data_7U91 # _model_server_result.job_id 2P2YvNk2TqTPcJp_F187QQ _model_server_result.datetime_utc '2024-11-26 18:38:33' _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 7u91 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 7U91 # _exptl.entry_id 7U91 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.374 _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)-7-(5-O-phosphono-beta-D-ribofuranosyl)-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 _cell.angle_gamma 90 _cell.entry_id 7U91 _cell.length_a 105.628 _cell.length_b 105.628 _cell.length_c 159.585 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U91 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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,D,H 1 1 B,E,F,G,I 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 E N N # _chem_comp.formula 'C17 H24 N5 O10 P' _chem_comp.formula_weight 489.374 _chem_comp.id 56B _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _chem_comp.type 'rna linking' _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 N2 C2 56B sing 1 n n C2 N1 56B sing 2 n n C2 N3 56B doub 3 n n N1 C6 56B sing 4 n n N3 C4 56B sing 5 n n C6 O6 56B doub 6 n n C6 C5 56B sing 7 n n C4 C5 56B doub 8 n y C4 N9 56B sing 9 n y C5 C7 56B sing 10 n y O4' C1' 56B sing 11 n n O4' C4' 56B sing 12 n n O3' C3' 56B sing 13 n n C1' N9 56B sing 14 n n C1' C2' 56B sing 15 n n N9 C8 56B sing 16 n y C4' C3' 56B sing 17 n n C4' C5' 56B sing 18 n n C7 C8 56B doub 19 n y C7 C9 56B sing 20 n n O2' C2' 56B sing 21 n n C3' C2' 56B sing 22 n n N10 C9 56B sing 23 n n N10 C10 56B sing 24 n n C12 C13 56B sing 25 n n C12 O12 56B sing 26 n n C12 C11 56B sing 27 n n C13 C14 56B doub 28 n n C14 C10 56B sing 29 n n C5' O5' 56B sing 30 n n C10 C11 56B sing 31 n n C11 O11 56B sing 32 n n OP2 P 56B sing 33 n n O5' P 56B sing 34 n n P OP1 56B doub 35 n n C2' H1 56B sing 36 n n O2' H2 56B sing 37 n n C1' H3 56B sing 38 n n N10 H4 56B sing 39 n n O11 H6 56B sing 40 n n C8 H7 56B sing 41 n n O12 H8 56B sing 42 n n N2 H9 56B sing 43 n n N2 H10 56B sing 44 n n C9 H11 56B sing 45 n n C9 H12 56B sing 46 n n N1 H13 56B sing 47 n n C10 H14 56B sing 48 n n C11 H15 56B sing 49 n n OP2 H16 56B sing 50 n n C12 H17 56B sing 51 n n C13 H18 56B sing 52 n n C14 H21 56B sing 53 n n O3' H23 56B sing 54 n n C4' H24 56B sing 55 n n C5' H25 56B sing 56 n n C5' H26 56B sing 57 n n C3' H27 56B sing 58 n n P OP3 56B sing 59 n n OP3 HOP3 56B sing 60 n n # _atom_sites.entry_id 7U91 _atom_sites.fract_transf_matrix[1][1] 0.009467 _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] 0.009467 _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] 0.006266 _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 56B A 1 401 401 56B QMP . D 3 NH4 A 1 402 1 NH4 NH4 . E 2 56B B 1 401 401 56B QMP . F 4 PEG B 1 402 402 PEG PEG . G 3 NH4 B 1 403 2 NH4 NH4 . H 5 HOH A 1 501 55 HOH HOH . H 5 HOH A 2 502 120 HOH HOH . H 5 HOH A 3 503 153 HOH HOH . H 5 HOH A 4 504 100 HOH HOH . H 5 HOH A 5 505 155 HOH HOH . H 5 HOH A 6 506 23 HOH HOH . H 5 HOH A 7 507 40 HOH HOH . H 5 HOH A 8 508 183 HOH HOH . H 5 HOH A 9 509 89 HOH HOH . H 5 HOH A 10 510 62 HOH HOH . H 5 HOH A 11 511 81 HOH HOH . H 5 HOH A 12 512 160 HOH HOH . H 5 HOH A 13 513 104 HOH HOH . H 5 HOH A 14 514 136 HOH HOH . H 5 HOH A 15 515 146 HOH HOH . H 5 HOH A 16 516 41 HOH HOH . H 5 HOH A 17 517 88 HOH HOH . H 5 HOH A 18 518 119 HOH HOH . H 5 HOH A 19 519 79 HOH HOH . H 5 HOH A 20 520 130 HOH HOH . H 5 HOH A 21 521 159 HOH HOH . H 5 HOH A 22 522 186 HOH HOH . H 5 HOH A 23 523 20 HOH HOH . H 5 HOH A 24 524 54 HOH HOH . H 5 HOH A 25 525 144 HOH HOH . H 5 HOH A 26 526 134 HOH HOH . H 5 HOH A 27 527 129 HOH HOH . H 5 HOH A 28 528 18 HOH HOH . H 5 HOH A 29 529 21 HOH HOH . H 5 HOH A 30 530 42 HOH HOH . H 5 HOH A 31 531 181 HOH HOH . H 5 HOH A 32 532 123 HOH HOH . H 5 HOH A 33 533 156 HOH HOH . H 5 HOH A 34 534 56 HOH HOH . H 5 HOH A 35 535 48 HOH HOH . H 5 HOH A 36 536 128 HOH HOH . H 5 HOH A 37 537 182 HOH HOH . H 5 HOH A 38 538 43 HOH HOH . H 5 HOH A 39 539 37 HOH HOH . H 5 HOH A 40 540 87 HOH HOH . H 5 HOH A 41 541 158 HOH HOH . H 5 HOH A 42 542 57 HOH HOH . H 5 HOH A 43 543 14 HOH HOH . H 5 HOH A 44 544 75 HOH HOH . H 5 HOH A 45 545 78 HOH HOH . H 5 HOH A 46 546 117 HOH HOH . H 5 HOH A 47 547 19 HOH HOH . H 5 HOH A 48 548 39 HOH HOH . H 5 HOH A 49 549 38 HOH HOH . H 5 HOH A 50 550 164 HOH HOH . H 5 HOH A 51 551 80 HOH HOH . H 5 HOH A 52 552 52 HOH HOH . H 5 HOH A 53 553 50 HOH HOH . H 5 HOH A 54 554 13 HOH HOH . H 5 HOH A 55 555 125 HOH HOH . H 5 HOH A 56 556 166 HOH HOH . H 5 HOH A 57 557 140 HOH HOH . H 5 HOH A 58 558 98 HOH HOH . H 5 HOH A 59 559 137 HOH HOH . H 5 HOH A 60 560 49 HOH HOH . H 5 HOH A 61 561 135 HOH HOH . H 5 HOH A 62 562 141 HOH HOH . H 5 HOH A 63 563 142 HOH HOH . H 5 HOH A 64 564 169 HOH HOH . H 5 HOH A 65 565 90 HOH HOH . H 5 HOH A 66 566 184 HOH HOH . H 5 HOH A 67 567 51 HOH HOH . H 5 HOH A 68 568 53 HOH HOH . H 5 HOH A 69 569 22 HOH HOH . H 5 HOH A 70 570 161 HOH HOH . H 5 HOH A 71 571 127 HOH HOH . H 5 HOH A 72 572 86 HOH HOH . H 5 HOH A 73 573 150 HOH HOH . H 5 HOH A 74 574 178 HOH HOH . H 5 HOH A 75 575 177 HOH HOH . H 5 HOH A 76 576 63 HOH HOH . H 5 HOH A 77 577 85 HOH HOH . H 5 HOH A 78 578 151 HOH HOH . H 5 HOH A 79 579 12 HOH HOH . H 5 HOH A 80 580 17 HOH HOH . H 5 HOH A 81 581 154 HOH HOH . H 5 HOH A 82 582 170 HOH HOH . H 5 HOH A 83 583 118 HOH HOH . I 5 HOH B 1 501 97 HOH HOH . I 5 HOH B 2 502 105 HOH HOH . I 5 HOH B 3 503 163 HOH HOH . I 5 HOH B 4 504 168 HOH HOH . I 5 HOH B 5 505 152 HOH HOH . I 5 HOH B 6 506 139 HOH HOH . I 5 HOH B 7 507 94 HOH HOH . I 5 HOH B 8 508 133 HOH HOH . I 5 HOH B 9 509 112 HOH HOH . I 5 HOH B 10 510 143 HOH HOH . I 5 HOH B 11 511 45 HOH HOH . I 5 HOH B 12 512 68 HOH HOH . I 5 HOH B 13 513 32 HOH HOH . I 5 HOH B 14 514 99 HOH HOH . I 5 HOH B 15 515 33 HOH HOH . I 5 HOH B 16 516 121 HOH HOH . I 5 HOH B 17 517 58 HOH HOH . I 5 HOH B 18 518 2 HOH HOH . I 5 HOH B 19 519 74 HOH HOH . I 5 HOH B 20 520 95 HOH HOH . I 5 HOH B 21 521 91 HOH HOH . I 5 HOH B 22 522 71 HOH HOH . I 5 HOH B 23 523 147 HOH HOH . I 5 HOH B 24 524 145 HOH HOH . I 5 HOH B 25 525 82 HOH HOH . I 5 HOH B 26 526 111 HOH HOH . I 5 HOH B 27 527 76 HOH HOH . I 5 HOH B 28 528 44 HOH HOH . I 5 HOH B 29 529 138 HOH HOH . I 5 HOH B 30 530 1 HOH HOH . I 5 HOH B 31 531 101 HOH HOH . I 5 HOH B 32 532 77 HOH HOH . I 5 HOH B 33 533 113 HOH HOH . I 5 HOH B 34 534 122 HOH HOH . I 5 HOH B 35 535 3 HOH HOH . I 5 HOH B 36 536 83 HOH HOH . I 5 HOH B 37 537 25 HOH HOH . I 5 HOH B 38 538 31 HOH HOH . I 5 HOH B 39 539 157 HOH HOH . I 5 HOH B 40 540 69 HOH HOH . I 5 HOH B 41 541 6 HOH HOH . I 5 HOH B 42 542 187 HOH HOH . I 5 HOH B 43 543 59 HOH HOH . I 5 HOH B 44 544 96 HOH HOH . I 5 HOH B 45 545 173 HOH HOH . I 5 HOH B 46 546 34 HOH HOH . I 5 HOH B 47 547 60 HOH HOH . I 5 HOH B 48 548 35 HOH HOH . I 5 HOH B 49 549 28 HOH HOH . I 5 HOH B 50 550 70 HOH HOH . I 5 HOH B 51 551 162 HOH HOH . I 5 HOH B 52 552 92 HOH HOH . I 5 HOH B 53 553 124 HOH HOH . I 5 HOH B 54 554 115 HOH HOH . I 5 HOH B 55 555 65 HOH HOH . I 5 HOH B 56 556 26 HOH HOH . I 5 HOH B 57 557 30 HOH HOH . I 5 HOH B 58 558 16 HOH HOH . I 5 HOH B 59 559 61 HOH HOH . I 5 HOH B 60 560 27 HOH HOH . I 5 HOH B 61 561 131 HOH HOH . I 5 HOH B 62 562 4 HOH HOH . I 5 HOH B 63 563 84 HOH HOH . I 5 HOH B 64 564 9 HOH HOH . I 5 HOH B 65 565 11 HOH HOH . I 5 HOH B 66 566 114 HOH HOH . I 5 HOH B 67 567 73 HOH HOH . I 5 HOH B 68 568 103 HOH HOH . I 5 HOH B 69 569 24 HOH HOH . I 5 HOH B 70 570 67 HOH HOH . I 5 HOH B 71 571 108 HOH HOH . I 5 HOH B 72 572 93 HOH HOH . I 5 HOH B 73 573 36 HOH HOH . I 5 HOH B 74 574 8 HOH HOH . I 5 HOH B 75 575 179 HOH HOH . I 5 HOH B 76 576 106 HOH HOH . I 5 HOH B 77 577 109 HOH HOH . I 5 HOH B 78 578 10 HOH HOH . I 5 HOH B 79 579 149 HOH HOH . I 5 HOH B 80 580 167 HOH HOH . I 5 HOH B 81 581 5 HOH HOH . I 5 HOH B 82 582 110 HOH HOH . I 5 HOH B 83 583 66 HOH HOH . I 5 HOH B 84 584 132 HOH HOH . I 5 HOH B 85 585 29 HOH HOH . I 5 HOH B 86 586 7 HOH HOH . I 5 HOH B 87 587 148 HOH HOH . I 5 HOH B 88 588 47 HOH HOH . I 5 HOH B 89 589 171 HOH HOH . I 5 HOH B 90 590 15 HOH HOH . I 5 HOH B 91 591 176 HOH HOH . I 5 HOH B 92 592 64 HOH HOH . I 5 HOH B 93 593 72 HOH HOH . I 5 HOH B 94 594 165 HOH HOH . I 5 HOH B 95 595 116 HOH HOH . I 5 HOH B 96 596 185 HOH HOH . I 5 HOH B 97 597 107 HOH HOH . I 5 HOH B 98 598 174 HOH HOH . I 5 HOH B 99 599 180 HOH HOH . I 5 HOH B 100 600 102 HOH HOH . I 5 HOH B 101 601 46 HOH HOH . I 5 HOH B 102 602 172 HOH HOH . I 5 HOH B 103 603 126 HOH HOH . I 5 HOH B 104 604 175 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 N N9 56B . . . C 2 71.245 14.509 68.334 1 40.36 ? N9 56B 401 A 1 HETATM 2 C C2' 56B . . . C 2 72.078 12.932 66.421 1 45.63 ? C2' 56B 401 A 1 HETATM 3 O O2' 56B . . . C 2 70.995 12.88 65.539 1 46.3 ? O2' 56B 401 A 1 HETATM 4 P P 56B . . . C 2 77.069 12.491 69.79 1 48.37 ? P 56B 401 A 1 HETATM 5 C C1' 56B . . . C 2 71.56 13.129 67.84 1 39.25 ? C1' 56B 401 A 1 HETATM 6 N N10 56B . . . C 2 71.029 19.323 69.115 1 50 ? N10 56B 401 A 1 HETATM 7 O O11 56B . . . C 2 72.883 21.44 71.468 1 63.24 ? O11 56B 401 A 1 HETATM 8 C C8 56B . . . C 2 71.998 15.69 68.084 1 41.52 ? C8 56B 401 A 1 HETATM 9 N N3 56B . . . C 2 69.273 13.998 69.78 1 32.22 ? N3 56B 401 A 1 HETATM 10 O O12 56B . . . C 2 70.646 21.746 73.387 1 60.5 ? O12 56B 401 A 1 HETATM 11 C C7 56B . . . C 2 71.458 16.781 68.781 1 44.99 ? C7 56B 401 A 1 HETATM 12 N N2 56B . . . C 2 67.403 13.588 71.156 1 31.18 ? N2 56B 401 A 1 HETATM 13 O O6 56B . . . C 2 69.192 17.855 70.809 1 41.88 ? O6 56B 401 A 1 HETATM 14 C C9 56B . . . C 2 71.972 18.211 68.738 1 48.23 ? C9 56B 401 A 1 HETATM 15 N N1 56B . . . C 2 68.328 15.778 70.973 1 38.63 ? N1 56B 401 A 1 HETATM 16 O O4' 56B . . . C 2 72.608 12.707 68.639 1 40.84 ? O4' 56B 401 A 1 HETATM 17 C C10 56B . . . C 2 71.435 20.634 69.73 1 51.98 ? C10 56B 401 A 1 HETATM 18 O O5' 56B . . . C 2 75.305 12.029 69.282 1 50.12 ? O5' 56B 401 A 1 HETATM 19 C C11 56B . . . C 2 71.799 20.592 71.283 1 57.74 ? C11 56B 401 A 1 HETATM 20 O OP2 56B . . . C 2 76.881 12.451 71.289 1 55.79 ? OP2 56B 401 A 1 HETATM 21 C C12 56B . . . C 2 70.48 21.083 72.11 1 54.35 ? C12 56B 401 A 1 HETATM 22 C C13 56B . . . C 2 69.85 21.924 71.017 1 57.58 ? C13 56B 401 A 1 HETATM 23 O OP1 56B . . . C 2 77.822 11.321 69.2 1 51.38 ? OP1 56B 401 A 1 HETATM 24 C C14 56B . . . C 2 70.336 21.675 69.797 1 53.77 ? C14 56B 401 A 1 HETATM 25 O O3' 56B . . . C 2 71.646 10.526 66.667 1 54.03 ? O3' 56B 401 A 1 HETATM 26 C C5 56B . . . C 2 70.327 16.216 69.512 1 42.54 ? C5 56B 401 A 1 HETATM 27 C C4 56B . . . C 2 70.234 14.841 69.236 1 39.4 ? C4 56B 401 A 1 HETATM 28 C C2 56B . . . C 2 68.331 14.491 70.645 1 34.51 ? C2 56B 401 A 1 HETATM 29 C C6 56B . . . C 2 69.3 16.691 70.442 1 40.05 ? C6 56B 401 A 1 HETATM 30 C C4' 56B . . . C 2 73.347 11.621 68.058 1 44.85 ? C4' 56B 401 A 1 HETATM 31 C C5' 56B . . . C 2 74.913 11.951 68.02 1 46.06 ? C5' 56B 401 A 1 HETATM 32 C C3' 56B . . . C 2 72.677 11.488 66.664 1 48.6 ? C3' 56B 401 A 1 HETATM 33 O OP3 56B . . . C 2 77.288 13.86 69.172 1 45.87 ? OP3 56B 401 A 1 # _model_server_stats.io_time_ms 104 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #