data_6YX5
#
_model_server_result.job_id            ufloYsgHz2I34XLEVA_yGQ 
_model_server_result.datetime_utc      '2024-11-28 22:52:55' 
_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              16 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           22 
#