data_5CCD # _model_server_result.job_id B4WWJJSnSEvn0tiXyYhwyQ _model_server_result.datetime_utc '2024-11-26 04:48:08' _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 5ccd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 5CCD # loop_ _exptl.entry_id _exptl.method 5CCD 'X-RAY DIFFRACTION' 5CCD 'NEUTRON DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 5CCD _cell.length_a 83.189 _cell.length_b 83.189 _cell.length_c 67.633 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 45.088667 # _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 '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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 5CCD _atom_sites.fract_transf_matrix[1][1] 0.012021 _atom_sites.fract_transf_matrix[1][2] 0.00694 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01388 _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] 0.014786 _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 SAH A 1 300 300 SAH SAH . C 3 DOD A 1 401 1035 DOD DOD . C 3 DOD A 2 402 1027 DOD DOD . C 3 DOD A 3 403 1093 DOD DOD . C 3 DOD A 4 404 1008 DOD DOD . C 3 DOD A 5 405 1092 DOD DOD . C 3 DOD A 6 406 1070 DOD DOD . C 3 DOD A 7 407 1056 DOD DOD . C 3 DOD A 8 408 1032 DOD DOD . C 3 DOD A 9 409 1099 DOD DOD . C 3 DOD A 10 410 1012 DOD DOD . C 3 DOD A 11 411 1103 DOD DOD . C 3 DOD A 12 412 1083 DOD DOD . C 3 DOD A 13 413 1097 DOD DOD . C 3 DOD A 14 414 1020 DOD DOD . C 3 DOD A 15 415 1090 DOD DOD . C 3 DOD A 16 416 1015 DOD DOD . C 3 DOD A 17 417 1051 DOD DOD . C 3 DOD A 18 418 1022 DOD DOD . C 3 DOD A 19 419 1013 DOD DOD . C 3 DOD A 20 420 1047 DOD DOD . C 3 DOD A 21 421 1021 DOD DOD . C 3 DOD A 22 422 1007 DOD DOD . C 3 DOD A 23 423 1095 DOD DOD . C 3 DOD A 24 424 1069 DOD DOD . C 3 DOD A 25 425 1005 DOD DOD . C 3 DOD A 26 426 1025 DOD DOD . C 3 DOD A 27 427 1009 DOD DOD . C 3 DOD A 28 428 1014 DOD DOD . C 3 DOD A 29 429 1011 DOD DOD . C 3 DOD A 30 430 1002 DOD DOD . C 3 DOD A 31 431 1114 DOD DOD . C 3 DOD A 32 432 1089 DOD DOD . C 3 DOD A 33 433 1017 DOD DOD . C 3 DOD A 34 434 1041 DOD DOD . C 3 DOD A 35 435 1004 DOD DOD . C 3 DOD A 36 436 1024 DOD DOD . C 3 DOD A 37 437 1006 DOD DOD . C 3 DOD A 38 438 1088 DOD DOD . C 3 DOD A 39 439 1045 DOD DOD . C 3 DOD A 40 440 1019 DOD DOD . C 3 DOD A 41 441 1010 DOD DOD . C 3 DOD A 42 442 1031 DOD DOD . C 3 DOD A 43 443 1054 DOD DOD . C 3 DOD A 44 444 1018 DOD DOD . C 3 DOD A 45 445 1026 DOD DOD . C 3 DOD A 46 446 1052 DOD DOD . C 3 DOD A 47 447 1028 DOD DOD . C 3 DOD A 48 448 1036 DOD DOD . C 3 DOD A 49 449 1003 DOD DOD . C 3 DOD A 50 450 1001 DOD DOD . C 3 DOD A 51 451 1023 DOD DOD . C 3 DOD A 52 452 1117 DOD DOD . C 3 DOD A 53 453 1034 DOD DOD . C 3 DOD A 54 454 1108 DOD DOD . C 3 DOD A 55 455 1038 DOD DOD . C 3 DOD A 56 456 1101 DOD DOD . C 3 DOD A 57 457 1115 DOD DOD . C 3 DOD A 58 458 1043 DOD DOD . C 3 DOD A 59 459 1102 DOD DOD . C 3 DOD A 60 460 1105 DOD DOD . C 3 DOD A 61 461 1081 DOD DOD . C 3 DOD A 62 462 1040 DOD DOD . C 3 DOD A 63 463 1111 DOD DOD . C 3 DOD A 64 464 1091 DOD DOD . C 3 DOD A 65 465 1094 DOD DOD . C 3 DOD A 66 466 1086 DOD DOD . C 3 DOD A 67 467 1116 DOD DOD . C 3 DOD A 68 468 1085 DOD DOD . C 3 DOD A 69 469 1106 DOD DOD . C 3 DOD A 70 470 1118 DOD DOD . C 3 DOD A 71 471 1096 DOD DOD . C 3 DOD A 72 472 1104 DOD DOD . C 3 DOD A 73 473 1098 DOD DOD . C 3 DOD A 74 474 1109 DOD DOD . C 3 DOD A 75 475 1112 DOD DOD . C 3 DOD A 76 476 1100 DOD DOD . C 3 DOD A 77 477 1113 DOD DOD . # 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 . . . B 2 33.96 -34.872 8.829 1 48.61 ? N SAH 300 A 1 HETATM 2 C CA SAH . . . B 2 33.081 -34.236 9.83 1 46.35 ? CA SAH 300 A 1 HETATM 3 C CB SAH . . . B 2 32.241 -35.288 10.579 1 42.19 ? CB SAH 300 A 1 HETATM 4 C CG SAH . . . B 2 30.764 -35.332 10.097 1 38.37 ? CG SAH 300 A 1 HETATM 5 S SD SAH . . . B 2 29.703 -36.466 11.096 1 35 ? SD SAH 300 A 1 HETATM 6 C C SAH . . . B 2 34.04 -33.569 10.813 1 47.14 ? C SAH 300 A 1 HETATM 7 O O SAH . . . B 2 33.788 -32.39 11.132 1 48.84 ? O SAH 300 A 1 HETATM 8 O OXT SAH . . . B 2 35.008 -34.256 11.213 1 46.9 ? OXT SAH 300 A 1 HETATM 9 C C5' SAH . . . B 2 28.557 -37.096 9.797 1 28.86 ? C5' SAH 300 A 1 HETATM 10 C C4' SAH . . . B 2 27.328 -36.202 9.491 1 26.5 ? C4' SAH 300 A 1 HETATM 11 O O4' SAH . . . B 2 26.493 -36.623 8.373 1 26.21 ? O4' SAH 300 A 1 HETATM 12 C C3' SAH . . . B 2 26.342 -36.093 10.647 1 24.65 ? C3' SAH 300 A 1 HETATM 13 O O3' SAH . . . B 2 25.694 -34.801 10.596 1 21.62 ? O3' SAH 300 A 1 HETATM 14 C C2' SAH . . . B 2 25.391 -37.28 10.385 1 23.8 ? C2' SAH 300 A 1 HETATM 15 O O2' SAH . . . B 2 24.009 -36.891 10.47 1 24.56 ? O2' SAH 300 A 1 HETATM 16 C C1' SAH . . . B 2 25.654 -37.69 8.925 1 23.38 ? C1' SAH 300 A 1 HETATM 17 N N9 SAH . . . B 2 26.077 -39.109 8.653 1 17.82 ? N9 SAH 300 A 1 HETATM 18 C C8 SAH . . . B 2 26.431 -39.514 7.414 1 16.94 ? C8 SAH 300 A 1 HETATM 19 N N7 SAH . . . B 2 26.785 -40.799 7.457 1 14.8 ? N7 SAH 300 A 1 HETATM 20 C C5 SAH . . . B 2 26.657 -41.216 8.731 1 14.03 ? C5 SAH 300 A 1 HETATM 21 C C6 SAH . . . B 2 26.875 -42.408 9.364 1 13.25 ? C6 SAH 300 A 1 HETATM 22 N N6 SAH . . . B 2 27.305 -43.41 8.627 1 13.3 ? N6 SAH 300 A 1 HETATM 23 N N1 SAH . . . B 2 26.673 -42.602 10.704 1 7.85 ? N1 SAH 300 A 1 HETATM 24 C C2 SAH . . . B 2 26.21 -41.527 11.502 1 11.4 ? C2 SAH 300 A 1 HETATM 25 N N3 SAH . . . B 2 25.988 -40.295 10.822 1 12.52 ? N3 SAH 300 A 1 HETATM 26 C C4 SAH . . . B 2 26.215 -40.164 9.48 1 13.81 ? C4 SAH 300 A 1 HETATM 27 H H2 SAH . . . B 2 26.036 -41.639 12.567 1 10.82 ? H2 SAH 300 A 1 HETATM 28 D DN1 SAH . . . B 2 34.356 -34.166 8.234 1 49.35 ? DN1 SAH 300 A 1 HETATM 29 D DN2 SAH . . . B 2 33.414 -35.483 8.266 1 49.95 ? DN2 SAH 300 A 1 HETATM 30 H HA SAH . . . B 2 32.414 -33.49 9.395 1 45.82 ? HA SAH 300 A 1 HETATM 31 H HB1 SAH . . . B 2 32.682 -36.257 10.349 1 42.05 ? HB1 SAH 300 A 1 HETATM 32 H HB2 SAH . . . B 2 32.282 -35.055 11.65 1 42.55 ? HB2 SAH 300 A 1 HETATM 33 H HG1 SAH . . . B 2 30.74 -35.635 9.053 1 38.49 ? HG1 SAH 300 A 1 HETATM 34 H HG2 SAH . . . B 2 30.353 -34.33 10.268 1 38.81 ? HG2 SAH 300 A 1 HETATM 35 H "H5'1" SAH . . . B 2 28.204 -38.085 10.09 1 30.19 ? "H5'1" SAH 300 A 1 HETATM 36 H "H5'2" SAH . . . B 2 29.176 -37.104 8.894 1 30.21 ? "H5'2" SAH 300 A 1 HETATM 37 H H4' SAH . . . B 2 27.705 -35.205 9.275 1 26.7 ? H4' SAH 300 A 1 HETATM 38 H H3' SAH . . . B 2 26.863 -36.244 11.595 1 24.17 ? H3' SAH 300 A 1 HETATM 39 D DO3' SAH . . . B 2 25.159 -34.646 11.422 1 21.5 ? DO3' SAH 300 A 1 HETATM 40 H H2' SAH . . . B 2 25.605 -38.1 11.067 1 24.3 ? H2' SAH 300 A 1 HETATM 41 D DO2' SAH . . . B 2 23.94 -35.892 10.416 1 28.42 ? DO2' SAH 300 A 1 HETATM 42 H H1' SAH . . . B 2 24.69 -37.589 8.433 1 23.59 ? H1' SAH 300 A 1 HETATM 43 H H8 SAH . . . B 2 26.427 -38.88 6.522 1 16.7 ? H8 SAH 300 A 1 HETATM 44 D DN61 SAH . . . B 2 27.454 -43.276 7.649 1 16.16 ? DN61 SAH 300 A 1 HETATM 45 D DN62 SAH . . . B 2 27.476 -44.298 9.045 1 15.28 ? DN62 SAH 300 A 1 HETATM 46 D DN3 SAH . . . B 2 34.695 -35.377 9.285 1 49.78 ? DN3 SAH 300 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #