data_5CCE # _model_server_result.job_id Ixp_7nRvCK8MHivw9AjA9Q _model_server_result.datetime_utc '2024-11-18 09:38:24' _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 5cce # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5CCE # loop_ _exptl.entry_id _exptl.method 5CCE 'NEUTRON DIFFRACTION' 5CCE '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 5CCE _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 5CCE _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,E _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' 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 '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 5CCE _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 2WP A 1 301 301 2WP 2WP . C 3 ADE A 1 302 302 ADE ADE . D 4 D8U A 1 303 501 D8U D8U . E 5 DOD A 1 401 1092 DOD DOD . E 5 DOD A 2 402 1064 DOD DOD . E 5 DOD A 3 403 1046 DOD DOD . E 5 DOD A 4 404 1056 DOD DOD . E 5 DOD A 5 405 1018 DOD DOD . E 5 DOD A 6 406 1067 DOD DOD . E 5 DOD A 7 407 1020 DOD DOD . E 5 DOD A 8 408 1058 DOD DOD . E 5 DOD A 9 409 1023 DOD DOD . E 5 DOD A 10 410 1041 DOD DOD . E 5 DOD A 11 411 1083 DOD DOD . E 5 DOD A 12 412 1007 DOD DOD . E 5 DOD A 13 413 1011 DOD DOD . E 5 DOD A 14 414 1071 DOD DOD . E 5 DOD A 15 415 1005 DOD DOD . E 5 DOD A 16 416 1002 DOD DOD . E 5 DOD A 17 417 1069 DOD DOD . E 5 DOD A 18 418 1001 DOD DOD . E 5 DOD A 19 419 1006 DOD DOD . E 5 DOD A 20 420 1022 DOD DOD . E 5 DOD A 21 421 1032 DOD DOD . E 5 DOD A 22 422 1015 DOD DOD . E 5 DOD A 23 423 1021 DOD DOD . E 5 DOD A 24 424 1014 DOD DOD . E 5 DOD A 25 425 1047 DOD DOD . E 5 DOD A 26 426 1091 DOD DOD . E 5 DOD A 27 427 1054 DOD DOD . E 5 DOD A 28 428 1003 DOD DOD . E 5 DOD A 29 429 1016 DOD DOD . E 5 DOD A 30 430 1008 DOD DOD . E 5 DOD A 31 431 1082 DOD DOD . E 5 DOD A 32 432 1013 DOD DOD . E 5 DOD A 33 433 1040 DOD DOD . E 5 DOD A 34 434 1070 DOD DOD . E 5 DOD A 35 435 1017 DOD DOD . E 5 DOD A 36 436 1035 DOD DOD . E 5 DOD A 37 437 1061 DOD DOD . E 5 DOD A 38 438 1030 DOD DOD . E 5 DOD A 39 439 1027 DOD DOD . E 5 DOD A 40 440 1012 DOD DOD . E 5 DOD A 41 441 1045 DOD DOD . E 5 DOD A 42 442 1004 DOD DOD . E 5 DOD A 43 443 1081 DOD DOD . E 5 DOD A 44 444 1009 DOD DOD . E 5 DOD A 45 445 1034 DOD DOD . E 5 DOD A 46 446 1087 DOD DOD . E 5 DOD A 47 447 1039 DOD DOD . E 5 DOD A 48 448 1028 DOD DOD . E 5 DOD A 49 449 1025 DOD DOD . E 5 DOD A 50 450 1024 DOD DOD . E 5 DOD A 51 451 1088 DOD DOD . E 5 DOD A 52 452 1052 DOD DOD . E 5 DOD A 53 453 1019 DOD DOD . E 5 DOD A 54 454 1051 DOD DOD . E 5 DOD A 55 455 1010 DOD DOD . E 5 DOD A 56 456 1089 DOD DOD . E 5 DOD A 57 457 1038 DOD DOD . E 5 DOD A 58 458 1090 DOD DOD . E 5 DOD A 59 459 1026 DOD DOD . E 5 DOD A 60 460 1044 DOD DOD . E 5 DOD A 61 461 1068 DOD DOD . E 5 DOD A 62 462 1063 DOD DOD . E 5 DOD A 63 463 1033 DOD DOD . E 5 DOD A 64 464 1043 DOD DOD . E 5 DOD A 65 465 1042 DOD DOD . E 5 DOD A 66 466 1036 DOD DOD . E 5 DOD A 67 467 1037 DOD DOD . E 5 DOD A 68 468 1031 DOD DOD . E 5 DOD A 69 469 1086 DOD DOD . E 5 DOD A 70 470 1085 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 C C1 2WP . . . B 2 25.276 -35.999 8.406 1 24.19 ? C1 2WP 301 A 1 HETATM 2 O O1 2WP . . . B 2 24.507 -34.787 8.279 1 21.64 ? O1 2WP 301 A 1 HETATM 3 C C2 2WP . . . B 2 25.1 -36.601 9.872 1 23.42 ? C2 2WP 301 A 1 HETATM 4 O O2 2WP . . . B 2 23.805 -36.582 10.333 1 24.58 ? O2 2WP 301 A 1 HETATM 5 C C3 2WP . . . B 2 26.083 -35.732 10.653 1 22.92 ? C3 2WP 301 A 1 HETATM 6 O O3 2WP . . . B 2 25.633 -34.414 10.901 1 20.15 ? O3 2WP 301 A 1 HETATM 7 C C4 2WP . . . B 2 27.265 -35.563 9.645 1 24.26 ? C4 2WP 301 A 1 HETATM 8 O O4 2WP . . . B 2 26.672 -35.629 8.341 1 24.14 ? O4 2WP 301 A 1 HETATM 9 C C5 2WP . . . B 2 28.314 -36.674 9.812 1 24.09 ? C5 2WP 301 A 1 HETATM 10 N N 2WP . . . B 2 33.417 -35.06 8.789 1 46.67 ? N 2WP 301 A 1 HETATM 11 C CA 2WP . . . B 2 32.821 -34.066 9.736 1 41.86 ? CA 2WP 301 A 1 HETATM 12 C CB 2WP . . . B 2 31.831 -34.794 10.694 1 37.08 ? CB 2WP 301 A 1 HETATM 13 C CG 2WP . . . B 2 30.542 -35.121 9.964 1 31.74 ? CG 2WP 301 A 1 HETATM 14 S SD 2WP . . . B 2 29.567 -36.235 11.078 1 25.41 ? SD 2WP 301 A 1 HETATM 15 C C 2WP . . . B 2 33.944 -33.468 10.661 1 40.86 ? C 2WP 301 A 1 HETATM 16 O O 2WP . . . B 2 34.929 -34.213 10.857 1 39.22 ? O 2WP 301 A 1 HETATM 17 O OXT 2WP . . . B 2 33.756 -32.333 11.123 1 41.02 ? OXT 2WP 301 A 1 HETATM 18 H H1 2WP . . . B 2 25.054 -36.643 7.705 1 23.39 ? H1 2WP 301 A 1 HETATM 19 D DO1 2WP . . . B 2 24.499 -34.548 7.489 1 25.46 ? DO1 2WP 301 A 1 HETATM 20 H H2 2WP . . . B 2 25.401 -37.544 9.849 1 26.49 ? H2 2WP 301 A 1 HETATM 21 D DO2 2WP . . . B 2 23.551 -35.804 10.402 1 28.06 ? DO2 2WP 301 A 1 HETATM 22 H H3 2WP . . . B 2 26.313 -36.174 11.515 1 24.19 ? H3 2WP 301 A 1 HETATM 23 D DO3 2WP . . . B 2 24.861 -34.438 11.185 1 21.18 ? DO3 2WP 301 A 1 HETATM 24 H H4 2WP . . . B 2 27.652 -34.658 9.772 1 24.29 ? H4 2WP 301 A 1 HETATM 25 H H51 2WP . . . B 2 28.726 -36.86 8.952 1 24.83 ? H51 2WP 301 A 1 HETATM 26 H H52 2WP . . . B 2 27.86 -37.477 10.107 1 24.25 ? H52 2WP 301 A 1 HETATM 27 D D10 2WP . . . B 2 34.021 -34.647 8.266 1 49.3 ? D10 2WP 301 A 1 HETATM 28 D D11 2WP . . . B 2 32.765 -35.408 8.271 1 49.01 ? D11 2WP 301 A 1 HETATM 29 H H13 2WP . . . B 2 32.388 -33.349 9.234 1 42.83 ? H13 2WP 301 A 1 HETATM 30 H H14 2WP . . . B 2 32.24 -35.605 11.022 1 36.88 ? H14 2WP 301 A 1 HETATM 31 H H15 2WP . . . B 2 31.65 -34.224 11.46 1 37.07 ? H15 2WP 301 A 1 HETATM 32 H H16 2WP . . . B 2 30.737 -35.557 9.121 1 32.46 ? H16 2WP 301 A 1 HETATM 33 H H17 2WP . . . B 2 30.055 -34.299 9.772 1 32.11 ? H17 2WP 301 A 1 HETATM 34 D DC 2WP . . . B 2 33.818 -35.72 9.253 1 49.1 ? DC 2WP 301 A 1 # _model_server_stats.io_time_ms 105 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 34 #