data_4OJT # _model_server_result.job_id X62RQa_UdloFNlbIuqV1WA _model_server_result.datetime_utc '2024-11-18 09:50:23' _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 4ojt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4OJT # _exptl.entry_id 4OJT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.299 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ribosylhomocysteine _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 4OJT _cell.length_a 81.241 _cell.length_b 81.241 _cell.length_c 67.456 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OJT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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' 5_556 x-y,-y,-z+4/3 1 0 0 0 -1 0 0 0 -1 0 0 89.941333 # _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 # _chem_comp.formula 'C9 H17 N O6 S' _chem_comp.formula_weight 267.299 _chem_comp.id 2WP _chem_comp.mon_nstd_flag . _chem_comp.name S-ribosylhomocysteine _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid' # 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 O1 C1 2WP sing 1 n n O4 C1 2WP sing 2 n n O4 C4 2WP sing 3 n n C1 C2 2WP sing 4 n n N CA 2WP sing 5 n n C4 C5 2WP sing 6 n n C4 C3 2WP sing 7 n n CA C 2WP sing 8 n n CA CB 2WP sing 9 n n C2 O2 2WP sing 10 n n C2 C3 2WP sing 11 n n C5 SD 2WP sing 12 n n CG CB 2WP sing 13 n n CG SD 2WP sing 14 n n C3 O3 2WP sing 15 n n C O 2WP doub 16 n n C OXT 2WP sing 17 n n C1 H1 2WP sing 18 n n O1 HO1 2WP sing 19 n n C2 H2 2WP sing 20 n n O2 HO2 2WP sing 21 n n C3 H3 2WP sing 22 n n O3 HO3 2WP sing 23 n n C4 H4 2WP sing 24 n n C5 H51 2WP sing 25 n n C5 H52 2WP sing 26 n n N H10 2WP sing 27 n n N H11 2WP sing 28 n n CA H13 2WP sing 29 n n CB H14 2WP sing 30 n n CB H15 2WP sing 31 n n CG H16 2WP sing 32 n n CG H17 2WP sing 33 n n OXT H18 2WP sing 34 n n # _atom_sites.entry_id 4OJT _atom_sites.fract_transf_matrix[1][1] 0.012309 _atom_sites.fract_transf_matrix[1][2] 0.007107 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014213 _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] 0.014824 _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 2WP A 1 301 231 2WP RHC . C 3 ADE A 1 302 232 ADE ADE . D 4 HOH A 1 401 1 HOH HOH . D 4 HOH A 2 402 2 HOH HOH . D 4 HOH A 3 403 3 HOH HOH . D 4 HOH A 4 404 4 HOH HOH . D 4 HOH A 5 405 5 HOH HOH . D 4 HOH A 6 406 6 HOH HOH . D 4 HOH A 7 407 7 HOH HOH . D 4 HOH A 8 408 8 HOH HOH . D 4 HOH A 9 409 9 HOH HOH . D 4 HOH A 10 410 10 HOH HOH . D 4 HOH A 11 411 11 HOH HOH . D 4 HOH A 12 412 12 HOH HOH . D 4 HOH A 13 413 13 HOH HOH . D 4 HOH A 14 414 14 HOH HOH . D 4 HOH A 15 415 15 HOH HOH . D 4 HOH A 16 416 16 HOH HOH . D 4 HOH A 17 417 17 HOH HOH . D 4 HOH A 18 418 18 HOH HOH . D 4 HOH A 19 419 19 HOH HOH . D 4 HOH A 20 420 20 HOH HOH . D 4 HOH A 21 421 21 HOH HOH . D 4 HOH A 22 422 22 HOH HOH . D 4 HOH A 23 423 23 HOH HOH . D 4 HOH A 24 424 24 HOH HOH . D 4 HOH A 25 425 25 HOH HOH . D 4 HOH A 26 426 26 HOH HOH . D 4 HOH A 27 427 27 HOH HOH . D 4 HOH A 28 428 28 HOH HOH . D 4 HOH A 29 429 29 HOH HOH . D 4 HOH A 30 430 30 HOH HOH . D 4 HOH A 31 431 31 HOH HOH . D 4 HOH A 32 432 32 HOH HOH . D 4 HOH A 33 433 33 HOH HOH . D 4 HOH A 34 434 34 HOH HOH . D 4 HOH A 35 435 35 HOH HOH . D 4 HOH A 36 436 36 HOH HOH . D 4 HOH A 37 437 37 HOH HOH . D 4 HOH A 38 438 38 HOH HOH . D 4 HOH A 39 439 39 HOH HOH . D 4 HOH A 40 440 40 HOH HOH . D 4 HOH A 41 441 41 HOH HOH . D 4 HOH A 42 442 42 HOH HOH . D 4 HOH A 43 443 43 HOH HOH . D 4 HOH A 44 444 44 HOH HOH . D 4 HOH A 45 445 45 HOH HOH . D 4 HOH A 46 446 46 HOH HOH . D 4 HOH A 47 447 47 HOH HOH . D 4 HOH A 48 448 48 HOH HOH . D 4 HOH A 49 449 49 HOH HOH . D 4 HOH A 50 450 50 HOH HOH . D 4 HOH A 51 451 51 HOH HOH . D 4 HOH A 52 452 52 HOH HOH . D 4 HOH A 53 453 53 HOH HOH . D 4 HOH A 54 454 54 HOH HOH . D 4 HOH A 55 455 55 HOH HOH . D 4 HOH A 56 456 56 HOH HOH . D 4 HOH A 57 457 57 HOH HOH . D 4 HOH A 58 458 58 HOH HOH . D 4 HOH A 59 459 59 HOH HOH . D 4 HOH A 60 460 60 HOH HOH . D 4 HOH A 61 461 61 HOH HOH . D 4 HOH A 62 462 62 HOH HOH . D 4 HOH A 63 463 63 HOH HOH . D 4 HOH A 64 464 64 HOH HOH . D 4 HOH A 65 465 65 HOH HOH . D 4 HOH A 66 466 66 HOH HOH . D 4 HOH A 67 467 67 HOH HOH . D 4 HOH A 68 468 68 HOH HOH . D 4 HOH A 69 469 69 HOH HOH . D 4 HOH A 70 470 70 HOH HOH . D 4 HOH A 71 471 71 HOH HOH . D 4 HOH A 72 472 72 HOH HOH . D 4 HOH A 73 473 73 HOH HOH . D 4 HOH A 74 474 74 HOH HOH . D 4 HOH A 75 475 75 HOH HOH . D 4 HOH A 76 476 76 HOH HOH . D 4 HOH A 77 477 77 HOH HOH . D 4 HOH A 78 478 78 HOH HOH . D 4 HOH A 79 479 79 HOH HOH . D 4 HOH A 80 480 80 HOH HOH . D 4 HOH A 81 481 81 HOH HOH . D 4 HOH A 82 482 82 HOH HOH . D 4 HOH A 83 483 83 HOH HOH . D 4 HOH A 84 484 84 HOH HOH . D 4 HOH A 85 485 85 HOH HOH . D 4 HOH A 86 486 86 HOH HOH . D 4 HOH A 87 487 87 HOH HOH . D 4 HOH A 88 488 88 HOH HOH . D 4 HOH A 89 489 89 HOH HOH . D 4 HOH A 90 490 90 HOH HOH . D 4 HOH A 91 491 91 HOH HOH . D 4 HOH A 92 492 92 HOH HOH . D 4 HOH A 93 493 93 HOH HOH . D 4 HOH A 94 494 94 HOH HOH . D 4 HOH A 95 495 95 HOH HOH . D 4 HOH A 96 496 96 HOH HOH . D 4 HOH A 97 497 97 HOH HOH . D 4 HOH A 98 498 98 HOH HOH . D 4 HOH A 99 499 99 HOH HOH . D 4 HOH A 100 500 100 HOH HOH . D 4 HOH A 101 501 101 HOH HOH . D 4 HOH A 102 502 103 HOH HOH . D 4 HOH A 103 503 104 HOH HOH . D 4 HOH A 104 504 105 HOH HOH . D 4 HOH A 105 505 106 HOH HOH . D 4 HOH A 106 506 107 HOH HOH . D 4 HOH A 107 507 108 HOH HOH . D 4 HOH A 108 508 109 HOH HOH . D 4 HOH A 109 509 110 HOH HOH . D 4 HOH A 110 510 111 HOH HOH . D 4 HOH A 111 511 112 HOH HOH . D 4 HOH A 112 512 113 HOH HOH . D 4 HOH A 113 513 114 HOH HOH . D 4 HOH A 114 514 115 HOH HOH . D 4 HOH A 115 515 116 HOH HOH . D 4 HOH A 116 516 117 HOH HOH . D 4 HOH A 117 517 118 HOH HOH . D 4 HOH A 118 518 119 HOH HOH . D 4 HOH A 119 519 120 HOH HOH . D 4 HOH A 120 520 121 HOH HOH . D 4 HOH A 121 521 122 HOH HOH . D 4 HOH A 122 522 123 HOH HOH . D 4 HOH A 123 523 125 HOH HOH . D 4 HOH A 124 524 126 HOH HOH . D 4 HOH A 125 525 127 HOH HOH . D 4 HOH A 126 526 128 HOH HOH . D 4 HOH A 127 527 129 HOH HOH . D 4 HOH A 128 528 130 HOH HOH . D 4 HOH A 129 529 131 HOH HOH . D 4 HOH A 130 530 132 HOH HOH . D 4 HOH A 131 531 133 HOH HOH . D 4 HOH A 132 532 135 HOH HOH . D 4 HOH A 133 533 136 HOH HOH . D 4 HOH A 134 534 137 HOH HOH . D 4 HOH A 135 535 138 HOH HOH . D 4 HOH A 136 536 139 HOH HOH . D 4 HOH A 137 537 140 HOH HOH . D 4 HOH A 138 538 141 HOH HOH . D 4 HOH A 139 539 142 HOH HOH . D 4 HOH A 140 540 144 HOH HOH . D 4 HOH A 141 541 145 HOH HOH . D 4 HOH A 142 542 146 HOH HOH . D 4 HOH A 143 543 148 HOH HOH . D 4 HOH A 144 544 149 HOH HOH . D 4 HOH A 145 545 150 HOH HOH . D 4 HOH A 146 546 151 HOH HOH . D 4 HOH A 147 547 153 HOH HOH . D 4 HOH A 148 548 155 HOH HOH . D 4 HOH A 149 549 156 HOH HOH . D 4 HOH A 150 550 157 HOH HOH . D 4 HOH A 151 551 158 HOH HOH . D 4 HOH A 152 552 159 HOH HOH . D 4 HOH A 153 553 160 HOH HOH . D 4 HOH A 154 554 162 HOH HOH . D 4 HOH A 155 555 163 HOH HOH . D 4 HOH A 156 556 164 HOH HOH . D 4 HOH A 157 557 166 HOH HOH . D 4 HOH A 158 558 168 HOH HOH . D 4 HOH A 159 559 169 HOH HOH . D 4 HOH A 160 560 170 HOH HOH . D 4 HOH A 161 561 172 HOH HOH . D 4 HOH A 162 562 173 HOH HOH . D 4 HOH A 163 563 174 HOH HOH . D 4 HOH A 164 564 175 HOH HOH . D 4 HOH A 165 565 176 HOH HOH . D 4 HOH A 166 566 178 HOH HOH . D 4 HOH A 167 567 179 HOH HOH . D 4 HOH A 168 568 180 HOH HOH . D 4 HOH A 169 569 181 HOH HOH . D 4 HOH A 170 570 186 HOH HOH . D 4 HOH A 171 571 187 HOH HOH . D 4 HOH A 172 572 188 HOH HOH . D 4 HOH A 173 573 189 HOH HOH . D 4 HOH A 174 574 190 HOH HOH . D 4 HOH A 175 575 191 HOH HOH . D 4 HOH A 176 576 193 HOH HOH . D 4 HOH A 177 577 194 HOH HOH . D 4 HOH A 178 578 195 HOH HOH . D 4 HOH A 179 579 196 HOH HOH . D 4 HOH A 180 580 197 HOH HOH . D 4 HOH A 181 581 199 HOH HOH . D 4 HOH A 182 582 200 HOH HOH . D 4 HOH A 183 583 202 HOH HOH . D 4 HOH A 184 584 203 HOH HOH . D 4 HOH A 185 585 204 HOH HOH . D 4 HOH A 186 586 205 HOH HOH . D 4 HOH A 187 587 206 HOH HOH . D 4 HOH A 188 588 208 HOH HOH . D 4 HOH A 189 589 212 HOH HOH . D 4 HOH A 190 590 213 HOH HOH . D 4 HOH A 191 591 214 HOH HOH . D 4 HOH A 192 592 217 HOH HOH . D 4 HOH A 193 593 219 HOH HOH . D 4 HOH A 194 594 221 HOH HOH . D 4 HOH A 195 595 222 HOH HOH . D 4 HOH A 196 596 223 HOH HOH . D 4 HOH A 197 597 224 HOH HOH . D 4 HOH A 198 598 225 HOH HOH . D 4 HOH A 199 599 226 HOH HOH . D 4 HOH A 200 600 227 HOH HOH . D 4 HOH A 201 601 230 HOH HOH . D 4 HOH A 202 602 231 HOH HOH . D 4 HOH A 203 603 232 HOH HOH . D 4 HOH A 204 604 233 HOH HOH . D 4 HOH A 205 605 235 HOH HOH . D 4 HOH A 206 606 237 HOH HOH . D 4 HOH A 207 607 238 HOH HOH . D 4 HOH A 208 608 240 HOH HOH . D 4 HOH A 209 609 241 HOH HOH . D 4 HOH A 210 610 242 HOH HOH . D 4 HOH A 211 611 244 HOH HOH . D 4 HOH A 212 612 246 HOH HOH . D 4 HOH A 213 613 248 HOH HOH . D 4 HOH A 214 614 250 HOH HOH . D 4 HOH A 215 615 251 HOH HOH . D 4 HOH A 216 616 253 HOH HOH . D 4 HOH A 217 617 257 HOH HOH . D 4 HOH A 218 618 259 HOH HOH . D 4 HOH A 219 619 268 HOH HOH . D 4 HOH A 220 620 269 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 2WP . . . B 2 38.744 -4.139 31.086 1 19.69 ? C1 2WP 301 A 1 HETATM 2 O O1 2WP . . . B 2 40.188 -4.156 30.997 1 16.01 ? O1 2WP 301 A 1 HETATM 3 C C2 2WP . . . B 2 38.293 -3.673 32.51 1 18.06 ? C2 2WP 301 A 1 HETATM 4 O O2 2WP . . . B 2 39.034 -2.598 32.979 1 15.95 ? O2 2WP 301 A 1 HETATM 5 C C3 2WP . . . B 2 38.585 -4.961 33.298 1 16.27 ? C3 2WP 301 A 1 HETATM 6 O O3 2WP . . . B 2 39.949 -5.235 33.393 1 15.82 ? O3 2WP 301 A 1 HETATM 7 C C4 2WP . . . B 2 38.024 -6.035 32.321 1 15.14 ? C4 2WP 301 A 1 HETATM 8 O O4 2WP . . . B 2 38.206 -5.461 31.011 1 17.68 ? O4 2WP 301 A 1 HETATM 9 C C5 2WP . . . B 2 36.528 -6.279 32.591 1 17.79 ? C5 2WP 301 A 1 HETATM 10 N N 2WP . . . B 2 35.377 -11.613 31.527 1 21.55 ? N 2WP 301 A 1 HETATM 11 C CA 2WP . . . B 2 36.492 -11.57 32.482 1 19.66 ? CA 2WP 301 A 1 HETATM 12 C CB 2WP . . . B 2 36.295 -10.347 33.425 1 19.78 ? CB 2WP 301 A 1 HETATM 13 C CG 2WP . . . B 2 36.453 -9.054 32.64 1 17.56 ? CG 2WP 301 A 1 HETATM 14 S SD 2WP . . . B 2 36.262 -7.641 33.801 1 17.46 ? SD 2WP 301 A 1 HETATM 15 C C 2WP . . . B 2 36.529 -12.88 33.349 1 20.22 ? C 2WP 301 A 1 HETATM 16 O O 2WP . . . B 2 35.412 -13.384 33.577 1 19.51 ? O 2WP 301 A 1 HETATM 17 O OXT 2WP . . . B 2 37.638 -13.31 33.726 1 22.19 ? OXT 2WP 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #