH . CA 7 HOH C 29 629 90 HOH HOH . CA 7 HOH C 30 630 72 HOH HOH . CA 7 HOH C 31 631 116 HOH HOH . CA 7 HOH C 32 632 107 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 O2 ENJ . . . D 2 -28.11 37.444 48.408 1 50.22 ? O2 ENJ 501 A 1 HETATM 2 O O1 ENJ . . . D 2 -27.997 41.795 47.051 1 50.88 ? O1 ENJ 501 A 1 HETATM 3 C C7 ENJ . . . D 2 -28.158 42.457 51.646 1 47.13 ? C7 ENJ 501 A 1 HETATM 4 C C6 ENJ . . . D 2 -26.47 39.629 49.205 1 43.51 ? C6 ENJ 501 A 1 HETATM 5 C C4 ENJ . . . D 2 -28.558 40.898 49.585 1 51.81 ? C4 ENJ 501 A 1 HETATM 6 C C3 ENJ . . . D 2 -27.647 41.684 50.499 1 47.83 ? C3 ENJ 501 A 1 HETATM 7 N N1 ENJ . . . D 2 -25.855 40.855 49.232 1 48.77 ? N1 ENJ 501 A 1 HETATM 8 C C5 ENJ . . . D 2 -27.81 39.607 49.283 1 48.99 ? C5 ENJ 501 A 1 HETATM 9 C C2 ENJ . . . D 2 -26.321 41.633 50.281 1 48.07 ? C2 ENJ 501 A 1 HETATM 10 C C1 ENJ . . . D 2 -28.49 38.308 49.181 1 51.15 ? C1 ENJ 501 A 1 HETATM 11 O O ENJ . . . D 2 -30.539 41.217 47.727 1 56.97 ? O ENJ 501 A 1 HETATM 12 C C1R ENJ . . . D 2 -24.375 40.78 49.132 1 47.73 ? C1R ENJ 501 A 1 HETATM 13 C C2R ENJ . . . D 2 -23.892 42.111 48.571 1 47.79 ? C2R ENJ 501 A 1 HETATM 14 C C3R ENJ . . . D 2 -22.571 42.358 49.249 1 47.11 ? C3R ENJ 501 A 1 HETATM 15 C C4R ENJ . . . D 2 -22.751 41.674 50.592 1 47.04 ? C4R ENJ 501 A 1 HETATM 16 C C5R ENJ . . . D 2 -23.367 42.654 51.582 1 42.36 ? C5R ENJ 501 A 1 HETATM 17 O O1P ENJ . . . D 2 -23.644 45.933 52.442 1 46.71 ? O1P ENJ 501 A 1 HETATM 18 O O21 ENJ . . . D 2 -29.325 43.184 48.613 1 55.85 ? O21 ENJ 501 A 1 HETATM 19 O O2P ENJ . . . D 2 -25.358 45.071 50.904 1 43.55 ? O2P ENJ 501 A 1 HETATM 20 O O2R ENJ . . . D 2 -23.724 42.034 47.158 1 48.29 ? O2R ENJ 501 A 1 HETATM 21 O O3P ENJ . . . D 2 -23.344 46.056 49.961 1 48.19 ? O3P ENJ 501 A 1 HETATM 22 O O3R ENJ . . . D 2 -21.513 41.779 48.472 1 44.77 ? O3R ENJ 501 A 1 HETATM 23 O O4R ENJ . . . D 2 -23.685 40.603 50.379 1 47.76 ? O4R ENJ 501 A 1 HETATM 24 O O5R ENJ . . . D 2 -22.989 43.913 51.127 1 41.29 ? O5R ENJ 501 A 1 HETATM 25 P P ENJ . . . D 2 -23.885 45.247 51.108 1 45.72 ? P ENJ 501 A 1 HETATM 26 S S ENJ . . . D 2 -29.107 41.801 48.256 1 66.67 ? S ENJ 501 A 1 HETATM 27 S S2 ENJ . . . D 2 -29.797 37.953 50.19 1 51.39 ? S2 ENJ 501 A 1 HETATM 28 S S7 ENJ . . . D 2 -29.485 42.123 52.42 1 48.08 ? S7 ENJ 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #