data_1K27 # _model_server_result.job_id LNEdajrvuRnn-w2usUerpg _model_server_result.datetime_utc '2024-11-08 14:43:38' _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 1k27 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 1K27 # _exptl.entry_id 1K27 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.377 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL _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 1K27 _cell.length_a 122.231 _cell.length_b 122.231 _cell.length_c 44.743 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K27 _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,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 122.231 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 61.1155 105.855151 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H19 N5 O2 S' _chem_comp.formula_weight 297.377 _chem_comp.id MTM _chem_comp.mon_nstd_flag . _chem_comp.name (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (1S)-1-(9-DEAZAADENIN-9-YL)-1,4,5-TRIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL # 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 CS S5' MTM sing 237 n n CS HCS1 MTM sing 238 n n CS HCS2 MTM sing 239 n n CS HCS3 MTM sing 240 n n S5' C5' MTM sing 241 n n C5' C4' MTM sing 242 n n C5' "H5'1" MTM sing 243 n n C5' "H5'2" MTM sing 244 n n C4' N4' MTM sing 245 n n C4' C3' MTM sing 246 n n C4' H4' MTM sing 247 n n N4' C1' MTM sing 248 n n N4' HN4 MTM sing 249 n n C2' O2' MTM sing 250 n n C2' C3' MTM sing 251 n n C2' C1' MTM sing 252 n n C2' H2' MTM sing 253 n n O2' "HO'2" MTM sing 254 n n C3' O3' MTM sing 255 n n C3' H3' MTM sing 256 n n O3' H3T MTM sing 257 n n C1' C9 MTM sing 258 n n C1' H1' MTM sing 259 n n C9 C8 MTM doub 260 n y C9 C4 MTM sing 261 n y C8 N7 MTM sing 262 n y C8 H8 MTM sing 263 n n N7 C5 MTM sing 264 n y N7 H7 MTM sing 265 n n C5 C6 MTM sing 266 n n C5 C4 MTM doub 267 n y C6 N6 MTM sing 268 n n C6 N1 MTM sing 269 n n C6 H6 MTM sing 270 n n N6 H61 MTM sing 271 n n N6 H62 MTM sing 272 n n N1 C2 MTM sing 273 n n N1 HN1 MTM sing 274 n n C2 N3 MTM doub 275 n n C2 H2 MTM sing 276 n n N3 C4 MTM sing 277 n n # _atom_sites.entry_id 1K27 _atom_sites.fract_transf_matrix[1][1] 0.008181 _atom_sites.fract_transf_matrix[1][2] 0.004723 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009447 _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] 0.02235 _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 PO4 A 1 301 301 PO4 PO4 . C 3 MTM A 1 401 401 MTM MTM . D 4 HOH A 1 501 501 HOH HOH . D 4 HOH A 2 502 502 HOH HOH . D 4 HOH A 3 503 503 HOH HOH . D 4 HOH A 4 504 504 HOH HOH . D 4 HOH A 5 505 505 HOH HOH . D 4 HOH A 6 506 506 HOH HOH . D 4 HOH A 7 507 507 HOH HOH . D 4 HOH A 8 508 508 HOH HOH . D 4 HOH A 9 509 509 HOH HOH . D 4 HOH A 10 510 510 HOH HOH . D 4 HOH A 11 511 511 HOH HOH . D 4 HOH A 12 512 512 HOH HOH . D 4 HOH A 13 513 513 HOH HOH . D 4 HOH A 14 514 514 HOH HOH . D 4 HOH A 15 515 515 HOH HOH . D 4 HOH A 16 516 516 HOH HOH . D 4 HOH A 17 517 517 HOH HOH . D 4 HOH A 18 518 518 HOH HOH . D 4 HOH A 19 519 519 HOH HOH . D 4 HOH A 20 520 520 HOH HOH . D 4 HOH A 21 521 521 HOH HOH . D 4 HOH A 22 522 522 HOH HOH . D 4 HOH A 23 523 523 HOH HOH . D 4 HOH A 24 524 524 HOH HOH . D 4 HOH A 25 525 525 HOH HOH . D 4 HOH A 26 526 526 HOH HOH . D 4 HOH A 27 527 527 HOH HOH . D 4 HOH A 28 528 528 HOH HOH . D 4 HOH A 29 529 529 HOH HOH . D 4 HOH A 30 530 530 HOH HOH . D 4 HOH A 31 531 531 HOH HOH . D 4 HOH A 32 532 532 HOH HOH . D 4 HOH A 33 533 533 HOH HOH . D 4 HOH A 34 534 534 HOH HOH . D 4 HOH A 35 535 535 HOH HOH . D 4 HOH A 36 536 536 HOH HOH . D 4 HOH A 37 537 537 HOH HOH . D 4 HOH A 38 538 538 HOH HOH . D 4 HOH A 39 539 539 HOH HOH . D 4 HOH A 40 540 540 HOH HOH . D 4 HOH A 41 541 541 HOH HOH . D 4 HOH A 42 542 542 HOH HOH . D 4 HOH A 43 543 543 HOH HOH . D 4 HOH A 44 544 544 HOH HOH . D 4 HOH A 45 545 545 HOH HOH . D 4 HOH A 46 546 546 HOH HOH . D 4 HOH A 47 547 547 HOH HOH . D 4 HOH A 48 548 548 HOH HOH . D 4 HOH A 49 549 549 HOH HOH . D 4 HOH A 50 550 550 HOH HOH . D 4 HOH A 51 551 551 HOH HOH . D 4 HOH A 52 552 552 HOH HOH . D 4 HOH A 53 553 553 HOH HOH . D 4 HOH A 54 554 554 HOH HOH . D 4 HOH A 55 555 555 HOH HOH . D 4 HOH A 56 556 556 HOH HOH . D 4 HOH A 57 557 557 HOH HOH . D 4 HOH A 58 558 558 HOH HOH . D 4 HOH A 59 559 559 HOH HOH . D 4 HOH A 60 560 560 HOH HOH . D 4 HOH A 61 561 561 HOH HOH . D 4 HOH A 62 562 562 HOH HOH . D 4 HOH A 63 563 563 HOH HOH . D 4 HOH A 64 564 564 HOH HOH . D 4 HOH A 65 565 565 HOH HOH . D 4 HOH A 66 566 566 HOH HOH . D 4 HOH A 67 567 567 HOH HOH . D 4 HOH A 68 568 568 HOH HOH . D 4 HOH A 69 569 569 HOH HOH . D 4 HOH A 70 570 570 HOH HOH . D 4 HOH A 71 571 571 HOH HOH . D 4 HOH A 72 572 572 HOH HOH . D 4 HOH A 73 573 573 HOH HOH . D 4 HOH A 74 574 574 HOH HOH . D 4 HOH A 75 575 575 HOH HOH . D 4 HOH A 76 576 576 HOH HOH . D 4 HOH A 77 577 577 HOH HOH . D 4 HOH A 78 578 578 HOH HOH . D 4 HOH A 79 579 579 HOH HOH . D 4 HOH A 80 580 580 HOH HOH . D 4 HOH A 81 581 581 HOH HOH . D 4 HOH A 82 582 582 HOH HOH . D 4 HOH A 83 583 583 HOH HOH . D 4 HOH A 84 584 584 HOH HOH . D 4 HOH A 85 585 585 HOH HOH . D 4 HOH A 86 586 586 HOH HOH . D 4 HOH A 87 587 587 HOH HOH . D 4 HOH A 88 588 588 HOH HOH . D 4 HOH A 89 589 589 HOH HOH . D 4 HOH A 90 590 590 HOH HOH . D 4 HOH A 91 591 591 HOH HOH . D 4 HOH A 92 592 592 HOH HOH . D 4 HOH A 93 593 593 HOH HOH . D 4 HOH A 94 594 594 HOH HOH . D 4 HOH A 95 595 595 HOH HOH . D 4 HOH A 96 596 596 HOH HOH . D 4 HOH A 97 597 597 HOH HOH . D 4 HOH A 98 598 598 HOH HOH . D 4 HOH A 99 599 599 HOH HOH . D 4 HOH A 100 600 600 HOH HOH . D 4 HOH A 101 601 601 HOH HOH . D 4 HOH A 102 602 602 HOH HOH . D 4 HOH A 103 603 603 HOH HOH . D 4 HOH A 104 604 604 HOH HOH . D 4 HOH A 105 605 605 HOH HOH . D 4 HOH A 106 606 606 HOH HOH . D 4 HOH A 107 607 607 HOH HOH . D 4 HOH A 108 608 608 HOH HOH . D 4 HOH A 109 609 609 HOH HOH . D 4 HOH A 110 610 610 HOH HOH . D 4 HOH A 111 611 611 HOH HOH . D 4 HOH A 112 612 612 HOH HOH . D 4 HOH A 113 613 613 HOH HOH . D 4 HOH A 114 614 614 HOH HOH . D 4 HOH A 115 615 615 HOH HOH . D 4 HOH A 116 616 616 HOH HOH . D 4 HOH A 117 617 617 HOH HOH . D 4 HOH A 118 618 618 HOH HOH . D 4 HOH A 119 619 619 HOH HOH . D 4 HOH A 120 620 620 HOH HOH . D 4 HOH A 121 621 621 HOH HOH . D 4 HOH A 122 622 622 HOH HOH . D 4 HOH A 123 623 623 HOH HOH . D 4 HOH A 124 624 624 HOH HOH . D 4 HOH A 125 625 625 HOH HOH . D 4 HOH A 126 626 626 HOH HOH . D 4 HOH A 127 627 627 HOH HOH . D 4 HOH A 128 628 628 HOH HOH . D 4 HOH A 129 629 629 HOH HOH . D 4 HOH A 130 630 630 HOH HOH . D 4 HOH A 131 631 631 HOH HOH . D 4 HOH A 132 632 632 HOH HOH . D 4 HOH A 133 633 633 HOH HOH . D 4 HOH A 134 634 634 HOH HOH . D 4 HOH A 135 635 635 HOH HOH . D 4 HOH A 136 636 636 HOH HOH . D 4 HOH A 137 637 637 HOH HOH . D 4 HOH A 138 638 638 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 CS MTM . . . C 3 58.521 13.493 31.901 1 17.82 ? CS MTM 401 A 1 HETATM 2 S S5' MTM . . . C 3 58.589 14.539 30.423 1 19.62 ? S5' MTM 401 A 1 HETATM 3 C C5' MTM . . . C 3 59.252 16.089 31.13 1 17.75 ? C5' MTM 401 A 1 HETATM 4 C C4' MTM . . . C 3 60.746 16.041 31.436 1 16.52 ? C4' MTM 401 A 1 HETATM 5 N N4' MTM . . . C 3 61.439 15.533 30.247 1 16.79 ? N4' MTM 401 A 1 HETATM 6 C C2' MTM . . . C 3 61.98 17.843 30.396 1 13.28 ? C2' MTM 401 A 1 HETATM 7 O O2' MTM . . . C 3 63.342 18.363 30.601 1 11.91 ? O2' MTM 401 A 1 HETATM 8 C C3' MTM . . . C 3 61.341 17.407 31.786 1 15.67 ? C3' MTM 401 A 1 HETATM 9 O O3' MTM . . . C 3 62.374 17.284 32.851 1 18.14 ? O3' MTM 401 A 1 HETATM 10 C C1' MTM . . . C 3 62.015 16.601 29.438 1 12.92 ? C1' MTM 401 A 1 HETATM 11 C C9 MTM . . . C 3 61.139 16.703 28.093 1 11.04 ? C9 MTM 401 A 1 HETATM 12 C C8 MTM . . . C 3 60.864 15.642 27.236 1 9.61 ? C8 MTM 401 A 1 HETATM 13 N N7 MTM . . . C 3 60.124 15.957 26.19 1 8.81 ? N7 MTM 401 A 1 HETATM 14 C C5 MTM . . . C 3 59.881 17.311 26.347 1 10.53 ? C5 MTM 401 A 1 HETATM 15 C C6 MTM . . . C 3 59.157 18.278 25.586 1 8.42 ? C6 MTM 401 A 1 HETATM 16 N N6 MTM . . . C 3 58.52 17.965 24.452 1 8.96 ? N6 MTM 401 A 1 HETATM 17 N N1 MTM . . . C 3 59.132 19.586 26.067 1 10.19 ? N1 MTM 401 A 1 HETATM 18 C C2 MTM . . . C 3 59.775 19.913 27.212 1 10.03 ? C2 MTM 401 A 1 HETATM 19 N N3 MTM . . . C 3 60.484 19.082 28.004 1 10.96 ? N3 MTM 401 A 1 HETATM 20 C C4 MTM . . . C 3 60.494 17.795 27.509 1 10.4 ? C4 MTM 401 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #