data_8DL3
#
_model_server_result.job_id            BqBkKAFodEQ1f04iKO_Q5w 
_model_server_result.datetime_utc      '2024-11-06 20:42:27' 
_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          8dl3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8DL3 
#
_exptl.entry_id    8DL3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              277.279 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one 
_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          90.33 
_cell.angle_gamma         90 
_cell.entry_id            8DL3 
_cell.length_a            42.726 
_cell.length_b            136.759 
_cell.length_c            52.606 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DL3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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           'C12 H15 N5 O3' 
_chem_comp.formula_weight    277.279 
_chem_comp.id                QEI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     queuine 
#
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
C1 C2 QEI sing 277 n n 
C1 C3 QEI sing 278 n n 
C1 N1 QEI sing 279 n n 
C2 C4 QEI sing 280 n n 
C2 O1 QEI sing 281 n n 
C3 C5 QEI doub 282 n n 
C4 C5 QEI sing 283 n n 
C4 O2 QEI sing 284 n n 
C6 N1 QEI sing 285 n n 
C6 C7 QEI sing 286 n n 
C9 C10 QEI doub 287 n y 
C9 C11 QEI sing 288 n n 
C9 C7 QEI sing 289 n y 
C10 N2 QEI sing 290 n y 
C10 N3 QEI sing 291 n n 
C11 N4 QEI sing 292 n n 
C11 O3 QEI doub 293 n n 
C7 C8 QEI doub 294 n y 
C8 N2 QEI sing 295 n y 
N3 C12 QEI doub 296 n n 
C12 N5 QEI sing 297 n n 
C12 N4 QEI sing 298 n n 
C1 H1 QEI sing 299 n n 
C2 H2 QEI sing 300 n n 
C3 H3 QEI sing 301 n n 
C4 H4 QEI sing 302 n n 
C5 H5 QEI sing 303 n n 
C6 H6 QEI sing 304 n n 
C6 H6A QEI sing 305 n n 
O1 HO1 QEI sing 306 n n 
O2 HO2 QEI sing 307 n n 
N1 HN1 QEI sing 308 n n 
C8 H8 QEI sing 309 n n 
N2 HN2 QEI sing 310 n n 
N5 HN5 QEI sing 311 n n 
N5 HN5A QEI sing 312 n n 
N4 HN4 QEI sing 313 n n 
#
_atom_sites.entry_id                     8DL3 
_atom_sites.fract_transf_matrix[1][1]    0.023405 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000137 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007312 
_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]    0.01901 
_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 QEI A 1 401 401 QEI QEI . 
D 2 QEI B 1 401 401 QEI QEI . 
E 3 HOH A 1 501 185 HOH HOH . 
E 3 HOH A 2 502 85 HOH HOH . 
E 3 HOH A 3 503 165 HOH HOH . 
E 3 HOH A 4 504 107 HOH HOH . 
E 3 HOH A 5 505 48 HOH HOH . 
E 3 HOH A 6 506 87 HOH HOH . 
E 3 HOH A 7 507 137 HOH HOH . 
E 3 HOH A 8 508 106 HOH HOH . 
E 3 HOH A 9 509 42 HOH HOH . 
E 3 HOH A 10 510 182 HOH HOH . 
E 3 HOH A 11 511 22 HOH HOH . 
E 3 HOH A 12 512 118 HOH HOH . 
E 3 HOH A 13 513 46 HOH HOH . 
E 3 HOH A 14 514 68 HOH HOH . 
E 3 HOH A 15 515 65 HOH HOH . 
E 3 HOH A 16 516 29 HOH HOH . 
E 3 HOH A 17 517 83 HOH HOH . 
E 3 HOH A 18 518 55 HOH HOH . 
E 3 HOH A 19 519 134 HOH HOH . 
E 3 HOH A 20 520 58 HOH HOH . 
E 3 HOH A 21 521 57 HOH HOH . 
E 3 HOH A 22 522 14 HOH HOH . 
E 3 HOH A 23 523 49 HOH HOH . 
E 3 HOH A 24 524 140 HOH HOH . 
E 3 HOH A 25 525 145 HOH HOH . 
E 3 HOH A 26 526 6 HOH HOH . 
E 3 HOH A 27 527 23 HOH HOH . 
E 3 HOH A 28 528 7 HOH HOH . 
E 3 HOH A 29 529 19 HOH HOH . 
E 3 HOH A 30 530 97 HOH HOH . 
E 3 HOH A 31 531 131 HOH HOH . 
E 3 HOH A 32 532 61 HOH HOH . 
E 3 HOH A 33 533 51 HOH HOH . 
E 3 HOH A 34 534 40 HOH HOH . 
E 3 HOH A 35 535 32 HOH HOH . 
E 3 HOH A 36 536 52 HOH HOH . 
E 3 HOH A 37 537 95 HOH HOH . 
E 3 HOH A 38 538 187 HOH HOH . 
E 3 HOH A 39 539 10 HOH HOH . 
E 3 HOH A 40 540 25 HOH HOH . 
E 3 HOH A 41 541 111 HOH HOH . 
E 3 HOH A 42 542 93 HOH HOH . 
E 3 HOH A 43 543 72 HOH HOH . 
E 3 HOH A 44 544 128 HOH HOH . 
E 3 HOH A 45 545 124 HOH HOH . 
E 3 HOH A 46 546 76 HOH HOH . 
E 3 HOH A 47 547 84 HOH HOH . 
E 3 HOH A 48 548 1 HOH HOH . 
E 3 HOH A 49 549 126 HOH HOH . 
E 3 HOH A 50 550 24 HOH HOH . 
E 3 HOH A 51 551 66 HOH HOH . 
E 3 HOH A 52 552 114 HOH HOH . 
E 3 HOH A 53 553 125 HOH HOH . 
E 3 HOH A 54 554 142 HOH HOH . 
E 3 HOH A 55 555 59 HOH HOH . 
E 3 HOH A 56 556 186 HOH HOH . 
E 3 HOH A 57 557 176 HOH HOH . 
E 3 HOH A 58 558 91 HOH HOH . 
E 3 HOH A 59 559 34 HOH HOH . 
E 3 HOH A 60 560 82 HOH HOH . 
E 3 HOH A 61 561 108 HOH HOH . 
E 3 HOH A 62 562 71 HOH HOH . 
E 3 HOH A 63 563 45 HOH HOH . 
E 3 HOH A 64 564 116 HOH HOH . 
E 3 HOH A 65 565 27 HOH HOH . 
E 3 HOH A 66 566 70 HOH HOH . 
E 3 HOH A 67 567 168 HOH HOH . 
E 3 HOH A 68 568 150 HOH HOH . 
E 3 HOH A 69 569 156 HOH HOH . 
E 3 HOH A 70 570 129 HOH HOH . 
E 3 HOH A 71 571 139 HOH HOH . 
E 3 HOH A 72 572 127 HOH HOH . 
E 3 HOH A 73 573 89 HOH HOH . 
E 3 HOH A 74 574 21 HOH HOH . 
E 3 HOH A 75 575 77 HOH HOH . 
E 3 HOH A 76 576 119 HOH HOH . 
E 3 HOH A 77 577 94 HOH HOH . 
E 3 HOH A 78 578 194 HOH HOH . 
E 3 HOH A 79 579 138 HOH HOH . 
E 3 HOH A 80 580 41 HOH HOH . 
E 3 HOH A 81 581 104 HOH HOH . 
E 3 HOH A 82 582 169 HOH HOH . 
E 3 HOH A 83 583 175 HOH HOH . 
E 3 HOH A 84 584 173 HOH HOH . 
E 3 HOH A 85 585 147 HOH HOH . 
E 3 HOH A 86 586 183 HOH HOH . 
E 3 HOH A 87 587 28 HOH HOH . 
E 3 HOH A 88 588 181 HOH HOH . 
E 3 HOH A 89 589 153 HOH HOH . 
E 3 HOH A 90 590 102 HOH HOH . 
E 3 HOH A 91 591 188 HOH HOH . 
F 3 HOH B 1 501 159 HOH HOH . 
F 3 HOH B 2 502 18 HOH HOH . 
F 3 HOH B 3 503 60 HOH HOH . 
F 3 HOH B 4 504 74 HOH HOH . 
F 3 HOH B 5 505 158 HOH HOH . 
F 3 HOH B 6 506 53 HOH HOH . 
F 3 HOH B 7 507 193 HOH HOH . 
F 3 HOH B 8 508 37 HOH HOH . 
F 3 HOH B 9 509 115 HOH HOH . 
F 3 HOH B 10 510 110 HOH HOH . 
F 3 HOH B 11 511 86 HOH HOH . 
F 3 HOH B 12 512 132 HOH HOH . 
F 3 HOH B 13 513 62 HOH HOH . 
F 3 HOH B 14 514 9 HOH HOH . 
F 3 HOH B 15 515 171 HOH HOH . 
F 3 HOH B 16 516 31 HOH HOH . 
F 3 HOH B 17 517 109 HOH HOH . 
F 3 HOH B 18 518 96 HOH HOH . 
F 3 HOH B 19 519 38 HOH HOH . 
F 3 HOH B 20 520 33 HOH HOH . 
F 3 HOH B 21 521 189 HOH HOH . 
F 3 HOH B 22 522 144 HOH HOH . 
F 3 HOH B 23 523 101 HOH HOH . 
F 3 HOH B 24 524 17 HOH HOH . 
F 3 HOH B 25 525 11 HOH HOH . 
F 3 HOH B 26 526 122 HOH HOH . 
F 3 HOH B 27 527 92 HOH HOH . 
F 3 HOH B 28 528 47 HOH HOH . 
F 3 HOH B 29 529 146 HOH HOH . 
F 3 HOH B 30 530 163 HOH HOH . 
F 3 HOH B 31 531 67 HOH HOH . 
F 3 HOH B 32 532 105 HOH HOH . 
F 3 HOH B 33 533 157 HOH HOH . 
F 3 HOH B 34 534 20 HOH HOH . 
F 3 HOH B 35 535 43 HOH HOH . 
F 3 HOH B 36 536 123 HOH HOH . 
F 3 HOH B 37 537 16 HOH HOH . 
F 3 HOH B 38 538 164 HOH HOH . 
F 3 HOH B 39 539 154 HOH HOH . 
F 3 HOH B 40 540 143 HOH HOH . 
F 3 HOH B 41 541 2 HOH HOH . 
F 3 HOH B 42 542 81 HOH HOH . 
F 3 HOH B 43 543 167 HOH HOH . 
F 3 HOH B 44 544 78 HOH HOH . 
F 3 HOH B 45 545 35 HOH HOH . 
F 3 HOH B 46 546 190 HOH HOH . 
F 3 HOH B 47 547 3 HOH HOH . 
F 3 HOH B 48 548 26 HOH HOH . 
F 3 HOH B 49 549 133 HOH HOH . 
F 3 HOH B 50 550 177 HOH HOH . 
F 3 HOH B 51 551 4 HOH HOH . 
F 3 HOH B 52 552 180 HOH HOH . 
F 3 HOH B 53 553 130 HOH HOH . 
F 3 HOH B 54 554 12 HOH HOH . 
F 3 HOH B 55 555 113 HOH HOH . 
F 3 HOH B 56 556 141 HOH HOH . 
F 3 HOH B 57 557 98 HOH HOH . 
F 3 HOH B 58 558 5 HOH HOH . 
F 3 HOH B 59 559 8 HOH HOH . 
F 3 HOH B 60 560 135 HOH HOH . 
F 3 HOH B 61 561 50 HOH HOH . 
F 3 HOH B 62 562 160 HOH HOH . 
F 3 HOH B 63 563 152 HOH HOH . 
F 3 HOH B 64 564 192 HOH HOH . 
F 3 HOH B 65 565 90 HOH HOH . 
F 3 HOH B 66 566 30 HOH HOH . 
F 3 HOH B 67 567 39 HOH HOH . 
F 3 HOH B 68 568 56 HOH HOH . 
F 3 HOH B 69 569 99 HOH HOH . 
F 3 HOH B 70 570 103 HOH HOH . 
F 3 HOH B 71 571 79 HOH HOH . 
F 3 HOH B 72 572 162 HOH HOH . 
F 3 HOH B 73 573 170 HOH HOH . 
F 3 HOH B 74 574 136 HOH HOH . 
F 3 HOH B 75 575 75 HOH HOH . 
F 3 HOH B 76 576 73 HOH HOH . 
F 3 HOH B 77 577 184 HOH HOH . 
F 3 HOH B 78 578 54 HOH HOH . 
F 3 HOH B 79 579 69 HOH HOH . 
F 3 HOH B 80 580 112 HOH HOH . 
F 3 HOH B 81 581 36 HOH HOH . 
F 3 HOH B 82 582 166 HOH HOH . 
F 3 HOH B 83 583 120 HOH HOH . 
F 3 HOH B 84 584 44 HOH HOH . 
F 3 HOH B 85 585 13 HOH HOH . 
F 3 HOH B 86 586 88 HOH HOH . 
F 3 HOH B 87 587 15 HOH HOH . 
F 3 HOH B 88 588 179 HOH HOH . 
F 3 HOH B 89 589 174 HOH HOH . 
F 3 HOH B 90 590 121 HOH HOH . 
F 3 HOH B 91 591 148 HOH HOH . 
F 3 HOH B 92 592 178 HOH HOH . 
F 3 HOH B 93 593 117 HOH HOH . 
F 3 HOH B 94 594 191 HOH HOH . 
F 3 HOH B 95 595 149 HOH HOH . 
F 3 HOH B 96 596 80 HOH HOH . 
F 3 HOH B 97 597 100 HOH HOH . 
F 3 HOH B 98 598 155 HOH HOH . 
F 3 HOH B 99 599 64 HOH HOH . 
F 3 HOH B 100 600 172 HOH HOH . 
F 3 HOH B 101 601 63 HOH HOH . 
F 3 HOH B 102 602 161 HOH HOH . 
F 3 HOH B 103 603 151 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 C1 QEI . . . C 2 1.235 -5.401 -1.666 1 35.95 ? C1 QEI 401 A 1 
HETATM 2 C C2 QEI . . . C 2 0.486 -5.944 -0.464 1 37.9 ? C2 QEI 401 A 1 
HETATM 3 C C3 QEI . . . C 2 1.921 -6.626 -2.205 1 38.63 ? C3 QEI 401 A 1 
HETATM 4 C C4 QEI . . . C 2 1.374 -7.08 0.022 1 36.69 ? C4 QEI 401 A 1 
HETATM 5 C C5 QEI . . . C 2 1.967 -7.569 -1.276 1 40.23 ? C5 QEI 401 A 1 
HETATM 6 C C6 QEI . . . C 2 1.54 -2.978 -1.367 1 36.74 ? C6 QEI 401 A 1 
HETATM 7 C C9 QEI . . . C 2 2.46 -2.156 1.027 1 34.39 ? C9 QEI 401 A 1 
HETATM 8 C C10 QEI . . . C 2 2.649 -0.793 1.553 1 33.63 ? C10 QEI 401 A 1 
HETATM 9 C C11 QEI . . . C 2 2.824 -3.302 1.89 1 32.2 ? C11 QEI 401 A 1 
HETATM 10 O O1 QEI . . . C 2 -0.801 -6.429 -0.855 1 35.89 ? O1 QEI 401 A 1 
HETATM 11 O O2 QEI . . . C 2 0.683 -8.072 0.767 1 37.45 ? O2 QEI 401 A 1 
HETATM 12 N N1 QEI . . . C 2 2.072 -4.317 -1.199 1 36.22 ? N1 QEI 401 A 1 
HETATM 13 C C7 QEI . . . C 2 1.931 -1.953 -0.328 1 35.53 ? C7 QEI 401 A 1 
HETATM 14 C C8 QEI . . . C 2 1.833 -0.578 -0.496 1 36.22 ? C8 QEI 401 A 1 
HETATM 15 N N2 QEI . . . C 2 2.249 0.08 0.61 1 36.61 ? N2 QEI 401 A 1 
HETATM 16 N N3 QEI . . . C 2 3.134 -0.664 2.809 1 33.26 ? N3 QEI 401 A 1 
HETATM 17 C C12 QEI . . . C 2 3.451 -1.766 3.557 1 32.77 ? C12 QEI 401 A 1 
HETATM 18 N N5 QEI . . . C 2 3.929 -1.567 4.821 1 29.66 ? N5 QEI 401 A 1 
HETATM 19 N N4 QEI . . . C 2 3.298 -3.033 3.104 1 32.72 ? N4 QEI 401 A 1 
HETATM 20 O O3 QEI . . . C 2 2.701 -4.479 1.49 1 34.47 ? O3 QEI 401 A 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#