data_6KDR # _model_server_result.job_id JcSDW2dbjl-sk5LVIhR9Qw _model_server_result.datetime_utc '2024-11-26 10:56:10' _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 6kdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 6KDR # _exptl.entry_id 6KDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 6KDR _cell.length_a 70.548 _cell.length_b 96.534 _cell.length_c 100.213 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 3 E N N ? 3 H N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide 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 N CA SAH sing 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 6KDR _atom_sites.fract_transf_matrix[1][1] 0.014175 _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] 0.010359 _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] 0.009979 _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 E 3 SAH A 1 301 2 SAH SAH . F 4 GOL A 1 302 1 GOL GOL . G 5 CL A 1 303 6 CL CL . H 3 SAH B 1 301 1 SAH SAH . I 4 GOL B 1 302 2 GOL GOL . J 4 GOL B 1 303 3 GOL GOL . K 5 CL B 1 304 5 CL CL . L 5 CL E 1 101 4 CL CL . M 6 HOH A 1 401 194 HOH HOH . M 6 HOH A 2 402 240 HOH HOH . M 6 HOH A 3 403 225 HOH HOH . M 6 HOH A 4 404 136 HOH HOH . M 6 HOH A 5 405 146 HOH HOH . M 6 HOH A 6 406 164 HOH HOH . M 6 HOH A 7 407 28 HOH HOH . M 6 HOH A 8 408 12 HOH HOH . M 6 HOH A 9 409 39 HOH HOH . M 6 HOH A 10 410 159 HOH HOH . M 6 HOH A 11 411 96 HOH HOH . M 6 HOH A 12 412 81 HOH HOH . M 6 HOH A 13 413 141 HOH HOH . M 6 HOH A 14 414 49 HOH HOH . M 6 HOH A 15 415 211 HOH HOH . M 6 HOH A 16 416 80 HOH HOH . M 6 HOH A 17 417 244 HOH HOH . M 6 HOH A 18 418 37 HOH HOH . M 6 HOH A 19 419 56 HOH HOH . M 6 HOH A 20 420 124 HOH HOH . M 6 HOH A 21 421 125 HOH HOH . M 6 HOH A 22 422 145 HOH HOH . M 6 HOH A 23 423 167 HOH HOH . M 6 HOH A 24 424 24 HOH HOH . M 6 HOH A 25 425 70 HOH HOH . M 6 HOH A 26 426 187 HOH HOH . M 6 HOH A 27 427 178 HOH HOH . M 6 HOH A 28 428 114 HOH HOH . M 6 HOH A 29 429 5 HOH HOH . M 6 HOH A 30 430 72 HOH HOH . M 6 HOH A 31 431 148 HOH HOH . M 6 HOH A 32 432 135 HOH HOH . M 6 HOH A 33 433 112 HOH HOH . M 6 HOH A 34 434 65 HOH HOH . M 6 HOH A 35 435 17 HOH HOH . M 6 HOH A 36 436 14 HOH HOH . M 6 HOH A 37 437 6 HOH HOH . M 6 HOH A 38 438 48 HOH HOH . M 6 HOH A 39 439 160 HOH HOH . M 6 HOH A 40 440 36 HOH HOH . M 6 HOH A 41 441 54 HOH HOH . M 6 HOH A 42 442 109 HOH HOH . M 6 HOH A 43 443 149 HOH HOH . M 6 HOH A 44 444 43 HOH HOH . M 6 HOH A 45 445 27 HOH HOH . M 6 HOH A 46 446 150 HOH HOH . M 6 HOH A 47 447 90 HOH HOH . M 6 HOH A 48 448 47 HOH HOH . M 6 HOH A 49 449 107 HOH HOH . M 6 HOH A 50 450 199 HOH HOH . M 6 HOH A 51 451 153 HOH HOH . M 6 HOH A 52 452 85 HOH HOH . M 6 HOH A 53 453 156 HOH HOH . M 6 HOH A 54 454 95 HOH HOH . M 6 HOH A 55 455 116 HOH HOH . M 6 HOH A 56 456 223 HOH HOH . M 6 HOH A 57 457 220 HOH HOH . M 6 HOH A 58 458 45 HOH HOH . M 6 HOH A 59 459 98 HOH HOH . M 6 HOH A 60 460 204 HOH HOH . M 6 HOH A 61 461 188 HOH HOH . M 6 HOH A 62 462 79 HOH HOH . M 6 HOH A 63 463 241 HOH HOH . M 6 HOH A 64 464 210 HOH HOH . M 6 HOH A 65 465 215 HOH HOH . M 6 HOH A 66 466 163 HOH HOH . M 6 HOH A 67 467 214 HOH HOH . M 6 HOH A 68 468 245 HOH HOH . M 6 HOH A 69 469 89 HOH HOH . M 6 HOH A 70 470 123 HOH HOH . M 6 HOH A 71 471 134 HOH HOH . M 6 HOH A 72 472 239 HOH HOH . M 6 HOH A 73 473 172 HOH HOH . M 6 HOH A 74 474 182 HOH HOH . M 6 HOH A 75 475 234 HOH HOH . M 6 HOH A 76 476 230 HOH HOH . M 6 HOH A 77 477 203 HOH HOH . M 6 HOH A 78 478 173 HOH HOH . N 6 HOH B 1 401 94 HOH HOH . N 6 HOH B 2 402 184 HOH HOH . N 6 HOH B 3 403 16 HOH HOH . N 6 HOH B 4 404 64 HOH HOH . N 6 HOH B 5 405 51 HOH HOH . N 6 HOH B 6 406 174 HOH HOH . N 6 HOH B 7 407 35 HOH HOH . N 6 HOH B 8 408 86 HOH HOH . N 6 HOH B 9 409 165 HOH HOH . N 6 HOH B 10 410 83 HOH HOH . N 6 HOH B 11 411 25 HOH HOH . N 6 HOH B 12 412 1 HOH HOH . N 6 HOH B 13 413 229 HOH HOH . N 6 HOH B 14 414 243 HOH HOH . N 6 HOH B 15 415 18 HOH HOH . N 6 HOH B 16 416 58 HOH HOH . N 6 HOH B 17 417 158 HOH HOH . N 6 HOH B 18 418 21 HOH HOH . N 6 HOH B 19 419 186 HOH HOH . N 6 HOH B 20 420 34 HOH HOH . N 6 HOH B 21 421 3 HOH HOH . N 6 HOH B 22 422 138 HOH HOH . N 6 HOH B 23 423 46 HOH HOH . N 6 HOH B 24 424 175 HOH HOH . N 6 HOH B 25 425 4 HOH HOH . N 6 HOH B 26 426 62 HOH HOH . N 6 HOH B 27 427 183 HOH HOH . N 6 HOH B 28 428 192 HOH HOH . N 6 HOH B 29 429 75 HOH HOH . N 6 HOH B 30 430 53 HOH HOH . N 6 HOH B 31 431 8 HOH HOH . N 6 HOH B 32 432 42 HOH HOH . N 6 HOH B 33 433 142 HOH HOH . N 6 HOH B 34 434 52 HOH HOH . N 6 HOH B 35 435 155 HOH HOH . N 6 HOH B 36 436 88 HOH HOH . N 6 HOH B 37 437 59 HOH HOH . N 6 HOH B 38 438 32 HOH HOH . N 6 HOH B 39 439 144 HOH HOH . N 6 HOH B 40 440 110 HOH HOH . N 6 HOH B 41 441 29 HOH HOH . N 6 HOH B 42 442 161 HOH HOH . N 6 HOH B 43 443 19 HOH HOH . N 6 HOH B 44 444 170 HOH HOH . N 6 HOH B 45 445 103 HOH HOH . N 6 HOH B 46 446 15 HOH HOH . N 6 HOH B 47 447 242 HOH HOH . N 6 HOH B 48 448 11 HOH HOH . N 6 HOH B 49 449 60 HOH HOH . N 6 HOH B 50 450 71 HOH HOH . N 6 HOH B 51 451 197 HOH HOH . N 6 HOH B 52 452 55 HOH HOH . N 6 HOH B 53 453 139 HOH HOH . N 6 HOH B 54 454 82 HOH HOH . N 6 HOH B 55 455 191 HOH HOH . N 6 HOH B 56 456 7 HOH HOH . N 6 HOH B 57 457 41 HOH HOH . N 6 HOH B 58 458 2 HOH HOH . N 6 HOH B 59 459 133 HOH HOH . N 6 HOH B 60 460 143 HOH HOH . N 6 HOH B 61 461 154 HOH HOH . N 6 HOH B 62 462 73 HOH HOH . N 6 HOH B 63 463 208 HOH HOH . N 6 HOH B 64 464 226 HOH HOH . N 6 HOH B 65 465 66 HOH HOH . N 6 HOH B 66 466 205 HOH HOH . N 6 HOH B 67 467 120 HOH HOH . N 6 HOH B 68 468 9 HOH HOH . N 6 HOH B 69 469 147 HOH HOH . N 6 HOH B 70 470 30 HOH HOH . N 6 HOH B 71 471 181 HOH HOH . N 6 HOH B 72 472 92 HOH HOH . N 6 HOH B 73 473 22 HOH HOH . N 6 HOH B 74 474 61 HOH HOH . N 6 HOH B 75 475 177 HOH HOH . N 6 HOH B 76 476 222 HOH HOH . N 6 HOH B 77 477 185 HOH HOH . N 6 HOH B 78 478 76 HOH HOH . N 6 HOH B 79 479 128 HOH HOH . N 6 HOH B 80 480 151 HOH HOH . N 6 HOH B 81 481 44 HOH HOH . N 6 HOH B 82 482 31 HOH HOH . N 6 HOH B 83 483 77 HOH HOH . N 6 HOH B 84 484 20 HOH HOH . N 6 HOH B 85 485 212 HOH HOH . N 6 HOH B 86 486 169 HOH HOH . N 6 HOH B 87 487 10 HOH HOH . N 6 HOH B 88 488 235 HOH HOH . N 6 HOH B 89 489 97 HOH HOH . N 6 HOH B 90 490 122 HOH HOH . N 6 HOH B 91 491 227 HOH HOH . N 6 HOH B 92 492 78 HOH HOH . N 6 HOH B 93 493 68 HOH HOH . N 6 HOH B 94 494 193 HOH HOH . N 6 HOH B 95 495 57 HOH HOH . N 6 HOH B 96 496 108 HOH HOH . N 6 HOH B 97 497 189 HOH HOH . N 6 HOH B 98 498 93 HOH HOH . N 6 HOH B 99 499 33 HOH HOH . N 6 HOH B 100 500 23 HOH HOH . N 6 HOH B 101 501 74 HOH HOH . N 6 HOH B 102 502 63 HOH HOH . N 6 HOH B 103 503 218 HOH HOH . N 6 HOH B 104 504 166 HOH HOH . N 6 HOH B 105 505 196 HOH HOH . N 6 HOH B 106 506 209 HOH HOH . N 6 HOH B 107 507 84 HOH HOH . N 6 HOH B 108 508 157 HOH HOH . N 6 HOH B 109 509 233 HOH HOH . N 6 HOH B 110 510 219 HOH HOH . N 6 HOH B 111 511 198 HOH HOH . N 6 HOH B 112 512 115 HOH HOH . N 6 HOH B 113 513 162 HOH HOH . N 6 HOH B 114 514 216 HOH HOH . N 6 HOH B 115 515 201 HOH HOH . N 6 HOH B 116 516 195 HOH HOH . N 6 HOH B 117 517 231 HOH HOH . N 6 HOH B 118 518 131 HOH HOH . N 6 HOH B 119 519 228 HOH HOH . N 6 HOH B 120 520 67 HOH HOH . N 6 HOH B 121 521 40 HOH HOH . N 6 HOH B 122 522 129 HOH HOH . N 6 HOH B 123 523 206 HOH HOH . N 6 HOH B 124 524 176 HOH HOH . N 6 HOH B 125 525 105 HOH HOH . N 6 HOH B 126 526 217 HOH HOH . N 6 HOH B 127 527 168 HOH HOH . N 6 HOH B 128 528 238 HOH HOH . N 6 HOH B 129 529 99 HOH HOH . N 6 HOH B 130 530 213 HOH HOH . N 6 HOH B 131 531 111 HOH HOH . N 6 HOH B 132 532 202 HOH HOH . N 6 HOH B 133 533 126 HOH HOH . N 6 HOH B 134 534 104 HOH HOH . N 6 HOH B 135 535 127 HOH HOH . N 6 HOH B 136 536 87 HOH HOH . N 6 HOH B 137 537 179 HOH HOH . N 6 HOH B 138 538 13 HOH HOH . N 6 HOH B 139 539 137 HOH HOH . N 6 HOH B 140 540 102 HOH HOH . N 6 HOH B 141 541 101 HOH HOH . N 6 HOH B 142 542 221 HOH HOH . N 6 HOH B 143 543 113 HOH HOH . N 6 HOH B 144 544 152 HOH HOH . N 6 HOH B 145 545 200 HOH HOH . N 6 HOH B 146 546 106 HOH HOH . N 6 HOH B 147 547 171 HOH HOH . N 6 HOH B 148 548 117 HOH HOH . N 6 HOH B 149 549 232 HOH HOH . N 6 HOH B 150 550 121 HOH HOH . N 6 HOH B 151 551 100 HOH HOH . N 6 HOH B 152 552 190 HOH HOH . N 6 HOH B 153 553 132 HOH HOH . N 6 HOH B 154 554 118 HOH HOH . N 6 HOH B 155 555 207 HOH HOH . N 6 HOH B 156 556 119 HOH HOH . N 6 HOH B 157 557 224 HOH HOH . O 6 HOH D 1 101 237 HOH HOH . O 6 HOH D 2 102 140 HOH HOH . P 6 HOH E 1 201 236 HOH HOH . P 6 HOH E 2 202 246 HOH HOH . P 6 HOH E 3 203 38 HOH HOH . P 6 HOH E 4 204 69 HOH HOH . P 6 HOH E 5 205 26 HOH HOH . P 6 HOH E 6 206 50 HOH HOH . P 6 HOH E 7 207 180 HOH HOH . P 6 HOH E 8 208 130 HOH HOH . P 6 HOH E 9 209 91 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 N SAH . . . H 3 -21.778 -35.505 -5.052 1 30.24 ? N SAH 301 B 1 HETATM 2 C CA SAH . . . H 3 -20.447 -36.081 -5.242 1 28.22 ? CA SAH 301 B 1 HETATM 3 C CB SAH . . . H 3 -19.643 -35.303 -6.282 1 28.68 ? CB SAH 301 B 1 HETATM 4 C CG SAH . . . H 3 -19.618 -33.784 -6.135 1 31.7 ? CG SAH 301 B 1 HETATM 5 S SD SAH . . . H 3 -18.575 -33.006 -7.403 1 31.04 ? SD SAH 301 B 1 HETATM 6 C C SAH . . . H 3 -19.674 -36.127 -3.928 1 32.78 ? C SAH 301 B 1 HETATM 7 O O SAH . . . H 3 -20.051 -35.48 -2.948 1 34.26 ? O SAH 301 B 1 HETATM 8 O OXT SAH . . . H 3 -18.662 -36.819 -3.819 1 31.49 ? OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . H 3 -20.021 -32.406 -8.319 1 28.39 ? C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . H 3 -20.559 -33.405 -9.343 1 27.41 ? C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . H 3 -21.752 -32.899 -9.911 1 27.53 ? O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . H 3 -19.598 -33.652 -10.502 1 29.69 ? C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . H 3 -19.431 -35.037 -10.675 1 29.56 ? O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . H 3 -20.295 -33.115 -11.731 1 29.46 ? C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . H 3 -20.069 -33.96 -12.831 1 28.58 ? O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . H 3 -21.757 -33.13 -11.306 1 25.85 ? C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . H 3 -22.591 -32.113 -11.967 1 26.84 ? N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . H 3 -22.377 -30.76 -12.045 1 27.93 ? C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . H 3 -23.411 -30.201 -12.728 1 25.84 ? N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . H 3 -24.275 -31.177 -13.08 1 26.01 ? C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . H 3 -25.475 -31.173 -13.781 1 25.35 ? C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . H 3 -25.986 -30.045 -14.251 1 25.4 ? N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . H 3 -26.14 -32.355 -13.984 1 25.98 ? N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . H 3 -25.626 -33.537 -13.504 1 27.97 ? C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . H 3 -24.435 -33.538 -12.811 1 26.17 ? N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . H 3 -23.772 -32.379 -12.604 1 27.91 ? C4 SAH 301 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #