data_7W93
#
_model_server_result.job_id            w1TyEPpV1yJjXw6MxPgP9g 
_model_server_result.datetime_utc      '2024-12-27 00:53:04' 
_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          7w93 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    7W93 
#
_exptl.entry_id    7W93 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              258.228 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione 
_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            7W93 
_cell.length_a            185.83 
_cell.length_b            185.83 
_cell.length_c            52.51 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7W93 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    'P 6c 2c' 
_symmetry.space_group_name_H-M     'P 63 2 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 
_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' 10_554 -y,-x,-z-1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -26.255 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 O ASN 250 A ASN 250 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? 
metalc ? metalc2 A OD1 ASN 250 A ASN 250 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? 
metalc ? metalc3 A O THR 252 A THR 252 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? 
metalc ? metalc4 A O ALA 286 A ALA 286 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? 
metalc ? metalc5 A O CYS 289 A CYS 289 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc6 A O TYR 291 A TYR 291 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? 
#
_chem_comp.formula           'C10 H14 N2 O6' 
_chem_comp.formula_weight    258.228 
_chem_comp.id                8IZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione 
_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
O15 C14 8IZ doub 1 n n 
C14 N13 8IZ sing 2 n n 
C14 N16 8IZ sing 3 n n 
N13 C11 8IZ sing 4 n n 
C17 N16 8IZ sing 5 n n 
N16 C18 8IZ sing 6 n n 
C11 O12 8IZ doub 7 n n 
C11 C10 8IZ sing 8 n n 
C18 C10 8IZ doub 9 n n 
C10 C03 8IZ sing 10 n n 
O01 C02 8IZ sing 11 n n 
C03 C02 8IZ sing 12 n n 
C03 O04 8IZ sing 13 n n 
C02 C08 8IZ sing 14 n n 
O04 C05 8IZ sing 15 n n 
C08 O09 8IZ sing 16 n n 
C08 C05 8IZ sing 17 n n 
C05 C06 8IZ sing 18 n n 
C06 O07 8IZ sing 19 n n 
C02 H1 8IZ sing 20 n n 
C03 H2 8IZ sing 21 n n 
C05 H3 8IZ sing 22 n n 
C06 H4 8IZ sing 23 n n 
C06 H5 8IZ sing 24 n n 
C08 H6 8IZ sing 25 n n 
C17 H7 8IZ sing 26 n n 
C17 H8 8IZ sing 27 n n 
C17 H9 8IZ sing 28 n n 
C18 H10 8IZ sing 29 n n 
N13 H11 8IZ sing 30 n n 
O01 H12 8IZ sing 31 n n 
O07 H13 8IZ sing 32 n n 
O09 H14 8IZ sing 33 n n 
#
_atom_sites.entry_id                     7W93 
_atom_sites.fract_transf_matrix[1][1]    0.005381 
_atom_sites.fract_transf_matrix[1][2]    0.003107 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006214 
_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]    0.019044 
_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 8IZ A 1 401 401 8IZ N1Y . 
C 3 K A 1 402 1 K K . 
D 4 HOH A 1 501 72 HOH HOH . 
D 4 HOH A 2 502 143 HOH HOH . 
D 4 HOH A 3 503 69 HOH HOH . 
D 4 HOH A 4 504 103 HOH HOH . 
D 4 HOH A 5 505 83 HOH HOH . 
D 4 HOH A 6 506 127 HOH HOH . 
D 4 HOH A 7 507 144 HOH HOH . 
D 4 HOH A 8 508 49 HOH HOH . 
D 4 HOH A 9 509 18 HOH HOH . 
D 4 HOH A 10 510 107 HOH HOH . 
D 4 HOH A 11 511 151 HOH HOH . 
D 4 HOH A 12 512 61 HOH HOH . 
D 4 HOH A 13 513 74 HOH HOH . 
D 4 HOH A 14 514 56 HOH HOH . 
D 4 HOH A 15 515 43 HOH HOH . 
D 4 HOH A 16 516 6 HOH HOH . 
D 4 HOH A 17 517 108 HOH HOH . 
D 4 HOH A 18 518 59 HOH HOH . 
D 4 HOH A 19 519 89 HOH HOH . 
D 4 HOH A 20 520 141 HOH HOH . 
D 4 HOH A 21 521 130 HOH HOH . 
D 4 HOH A 22 522 32 HOH HOH . 
D 4 HOH A 23 523 66 HOH HOH . 
D 4 HOH A 24 524 114 HOH HOH . 
D 4 HOH A 25 525 42 HOH HOH . 
D 4 HOH A 26 526 157 HOH HOH . 
D 4 HOH A 27 527 91 HOH HOH . 
D 4 HOH A 28 528 95 HOH HOH . 
D 4 HOH A 29 529 41 HOH HOH . 
D 4 HOH A 30 530 124 HOH HOH . 
D 4 HOH A 31 531 110 HOH HOH . 
D 4 HOH A 32 532 40 HOH HOH . 
D 4 HOH A 33 533 16 HOH HOH . 
D 4 HOH A 34 534 158 HOH HOH . 
D 4 HOH A 35 535 60 HOH HOH . 
D 4 HOH A 36 536 31 HOH HOH . 
D 4 HOH A 37 537 36 HOH HOH . 
D 4 HOH A 38 538 126 HOH HOH . 
D 4 HOH A 39 539 12 HOH HOH . 
D 4 HOH A 40 540 25 HOH HOH . 
D 4 HOH A 41 541 34 HOH HOH . 
D 4 HOH A 42 542 35 HOH HOH . 
D 4 HOH A 43 543 17 HOH HOH . 
D 4 HOH A 44 544 147 HOH HOH . 
D 4 HOH A 45 545 22 HOH HOH . 
D 4 HOH A 46 546 33 HOH HOH . 
D 4 HOH A 47 547 30 HOH HOH . 
D 4 HOH A 48 548 13 HOH HOH . 
D 4 HOH A 49 549 73 HOH HOH . 
D 4 HOH A 50 550 156 HOH HOH . 
D 4 HOH A 51 551 84 HOH HOH . 
D 4 HOH A 52 552 28 HOH HOH . 
D 4 HOH A 53 553 79 HOH HOH . 
D 4 HOH A 54 554 96 HOH HOH . 
D 4 HOH A 55 555 142 HOH HOH . 
D 4 HOH A 56 556 123 HOH HOH . 
D 4 HOH A 57 557 44 HOH HOH . 
D 4 HOH A 58 558 14 HOH HOH . 
D 4 HOH A 59 559 76 HOH HOH . 
D 4 HOH A 60 560 106 HOH HOH . 
D 4 HOH A 61 561 82 HOH HOH . 
D 4 HOH A 62 562 117 HOH HOH . 
D 4 HOH A 63 563 20 HOH HOH . 
D 4 HOH A 64 564 118 HOH HOH . 
D 4 HOH A 65 565 8 HOH HOH . 
D 4 HOH A 66 566 120 HOH HOH . 
D 4 HOH A 67 567 5 HOH HOH . 
D 4 HOH A 68 568 52 HOH HOH . 
D 4 HOH A 69 569 75 HOH HOH . 
D 4 HOH A 70 570 10 HOH HOH . 
D 4 HOH A 71 571 88 HOH HOH . 
D 4 HOH A 72 572 15 HOH HOH . 
D 4 HOH A 73 573 113 HOH HOH . 
D 4 HOH A 74 574 65 HOH HOH . 
D 4 HOH A 75 575 7 HOH HOH . 
D 4 HOH A 76 576 93 HOH HOH . 
D 4 HOH A 77 577 80 HOH HOH . 
D 4 HOH A 78 578 51 HOH HOH . 
D 4 HOH A 79 579 63 HOH HOH . 
D 4 HOH A 80 580 164 HOH HOH . 
D 4 HOH A 81 581 160 HOH HOH . 
D 4 HOH A 82 582 121 HOH HOH . 
D 4 HOH A 83 583 94 HOH HOH . 
D 4 HOH A 84 584 38 HOH HOH . 
D 4 HOH A 85 585 1 HOH HOH . 
D 4 HOH A 86 586 136 HOH HOH . 
D 4 HOH A 87 587 19 HOH HOH . 
D 4 HOH A 88 588 70 HOH HOH . 
D 4 HOH A 89 589 21 HOH HOH . 
D 4 HOH A 90 590 122 HOH HOH . 
D 4 HOH A 91 591 133 HOH HOH . 
D 4 HOH A 92 592 68 HOH HOH . 
D 4 HOH A 93 593 55 HOH HOH . 
D 4 HOH A 94 594 85 HOH HOH . 
D 4 HOH A 95 595 131 HOH HOH . 
D 4 HOH A 96 596 99 HOH HOH . 
D 4 HOH A 97 597 53 HOH HOH . 
D 4 HOH A 98 598 46 HOH HOH . 
D 4 HOH A 99 599 62 HOH HOH . 
D 4 HOH A 100 600 39 HOH HOH . 
D 4 HOH A 101 601 148 HOH HOH . 
D 4 HOH A 102 602 129 HOH HOH . 
D 4 HOH A 103 603 102 HOH HOH . 
D 4 HOH A 104 604 37 HOH HOH . 
D 4 HOH A 105 605 47 HOH HOH . 
D 4 HOH A 106 606 112 HOH HOH . 
D 4 HOH A 107 607 2 HOH HOH . 
D 4 HOH A 108 608 119 HOH HOH . 
D 4 HOH A 109 609 45 HOH HOH . 
D 4 HOH A 110 610 11 HOH HOH . 
D 4 HOH A 111 611 4 HOH HOH . 
D 4 HOH A 112 612 27 HOH HOH . 
D 4 HOH A 113 613 125 HOH HOH . 
D 4 HOH A 114 614 71 HOH HOH . 
D 4 HOH A 115 615 146 HOH HOH . 
D 4 HOH A 116 616 23 HOH HOH . 
D 4 HOH A 117 617 86 HOH HOH . 
D 4 HOH A 118 618 9 HOH HOH . 
D 4 HOH A 119 619 78 HOH HOH . 
D 4 HOH A 120 620 132 HOH HOH . 
D 4 HOH A 121 621 115 HOH HOH . 
D 4 HOH A 122 622 48 HOH HOH . 
D 4 HOH A 123 623 90 HOH HOH . 
D 4 HOH A 124 624 137 HOH HOH . 
D 4 HOH A 125 625 154 HOH HOH . 
D 4 HOH A 126 626 3 HOH HOH . 
D 4 HOH A 127 627 104 HOH HOH . 
D 4 HOH A 128 628 159 HOH HOH . 
D 4 HOH A 129 629 87 HOH HOH . 
D 4 HOH A 130 630 155 HOH HOH . 
D 4 HOH A 131 631 161 HOH HOH . 
D 4 HOH A 132 632 109 HOH HOH . 
D 4 HOH A 133 633 26 HOH HOH . 
D 4 HOH A 134 634 152 HOH HOH . 
D 4 HOH A 135 635 163 HOH HOH . 
D 4 HOH A 136 636 92 HOH HOH . 
D 4 HOH A 137 637 101 HOH HOH . 
D 4 HOH A 138 638 98 HOH HOH . 
D 4 HOH A 139 639 162 HOH HOH . 
D 4 HOH A 140 640 100 HOH HOH . 
D 4 HOH A 141 641 111 HOH HOH . 
D 4 HOH A 142 642 153 HOH HOH . 
D 4 HOH A 143 643 150 HOH HOH . 
D 4 HOH A 144 644 165 HOH HOH . 
D 4 HOH A 145 645 105 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 C10 8IZ . . . B 2 74.755 -26.993 -9.482 1 42.31 ? C10 8IZ 401 A 1 
HETATM 2 C C02 8IZ . . . B 2 73.107 -28.655 -8.297 1 41.65 ? C02 8IZ 401 A 1 
HETATM 3 C C03 8IZ . . . B 2 73.752 -27.284 -8.364 1 42.74 ? C03 8IZ 401 A 1 
HETATM 4 C C05 8IZ . . . B 2 73.411 -27.311 -6.078 1 43.84 ? C05 8IZ 401 A 1 
HETATM 5 C C06 8IZ . . . B 2 74.124 -27.472 -4.647 1 43.43 ? C06 8IZ 401 A 1 
HETATM 6 C C08 8IZ . . . B 2 72.794 -28.64 -6.713 1 46.41 ? C08 8IZ 401 A 1 
HETATM 7 C C11 8IZ . . . B 2 74.86 -25.725 -10.189 1 42.87 ? C11 8IZ 401 A 1 
HETATM 8 C C14 8IZ . . . B 2 76.79 -26.416 -11.391 1 39.5 ? C14 8IZ 401 A 1 
HETATM 9 C C17 8IZ . . . B 2 77.764 -28.918 -10.838 1 46.81 ? C17 8IZ 401 A 1 
HETATM 10 C C18 8IZ . . . B 2 75.714 -28.002 -9.645 1 39.2 ? C18 8IZ 401 A 1 
HETATM 11 N N13 8IZ . . . B 2 75.858 -25.403 -11.189 1 37.22 ? N13 8IZ 401 A 1 
HETATM 12 N N16 8IZ . . . B 2 76.717 -27.781 -10.59 1 43.44 ? N16 8IZ 401 A 1 
HETATM 13 O O01 8IZ . . . B 2 72.009 -28.72 -9.161 1 42.28 ? O01 8IZ 401 A 1 
HETATM 14 O O04 8IZ . . . B 2 74.34 -27.027 -7.113 1 41.75 ? O04 8IZ 401 A 1 
HETATM 15 O O07 8IZ . . . B 2 74.611 -26.217 -4.244 1 42.75 ? O07 8IZ 401 A 1 
HETATM 16 O O09 8IZ . . . B 2 71.422 -28.548 -6.551 1 43.14 ? O09 8IZ 401 A 1 
HETATM 17 O O12 8IZ . . . B 2 74.041 -24.824 -10.044 1 40.93 ? O12 8IZ 401 A 1 
HETATM 18 O O15 8IZ . . . B 2 77.684 -26.233 -12.212 1 40.86 ? O15 8IZ 401 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#