data_6YX5 # _model_server_result.job_id BFY08JS1DlYDDQLB2Ehoog _model_server_result.datetime_utc '2024-11-14 20:54:34' _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 6yx5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":204}' # _entry.id 6YX5 # _exptl.entry_id 6YX5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 352.238 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate' _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 6YX5 _cell.length_a 142.309 _cell.length_b 142.309 _cell.length_c 76.616 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YX5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _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 _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 6 _struct_asym.id F _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 OH TYR 75 A TYR 77 1_555 F P14 LJN . A LJN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale2 F C56 LJN . A LJN 204 1_555 B SG CYS 185 B CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? metalc ? metalc1 A OG1 THR 20 A THR 22 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc2 A OG1 THR 38 A THR 40 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc3 C MG MG . A MG 201 1_555 D O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc4 C MG MG . A MG 201 1_555 D O2G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 C MG MG . A MG 201 1_555 N O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc6 C MG MG . A MG 201 1_555 N O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? # _chem_comp.formula 'C10 H17 N4 O8 P' _chem_comp.formula_weight 352.238 _chem_comp.id LJN _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate' _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 N28 N27 LJN doub 269 n y N28 C29 LJN sing 270 n y N27 N26 LJN sing 271 n y C29 C31 LJN sing 272 n n C29 C30 LJN doub 273 n y C31 N32 LJN sing 274 n n O35 C33 LJN doub 275 n n N26 C30 LJN sing 276 n y N26 C22 LJN sing 277 n n C33 N32 LJN sing 278 n n C33 C56 LJN sing 279 n n O25 C21 LJN sing 280 n n C21 C22 LJN sing 281 n n C21 C20 LJN sing 282 n n C22 O23 LJN sing 283 n n C20 O24 LJN sing 284 n n C20 C19 LJN sing 285 n n O23 C19 LJN sing 286 n n C19 C18 LJN sing 287 n n O17 C18 LJN sing 288 n n O17 P14 LJN sing 289 n n O15 P14 LJN sing 290 n n P14 O16 LJN doub 291 n n C18 H1 LJN sing 292 n n C18 H2 LJN sing 293 n n C19 H3 LJN sing 294 n n C20 H4 LJN sing 295 n n C21 H5 LJN sing 296 n n C22 H6 LJN sing 297 n n C30 H7 LJN sing 298 n n C31 H8 LJN sing 299 n n C31 H9 LJN sing 300 n n C56 H10 LJN sing 301 n n C56 H11 LJN sing 302 n n C56 H12 LJN sing 303 n n N32 H13 LJN sing 304 n n O15 H14 LJN sing 305 n n O24 H16 LJN sing 306 n n O25 H17 LJN sing 307 n n P14 O1 LJN sing 308 n n O1 H15 LJN sing 309 n n # _atom_sites.entry_id 6YX5 _atom_sites.fract_transf_matrix[1][1] 0.007027 _atom_sites.fract_transf_matrix[1][2] 0.004057 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008114 _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] 0.013052 _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 3 MG A 1 201 202 MG MG . D 4 GNP A 1 202 203 GNP GNP . E 5 GLC A 1 203 303 GLC GLC . F 6 LJN A 1 204 400 LJN LIG . G 7 SO4 A 1 205 2 SO4 SO4 . H 7 SO4 A 1 206 9 SO4 SO4 . I 5 GLC B 1 401 500 GLC GLC . J 5 GLC B 1 402 600 GLC GLC . K 7 SO4 B 1 403 5 SO4 SO4 . L 7 SO4 B 1 404 6 SO4 SO4 . M 7 SO4 B 1 405 8 SO4 SO4 . N 8 HOH A 1 301 23 HOH HOH . N 8 HOH A 2 302 33 HOH HOH . N 8 HOH A 3 303 61 HOH HOH . N 8 HOH A 4 304 1 HOH HOH . N 8 HOH A 5 305 84 HOH HOH . N 8 HOH A 6 306 12 HOH HOH . N 8 HOH A 7 307 101 HOH HOH . N 8 HOH A 8 308 26 HOH HOH . N 8 HOH A 9 309 83 HOH HOH . N 8 HOH A 10 310 119 HOH HOH . N 8 HOH A 11 311 52 HOH HOH . N 8 HOH A 12 312 80 HOH HOH . N 8 HOH A 13 313 25 HOH HOH . N 8 HOH A 14 314 48 HOH HOH . N 8 HOH A 15 315 70 HOH HOH . N 8 HOH A 16 316 92 HOH HOH . N 8 HOH A 17 317 37 HOH HOH . N 8 HOH A 18 318 55 HOH HOH . N 8 HOH A 19 319 102 HOH HOH . N 8 HOH A 20 320 17 HOH HOH . N 8 HOH A 21 321 104 HOH HOH . N 8 HOH A 22 322 59 HOH HOH . N 8 HOH A 23 323 3 HOH HOH . N 8 HOH A 24 324 103 HOH HOH . N 8 HOH A 25 325 116 HOH HOH . N 8 HOH A 26 326 117 HOH HOH . N 8 HOH A 27 327 73 HOH HOH . O 8 HOH B 1 501 72 HOH HOH . O 8 HOH B 2 502 11 HOH HOH . O 8 HOH B 3 503 98 HOH HOH . O 8 HOH B 4 504 121 HOH HOH . O 8 HOH B 5 505 53 HOH HOH . O 8 HOH B 6 506 40 HOH HOH . O 8 HOH B 7 507 15 HOH HOH . O 8 HOH B 8 508 4 HOH HOH . O 8 HOH B 9 509 49 HOH HOH . O 8 HOH B 10 510 2 HOH HOH . O 8 HOH B 11 511 66 HOH HOH . O 8 HOH B 12 512 20 HOH HOH . O 8 HOH B 13 513 6 HOH HOH . O 8 HOH B 14 514 107 HOH HOH . O 8 HOH B 15 515 93 HOH HOH . O 8 HOH B 16 516 60 HOH HOH . O 8 HOH B 17 517 111 HOH HOH . O 8 HOH B 18 518 38 HOH HOH . O 8 HOH B 19 519 13 HOH HOH . O 8 HOH B 20 520 94 HOH HOH . O 8 HOH B 21 521 27 HOH HOH . O 8 HOH B 22 522 75 HOH HOH . O 8 HOH B 23 523 118 HOH HOH . O 8 HOH B 24 524 67 HOH HOH . O 8 HOH B 25 525 16 HOH HOH . O 8 HOH B 26 526 96 HOH HOH . O 8 HOH B 27 527 30 HOH HOH . O 8 HOH B 28 528 10 HOH HOH . O 8 HOH B 29 529 63 HOH HOH . O 8 HOH B 30 530 22 HOH HOH . O 8 HOH B 31 531 122 HOH HOH . O 8 HOH B 32 532 62 HOH HOH . O 8 HOH B 33 533 31 HOH HOH . O 8 HOH B 34 534 54 HOH HOH . O 8 HOH B 35 535 90 HOH HOH . O 8 HOH B 36 536 34 HOH HOH . O 8 HOH B 37 537 28 HOH HOH . O 8 HOH B 38 538 9 HOH HOH . O 8 HOH B 39 539 8 HOH HOH . O 8 HOH B 40 540 42 HOH HOH . O 8 HOH B 41 541 65 HOH HOH . O 8 HOH B 42 542 43 HOH HOH . O 8 HOH B 43 543 24 HOH HOH . O 8 HOH B 44 544 18 HOH HOH . O 8 HOH B 45 545 35 HOH HOH . O 8 HOH B 46 546 39 HOH HOH . O 8 HOH B 47 547 36 HOH HOH . O 8 HOH B 48 548 82 HOH HOH . O 8 HOH B 49 549 19 HOH HOH . O 8 HOH B 50 550 14 HOH HOH . O 8 HOH B 51 551 46 HOH HOH . O 8 HOH B 52 552 68 HOH HOH . O 8 HOH B 53 553 89 HOH HOH . O 8 HOH B 54 554 99 HOH HOH . O 8 HOH B 55 555 21 HOH HOH . O 8 HOH B 56 556 85 HOH HOH . O 8 HOH B 57 557 112 HOH HOH . O 8 HOH B 58 558 57 HOH HOH . O 8 HOH B 59 559 110 HOH HOH . O 8 HOH B 60 560 100 HOH HOH . O 8 HOH B 61 561 81 HOH HOH . O 8 HOH B 62 562 51 HOH HOH . O 8 HOH B 63 563 74 HOH HOH . O 8 HOH B 64 564 71 HOH HOH . O 8 HOH B 65 565 88 HOH HOH . O 8 HOH B 66 566 76 HOH HOH . O 8 HOH B 67 567 108 HOH HOH . O 8 HOH B 68 568 7 HOH HOH . O 8 HOH B 69 569 87 HOH HOH . O 8 HOH B 70 570 95 HOH HOH . O 8 HOH B 71 571 86 HOH HOH . O 8 HOH B 72 572 78 HOH HOH . O 8 HOH B 73 573 113 HOH HOH . O 8 HOH B 74 574 115 HOH HOH . O 8 HOH B 75 575 47 HOH HOH . O 8 HOH B 76 576 109 HOH HOH . O 8 HOH B 77 577 58 HOH HOH . O 8 HOH B 78 578 105 HOH HOH . O 8 HOH B 79 579 64 HOH HOH . O 8 HOH B 80 580 77 HOH HOH . O 8 HOH B 81 581 29 HOH HOH . O 8 HOH B 82 582 120 HOH HOH . O 8 HOH B 83 583 50 HOH HOH . O 8 HOH B 84 584 41 HOH HOH . O 8 HOH B 85 585 91 HOH HOH . O 8 HOH B 86 586 106 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 C C18 LJN . . . F 6 -18.029 -52.662 -0.067 1 87.62 ? C18 LJN 204 A 1 HETATM 2 C C19 LJN . . . F 6 -16.587 -53.018 -0.373 1 93.03 ? C19 LJN 204 A 1 HETATM 3 C C20 LJN . . . F 6 -16.03 -54.021 0.629 1 94.64 ? C20 LJN 204 A 1 HETATM 4 C C21 LJN . . . F 6 -14.548 -53.702 0.701 1 97.14 ? C21 LJN 204 A 1 HETATM 5 C C22 LJN . . . F 6 -14.403 -52.375 -0.051 1 97.03 ? C22 LJN 204 A 1 HETATM 6 C C29 LJN . . . F 6 -12.423 -49.701 1.435 1 81.24 ? C29 LJN 204 A 1 HETATM 7 C C30 LJN . . . F 6 -13.072 -50.213 0.326 1 87.73 ? C30 LJN 204 A 1 HETATM 8 C C31 LJN . . . F 6 -11.68 -48.402 1.457 1 74.3 ? C31 LJN 204 A 1 HETATM 9 C C33 LJN . . . F 6 -11.941 -46.485 2.89 1 68.08 ? C33 LJN 204 A 1 HETATM 10 C C56 LJN . . . F 6 -11.91 -45.896 4.286 1 51.48 ? C56 LJN 204 A 1 HETATM 11 N N26 LJN . . . F 6 -13.606 -51.368 0.698 1 86.57 ? N26 LJN 204 A 1 HETATM 12 N N27 LJN . . . F 6 -13.318 -51.637 2.036 1 86.94 ? N27 LJN 204 A 1 HETATM 13 N N28 LJN . . . F 6 -12.559 -50.547 2.479 1 82.56 ? N28 LJN 204 A 1 HETATM 14 N N32 LJN . . . F 6 -11.81 -47.801 2.765 1 64.13 ? N32 LJN 204 A 1 HETATM 15 O O15 LJN . . . F 6 -20.874 -53.343 1.328 1 66.58 ? O15 LJN 204 A 1 HETATM 16 O O17 LJN . . . F 6 -18.727 -53.889 0.131 1 77.86 ? O17 LJN 204 A 1 HETATM 17 O O23 LJN . . . F 6 -15.725 -51.882 -0.308 1 92.6 ? O23 LJN 204 A 1 HETATM 18 O O24 LJN . . . F 6 -16.286 -55.371 0.231 1 92.22 ? O24 LJN 204 A 1 HETATM 19 O O25 LJN . . . F 6 -13.734 -54.727 0.116 1 88.12 ? O25 LJN 204 A 1 HETATM 20 O O35 LJN . . . F 6 -12.046 -45.757 1.919 1 70.1 ? O35 LJN 204 A 1 HETATM 21 P P14 LJN . . . F 6 -19.603 -54.148 1.452 1 59.76 ? P14 LJN 204 A 1 HETATM 22 O O1 LJN . . . F 6 -18.828 -53.658 2.648 1 68.26 ? O1 LJN 204 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 473 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 22 #