data_4YR7
#
_model_server_result.job_id            08SbvebQ2T0Oh9i4LkcxXw 
_model_server_result.datetime_utc      '2024-12-26 12:14:22' 
_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          4yr7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    4YR7 
#
_exptl.entry_id    4YR7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              176.94 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-deoxy-alpha-L-xylulofuranose-1,2-borate 
_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            4YR7 
_cell.length_a            74.45 
_cell.length_b            85.23 
_cell.length_c            133.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YR7 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 D N N 
#
_chem_comp.formula           'C5 H10 B O6 -1' 
_chem_comp.formula_weight    176.94 
_chem_comp.id                A1B 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-deoxy-alpha-L-xylulofuranose-1,2-borate 
_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
O12 C7 A1B sing 1 n n 
C6 O5 A1B sing 2 n n 
C6 C7 A1B sing 3 n n 
O5 C4 A1B sing 4 n n 
C7 C8 A1B sing 5 n n 
C11 C4 A1B sing 6 n n 
C4 C8 A1B sing 7 n n 
C4 O3 A1B sing 8 n n 
C8 O1 A1B sing 9 n n 
O3 B A1B sing 10 n n 
O1 B A1B sing 11 n n 
B O9 A1B sing 12 n n 
B O10 A1B sing 13 n n 
C8 H1 A1B sing 14 n n 
C7 H2 A1B sing 15 n n 
O12 H3 A1B sing 16 n n 
C6 H4 A1B sing 17 n n 
C6 H5 A1B sing 18 n n 
C11 H6 A1B sing 19 n n 
C11 H7 A1B sing 20 n n 
C11 H8 A1B sing 21 n n 
O10 H9 A1B sing 22 n n 
O9 H10 A1B sing 23 n n 
#
_atom_sites.entry_id                     4YR7 
_atom_sites.fract_transf_matrix[1][1]    0.013432 
_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]    0.011733 
_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]    0.007485 
_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 A1B A 1 401 1 A1B A1B . 
D 2 A1B B 1 401 1 A1B A1B . 
E 3 HOH A 1 501 131 HOH HOH . 
E 3 HOH A 2 502 106 HOH HOH . 
E 3 HOH A 3 503 150 HOH HOH . 
E 3 HOH A 4 504 188 HOH HOH . 
E 3 HOH A 5 505 179 HOH HOH . 
E 3 HOH A 6 506 97 HOH HOH . 
E 3 HOH A 7 507 139 HOH HOH . 
E 3 HOH A 8 508 89 HOH HOH . 
E 3 HOH A 9 509 161 HOH HOH . 
E 3 HOH A 10 510 6 HOH HOH . 
E 3 HOH A 11 511 71 HOH HOH . 
E 3 HOH A 12 512 15 HOH HOH . 
E 3 HOH A 13 513 10 HOH HOH . 
E 3 HOH A 14 514 37 HOH HOH . 
E 3 HOH A 15 515 105 HOH HOH . 
E 3 HOH A 16 516 16 HOH HOH . 
E 3 HOH A 17 517 86 HOH HOH . 
E 3 HOH A 18 518 2 HOH HOH . 
E 3 HOH A 19 519 123 HOH HOH . 
E 3 HOH A 20 520 121 HOH HOH . 
E 3 HOH A 21 521 154 HOH HOH . 
E 3 HOH A 22 522 167 HOH HOH . 
E 3 HOH A 23 523 158 HOH HOH . 
E 3 HOH A 24 524 1 HOH HOH . 
E 3 HOH A 25 525 133 HOH HOH . 
E 3 HOH A 26 526 173 HOH HOH . 
E 3 HOH A 27 527 187 HOH HOH . 
E 3 HOH A 28 528 93 HOH HOH . 
E 3 HOH A 29 529 81 HOH HOH . 
E 3 HOH A 30 530 160 HOH HOH . 
E 3 HOH A 31 531 25 HOH HOH . 
E 3 HOH A 32 532 8 HOH HOH . 
E 3 HOH A 33 533 109 HOH HOH . 
E 3 HOH A 34 534 195 HOH HOH . 
E 3 HOH A 35 535 163 HOH HOH . 
E 3 HOH A 36 536 77 HOH HOH . 
E 3 HOH A 37 537 53 HOH HOH . 
E 3 HOH A 38 538 136 HOH HOH . 
E 3 HOH A 39 539 101 HOH HOH . 
E 3 HOH A 40 540 102 HOH HOH . 
E 3 HOH A 41 541 104 HOH HOH . 
E 3 HOH A 42 542 41 HOH HOH . 
E 3 HOH A 43 543 111 HOH HOH . 
E 3 HOH A 44 544 29 HOH HOH . 
E 3 HOH A 45 545 153 HOH HOH . 
E 3 HOH A 46 546 44 HOH HOH . 
E 3 HOH A 47 547 3 HOH HOH . 
E 3 HOH A 48 548 165 HOH HOH . 
E 3 HOH A 49 549 66 HOH HOH . 
E 3 HOH A 50 550 61 HOH HOH . 
E 3 HOH A 51 551 9 HOH HOH . 
E 3 HOH A 52 552 191 HOH HOH . 
E 3 HOH A 53 553 84 HOH HOH . 
E 3 HOH A 54 554 5 HOH HOH . 
E 3 HOH A 55 555 17 HOH HOH . 
E 3 HOH A 56 556 186 HOH HOH . 
E 3 HOH A 57 557 124 HOH HOH . 
E 3 HOH A 58 558 43 HOH HOH . 
E 3 HOH A 59 559 40 HOH HOH . 
E 3 HOH A 60 560 155 HOH HOH . 
E 3 HOH A 61 561 120 HOH HOH . 
E 3 HOH A 62 562 183 HOH HOH . 
E 3 HOH A 63 563 119 HOH HOH . 
E 3 HOH A 64 564 169 HOH HOH . 
E 3 HOH A 65 565 137 HOH HOH . 
E 3 HOH A 66 566 22 HOH HOH . 
E 3 HOH A 67 567 141 HOH HOH . 
E 3 HOH A 68 568 185 HOH HOH . 
E 3 HOH A 69 569 11 HOH HOH . 
E 3 HOH A 70 570 36 HOH HOH . 
E 3 HOH A 71 571 129 HOH HOH . 
E 3 HOH A 72 572 80 HOH HOH . 
E 3 HOH A 73 573 125 HOH HOH . 
E 3 HOH A 74 574 50 HOH HOH . 
E 3 HOH A 75 575 122 HOH HOH . 
E 3 HOH A 76 576 73 HOH HOH . 
E 3 HOH A 77 577 166 HOH HOH . 
E 3 HOH A 78 578 83 HOH HOH . 
E 3 HOH A 79 579 69 HOH HOH . 
E 3 HOH A 80 580 26 HOH HOH . 
E 3 HOH A 81 581 103 HOH HOH . 
E 3 HOH A 82 582 27 HOH HOH . 
E 3 HOH A 83 583 78 HOH HOH . 
E 3 HOH A 84 584 64 HOH HOH . 
E 3 HOH A 85 585 67 HOH HOH . 
E 3 HOH A 86 586 157 HOH HOH . 
E 3 HOH A 87 587 87 HOH HOH . 
E 3 HOH A 88 588 52 HOH HOH . 
E 3 HOH A 89 589 45 HOH HOH . 
E 3 HOH A 90 590 94 HOH HOH . 
E 3 HOH A 91 591 138 HOH HOH . 
E 3 HOH A 92 592 115 HOH HOH . 
E 3 HOH A 93 593 172 HOH HOH . 
E 3 HOH A 94 594 24 HOH HOH . 
E 3 HOH A 95 595 128 HOH HOH . 
E 3 HOH A 96 596 130 HOH HOH . 
E 3 HOH A 97 597 177 HOH HOH . 
E 3 HOH A 98 598 182 HOH HOH . 
E 3 HOH A 99 599 88 HOH HOH . 
E 3 HOH A 100 600 58 HOH HOH . 
E 3 HOH A 101 601 145 HOH HOH . 
E 3 HOH A 102 602 75 HOH HOH . 
E 3 HOH A 103 603 4 HOH HOH . 
F 3 HOH B 1 501 190 HOH HOH . 
F 3 HOH B 2 502 107 HOH HOH . 
F 3 HOH B 3 503 28 HOH HOH . 
F 3 HOH B 4 504 72 HOH HOH . 
F 3 HOH B 5 505 117 HOH HOH . 
F 3 HOH B 6 506 193 HOH HOH . 
F 3 HOH B 7 507 151 HOH HOH . 
F 3 HOH B 8 508 146 HOH HOH . 
F 3 HOH B 9 509 176 HOH HOH . 
F 3 HOH B 10 510 79 HOH HOH . 
F 3 HOH B 11 511 116 HOH HOH . 
F 3 HOH B 12 512 168 HOH HOH . 
F 3 HOH B 13 513 48 HOH HOH . 
F 3 HOH B 14 514 42 HOH HOH . 
F 3 HOH B 15 515 19 HOH HOH . 
F 3 HOH B 16 516 62 HOH HOH . 
F 3 HOH B 17 517 38 HOH HOH . 
F 3 HOH B 18 518 13 HOH HOH . 
F 3 HOH B 19 519 149 HOH HOH . 
F 3 HOH B 20 520 70 HOH HOH . 
F 3 HOH B 21 521 54 HOH HOH . 
F 3 HOH B 22 522 31 HOH HOH . 
F 3 HOH B 23 523 12 HOH HOH . 
F 3 HOH B 24 524 113 HOH HOH . 
F 3 HOH B 25 525 118 HOH HOH . 
F 3 HOH B 26 526 68 HOH HOH . 
F 3 HOH B 27 527 33 HOH HOH . 
F 3 HOH B 28 528 63 HOH HOH . 
F 3 HOH B 29 529 134 HOH HOH . 
F 3 HOH B 30 530 30 HOH HOH . 
F 3 HOH B 31 531 98 HOH HOH . 
F 3 HOH B 32 532 175 HOH HOH . 
F 3 HOH B 33 533 20 HOH HOH . 
F 3 HOH B 34 534 184 HOH HOH . 
F 3 HOH B 35 535 112 HOH HOH . 
F 3 HOH B 36 536 57 HOH HOH . 
F 3 HOH B 37 537 21 HOH HOH . 
F 3 HOH B 38 538 135 HOH HOH . 
F 3 HOH B 39 539 132 HOH HOH . 
F 3 HOH B 40 540 76 HOH HOH . 
F 3 HOH B 41 541 85 HOH HOH . 
F 3 HOH B 42 542 140 HOH HOH . 
F 3 HOH B 43 543 7 HOH HOH . 
F 3 HOH B 44 544 152 HOH HOH . 
F 3 HOH B 45 545 49 HOH HOH . 
F 3 HOH B 46 546 34 HOH HOH . 
F 3 HOH B 47 547 100 HOH HOH . 
F 3 HOH B 48 548 194 HOH HOH . 
F 3 HOH B 49 549 148 HOH HOH . 
F 3 HOH B 50 550 126 HOH HOH . 
F 3 HOH B 51 551 114 HOH HOH . 
F 3 HOH B 52 552 46 HOH HOH . 
F 3 HOH B 53 553 110 HOH HOH . 
F 3 HOH B 54 554 162 HOH HOH . 
F 3 HOH B 55 555 65 HOH HOH . 
F 3 HOH B 56 556 99 HOH HOH . 
F 3 HOH B 57 557 32 HOH HOH . 
F 3 HOH B 58 558 108 HOH HOH . 
F 3 HOH B 59 559 178 HOH HOH . 
F 3 HOH B 60 560 192 HOH HOH . 
F 3 HOH B 61 561 56 HOH HOH . 
F 3 HOH B 62 562 35 HOH HOH . 
F 3 HOH B 63 563 156 HOH HOH . 
F 3 HOH B 64 564 39 HOH HOH . 
F 3 HOH B 65 565 164 HOH HOH . 
F 3 HOH B 66 566 174 HOH HOH . 
F 3 HOH B 67 567 14 HOH HOH . 
F 3 HOH B 68 568 18 HOH HOH . 
F 3 HOH B 69 569 74 HOH HOH . 
F 3 HOH B 70 570 82 HOH HOH . 
F 3 HOH B 71 571 51 HOH HOH . 
F 3 HOH B 72 572 144 HOH HOH . 
F 3 HOH B 73 573 92 HOH HOH . 
F 3 HOH B 74 574 95 HOH HOH . 
F 3 HOH B 75 575 189 HOH HOH . 
F 3 HOH B 76 576 171 HOH HOH . 
F 3 HOH B 77 577 60 HOH HOH . 
F 3 HOH B 78 578 142 HOH HOH . 
F 3 HOH B 79 579 147 HOH HOH . 
F 3 HOH B 80 580 91 HOH HOH . 
F 3 HOH B 81 581 59 HOH HOH . 
F 3 HOH B 82 582 47 HOH HOH . 
F 3 HOH B 83 583 170 HOH HOH . 
F 3 HOH B 84 584 143 HOH HOH . 
F 3 HOH B 85 585 23 HOH HOH . 
F 3 HOH B 86 586 55 HOH HOH . 
F 3 HOH B 87 587 90 HOH HOH . 
F 3 HOH B 88 588 96 HOH HOH . 
F 3 HOH B 89 589 181 HOH HOH . 
F 3 HOH B 90 590 159 HOH HOH . 
F 3 HOH B 91 591 127 HOH HOH . 
F 3 HOH B 92 592 180 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 C8 A1B . . . C 2 -8.74 -18.257 14.311 1 47.5 ? C8 A1B 401 A 1 
HETATM 2 O O1 A1B . . . C 2 -8.608 -17.324 13.239 1 43.59 ? O1 A1B 401 A 1 
HETATM 3 C C7 A1B . . . C 2 -9.363 -17.64 15.441 1 50.54 ? C7 A1B 401 A 1 
HETATM 4 O O12 A1B . . . C 2 -10.127 -18.6 16.102 1 41.78 ? O12 A1B 401 A 1 
HETATM 5 C C6 A1B . . . C 2 -8.249 -17.18 16.286 1 46.67 ? C6 A1B 401 A 1 
HETATM 6 O O5 A1B . . . C 2 -7.216 -18.12 16.059 1 45.51 ? O5 A1B 401 A 1 
HETATM 7 C C4 A1B . . . C 2 -7.403 -18.629 14.759 1 47.1 ? C4 A1B 401 A 1 
HETATM 8 C C11 A1B . . . C 2 -7.241 -20.104 14.791 1 48.73 ? C11 A1B 401 A 1 
HETATM 9 O O3 A1B . . . C 2 -6.51 -18.065 13.89 1 44.62 ? O3 A1B 401 A 1 
HETATM 10 B B A1B . . . C 2 -7.242 -17.455 12.808 1 41.78 ? B A1B 401 A 1 
HETATM 11 O O10 A1B . . . C 2 -7.102 -18.277 11.623 1 34.71 ? O10 A1B 401 A 1 
HETATM 12 O O9 A1B . . . C 2 -6.778 -16.127 12.487 1 43.4 ? O9 A1B 401 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           12 
#