data_6HUX # _model_server_result.job_id ChdUjYimg-xs9D-8tLdlSQ _model_server_result.datetime_utc '2024-11-07 02:39:52' _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 6hux # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":412}' # _entry.id 6HUX # _exptl.entry_id 6HUX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 787.685 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol _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 120 _cell.entry_id 6HUX _cell.length_a 124.281 _cell.length_b 124.281 _cell.length_c 150.086 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HUX _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_567 x-y+2/3,-y+4/3,-z+7/3 1 0 0 0 -1 0 0 0 -1 0 143.507338 350.200667 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id M _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 OD2 ASP 86 A ASP 86 1_555 L NA NA . A NA 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc2 A OG1 THR 112 A THR 112 1_555 L NA NA . A NA 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.195 ? metalc ? metalc3 A OE1 GLU 245 A GLU 245 1_555 N MG MG . A MG 413 11_567 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc4 A OE1 GLU 265 A GLU 265 1_555 N MG MG . A MG 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 A OE2 GLU 265 A GLU 265 1_555 N MG MG . A MG 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? # _chem_comp.formula 'C31 H44 N6 O16 P 1' _chem_comp.formula_weight 787.685 _chem_comp.id E4M _chem_comp.mon_nstd_flag . _chem_comp.name 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol _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 N1 C2 E4M doub 89 n n N1 C8A E4M sing 90 n n C2 N3 E4M sing 91 n n C2 NA2 E4M sing 92 n n N3 C4 E4M sing 93 n n N3 HN3 E4M sing 94 n n C4 C4A E4M sing 95 n n C4 OH4 E4M doub 96 n n N5 C6 E4M sing 97 n n N5 C10 E4M doub 98 n n N5 C4A E4M sing 99 n n C6 C7 E4M sing 100 n n C6 C9 E4M sing 101 n n C6 H6 E4M sing 102 n n C7 N8 E4M sing 103 n n C7 C7M E4M sing 104 n n C7 H7 E4M sing 105 n n N8 C8A E4M sing 106 n n N8 HN8 E4M sing 107 n n C9 N10 E4M sing 108 n n C9 C9M E4M sing 109 n n C9 H9 E4M sing 110 n n PA O2A E4M sing 111 n n PA O1A E4M sing 112 n n PA O3A E4M doub 113 n n PA O5J E4M sing 114 n n C10 N10 E4M sing 115 n n C10 H10 E4M sing 116 n n N10 C14 E4M sing 117 n n C11 C12 E4M doub 118 n y C11 C16 E4M sing 119 n y C11 CX1 E4M sing 120 n n C12 C13 E4M sing 121 n y C12 H12 E4M sing 122 n n C13 C14 E4M doub 123 n y C13 H13 E4M sing 124 n n C14 C15 E4M sing 125 n y C15 C16 E4M doub 126 n y C15 H15 E4M sing 127 n n C16 H16 E4M sing 128 n n O2A C27 E4M sing 129 n n C1J C2J E4M sing 130 n n C1J O4J E4M sing 131 n n C1J OX5 E4M sing 132 n n C1J H1J E4M sing 133 n n O1A HO1A E4M sing 134 n n C2J O2J E4M sing 135 n n C2J C3J E4M sing 136 n n C2J H2J E4M sing 137 n n O2J HO2J E4M sing 138 n n C3J O3J E4M sing 139 n n C3J C4J E4M sing 140 n n C3J H3J E4M sing 141 n n O3J HO3J E4M sing 142 n n C4A C8A E4M doub 143 n n C4J O4J E4M sing 144 n n C4J C5J E4M sing 145 n n C4J H4J E4M sing 146 n n C5J O5J E4M sing 147 n n C5J H5J E4M sing 148 n n C5J H5JA E4M sing 149 n n C7M H7M E4M sing 150 n n C7M H7MA E4M sing 151 n n C7M H7MB E4M sing 152 n n C9M H9M E4M sing 153 n n C9M H9MA E4M sing 154 n n C9M H9MB E4M sing 155 n n NA2 HNA2 E4M sing 156 n n NA2 HNAA E4M sing 157 n n CX1 CX2 E4M sing 158 n n CX1 HX1 E4M sing 159 n n CX1 HX1A E4M sing 160 n n CX2 OX2 E4M sing 161 n n CX2 CX3 E4M sing 162 n n CX2 HX2 E4M sing 163 n n OX2 HOX2 E4M sing 164 n n CX3 OX3 E4M sing 165 n n CX3 CX4 E4M sing 166 n n CX3 HX3 E4M sing 167 n n OX3 HOX3 E4M sing 168 n n CX4 OX4 E4M sing 169 n n CX4 CX5 E4M sing 170 n n CX4 HX4 E4M sing 171 n n OX4 HOX4 E4M sing 172 n n CX5 OX5 E4M sing 173 n n CX5 HX5 E4M sing 174 n n CX5 HX5A E4M sing 175 n n C27 C28 E4M sing 176 n n C28 C29 E4M sing 177 n n C29 C30 E4M sing 178 n n C30 O13 E4M doub 179 n n C30 O14 E4M sing 180 n n C27 C31 E4M sing 181 n n C31 O15 E4M doub 182 n n C31 O16 E4M sing 183 n n C27 H38 E4M sing 184 n n C28 H39 E4M sing 185 n n C28 H40 E4M sing 186 n n C29 H41 E4M sing 187 n n C29 H42 E4M sing 188 n n O14 H43 E4M sing 189 n n O16 H44 E4M sing 190 n n # _atom_sites.entry_id 6HUX _atom_sites.fract_transf_matrix[1][1] 0.008046 _atom_sites.fract_transf_matrix[1][2] 0.004646 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009291 _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] 0.006663 _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 ACT A 1 401 3 ACT ACT . C 2 ACT A 1 402 7 ACT ACT . D 2 ACT A 1 403 8 ACT ACT . E 2 ACT A 1 404 10 ACT ACT . F 2 ACT A 1 405 11 ACT ACT . G 2 ACT A 1 406 12 ACT ACT . H 2 ACT A 1 407 13 ACT ACT . I 2 ACT A 1 408 14 ACT ACT . J 2 ACT A 1 409 15 ACT ACT . K 3 FE9 A 1 410 401 FE9 FE9 . L 4 NA A 1 411 1 NA NA . M 5 E4M A 1 412 1 E4M E4M . N 6 MG A 1 413 1 MG MG . O 7 SO4 A 1 414 1 SO4 SO4 . P 7 SO4 A 1 415 2 SO4 SO4 . Q 7 SO4 A 1 416 3 SO4 SO4 . R 7 SO4 A 1 417 4 SO4 SO4 . S 7 SO4 A 1 418 5 SO4 SO4 . T 7 SO4 A 1 419 7 SO4 SO4 . U 7 SO4 A 1 420 8 SO4 SO4 . V 8 EDO A 1 421 1 EDO EDO . W 8 EDO A 1 422 2 EDO EDO . X 8 EDO A 1 423 3 EDO EDO . Y 9 CL A 1 424 1 CL CL . Z 10 HOH A 1 501 38 HOH HOH . Z 10 HOH A 2 502 36 HOH HOH . Z 10 HOH A 3 503 7 HOH HOH . Z 10 HOH A 4 504 17 HOH HOH . Z 10 HOH A 5 505 22 HOH HOH . Z 10 HOH A 6 506 58 HOH HOH . Z 10 HOH A 7 507 41 HOH HOH . Z 10 HOH A 8 508 4 HOH HOH . Z 10 HOH A 9 509 29 HOH HOH . Z 10 HOH A 10 510 64 HOH HOH . Z 10 HOH A 11 511 12 HOH HOH . Z 10 HOH A 12 512 63 HOH HOH . Z 10 HOH A 13 513 45 HOH HOH . Z 10 HOH A 14 514 27 HOH HOH . Z 10 HOH A 15 515 51 HOH HOH . Z 10 HOH A 16 516 42 HOH HOH . Z 10 HOH A 17 517 32 HOH HOH . Z 10 HOH A 18 518 43 HOH HOH . Z 10 HOH A 19 519 47 HOH HOH . Z 10 HOH A 20 520 19 HOH HOH . Z 10 HOH A 21 521 24 HOH HOH . Z 10 HOH A 22 522 5 HOH HOH . Z 10 HOH A 23 523 26 HOH HOH . Z 10 HOH A 24 524 21 HOH HOH . Z 10 HOH A 25 525 20 HOH HOH . Z 10 HOH A 26 526 60 HOH HOH . Z 10 HOH A 27 527 52 HOH HOH . Z 10 HOH A 28 528 54 HOH HOH . Z 10 HOH A 29 529 16 HOH HOH . Z 10 HOH A 30 530 62 HOH HOH . Z 10 HOH A 31 531 31 HOH HOH . Z 10 HOH A 32 532 30 HOH HOH . Z 10 HOH A 33 533 39 HOH HOH . Z 10 HOH A 34 534 37 HOH HOH . Z 10 HOH A 35 535 1 HOH HOH . Z 10 HOH A 36 536 46 HOH HOH . Z 10 HOH A 37 537 49 HOH HOH . Z 10 HOH A 38 538 11 HOH HOH . Z 10 HOH A 39 539 55 HOH HOH . Z 10 HOH A 40 540 56 HOH HOH . Z 10 HOH A 41 541 10 HOH HOH . Z 10 HOH A 42 542 44 HOH HOH . Z 10 HOH A 43 543 50 HOH HOH . Z 10 HOH A 44 544 40 HOH HOH . Z 10 HOH A 45 545 59 HOH HOH . Z 10 HOH A 46 546 65 HOH HOH . Z 10 HOH A 47 547 8 HOH HOH . Z 10 HOH A 48 548 61 HOH HOH . Z 10 HOH A 49 549 53 HOH HOH . Z 10 HOH A 50 550 13 HOH HOH . Z 10 HOH A 51 551 3 HOH HOH . Z 10 HOH A 52 552 23 HOH HOH . Z 10 HOH A 53 553 57 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 N N1 E4M . . . M 5 -28.767 87.16 181.861 1 48.88 ? N1 E4M 412 A 1 HETATM 2 C C2 E4M . . . M 5 -29.785 87.362 180.992 1 45.92 ? C2 E4M 412 A 1 HETATM 3 N N3 E4M . . . M 5 -30.989 87.837 181.392 1 43.96 ? N3 E4M 412 A 1 HETATM 4 C C4 E4M . . . M 5 -31.252 88.117 182.688 1 50.07 ? C4 E4M 412 A 1 HETATM 5 N N5 E4M . . . M 5 -30.244 88.166 185.076 1 59.27 ? N5 E4M 412 A 1 HETATM 6 C C6 E4M . . . M 5 -28.988 88.536 185.737 1 56.1 ? C6 E4M 412 A 1 HETATM 7 C C7 E4M . . . M 5 -28.046 87.343 185.498 1 50.27 ? C7 E4M 412 A 1 HETATM 8 N N8 E4M . . . M 5 -27.869 87.177 184.057 1 51.19 ? N8 E4M 412 A 1 HETATM 9 C C9 E4M . . . M 5 -29.444 88.633 187.179 1 54.08 ? C9 E4M 412 A 1 HETATM 10 C C10 E4M . . . M 5 -31.241 88.061 185.854 1 58.47 ? C10 E4M 412 A 1 HETATM 11 N N10 E4M . . . M 5 -30.817 88.13 187.051 1 55.34 ? N10 E4M 412 A 1 HETATM 12 C C11 E4M . . . M 5 -32.881 86.814 190.475 1 51.81 ? C11 E4M 412 A 1 HETATM 13 C C12 E4M . . . M 5 -33.384 86.542 189.197 1 53.22 ? C12 E4M 412 A 1 HETATM 14 C C13 E4M . . . M 5 -32.715 86.985 188.05 1 51.32 ? C13 E4M 412 A 1 HETATM 15 C C14 E4M . . . M 5 -31.526 87.699 188.183 1 49.87 ? C14 E4M 412 A 1 HETATM 16 C C15 E4M . . . M 5 -31.004 87.938 189.464 1 48.7 ? C15 E4M 412 A 1 HETATM 17 C C16 E4M . . . M 5 -31.676 87.499 190.609 1 49.96 ? C16 E4M 412 A 1 HETATM 18 C C4A E4M . . . M 5 -30.182 87.911 183.694 1 50.62 ? C4A E4M 412 A 1 HETATM 19 C C7M E4M . . . M 5 -26.684 87.534 186.162 1 45.76 ? C7M E4M 412 A 1 HETATM 20 C C8A E4M . . . M 5 -28.894 87.404 183.186 1 49.2 ? C8A E4M 412 A 1 HETATM 21 C C9M E4M . . . M 5 -29.355 90.091 187.622 1 46.96 ? C9M E4M 412 A 1 HETATM 22 N NA2 E4M . . . M 5 -29.55 87.097 179.68 1 43.85 ? NA2 E4M 412 A 1 HETATM 23 O OH4 E4M . . . M 5 -32.377 88.529 183.041 1 52.57 ? OH4 E4M 412 A 1 HETATM 24 C CX1 E4M . . . M 5 -33.584 86.274 191.696 1 59.89 ? CX1 E4M 412 A 1 HETATM 25 C CX2 E4M . . . M 5 -34.575 87.224 192.346 1 69.8 ? CX2 E4M 412 A 1 HETATM 26 O OX2 E4M . . . M 5 -33.85 88.36 192.834 1 72.08 ? OX2 E4M 412 A 1 HETATM 27 C CX3 E4M . . . M 5 -35.332 86.491 193.469 1 70.61 ? CX3 E4M 412 A 1 HETATM 28 O OX3 E4M . . . M 5 -36.385 87.305 194.014 1 67.8 ? OX3 E4M 412 A 1 HETATM 29 C CX4 E4M . . . M 5 -34.387 85.999 194.566 1 76.45 ? CX4 E4M 412 A 1 HETATM 30 O OX4 E4M . . . M 5 -35.044 85.938 195.837 1 81.52 ? OX4 E4M 412 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #