data_5TMP # _model_server_result.job_id D4vATJFAv7ewtl8WtYDSYQ _model_server_result.datetime_utc '2024-11-24 10:46:05' _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 5tmp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":214}' # _entry.id 5TMP # _exptl.entry_id 5TMP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 911.327 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE" _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 5TMP _cell.length_a 152.1 _cell.length_b 152.1 _cell.length_c 75.6 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TMP _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # 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 hexameric 6 software_defined_assembly 2 PQS dimeric 2 software_defined_assembly 3 # 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 1,2,3,4,5,6 A,B,C 3 1,5 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 76.05 131.722464 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -76.05 131.722464 0 4 'crystal symmetry operation' 10_455 y-1/3,x+1/3,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -76.05 43.907488 25.2 5 'crystal symmetry operation' 11_565 x-y+2/3,-y+4/3,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 175.629952 25.2 6 'crystal symmetry operation' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 76.05 43.907488 25.2 # _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 'C20 H24 N10 O22 P5 -5' _chem_comp.formula_weight 911.327 _chem_comp.id Z5A _chem_comp.mon_nstd_flag . _chem_comp.name "P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE" _chem_comp.type non-polymer _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 N1T C2T Z5A sing 363 n n N1T C6T Z5A sing 364 n n N1T C1' Z5A sing 365 n n C2T O2T Z5A doub 366 n n C2T N3T Z5A sing 367 n n N3T C4T Z5A sing 368 n n N3T H3T Z5A sing 369 n n C4T O4T Z5A doub 370 n n C4T C5T Z5A sing 371 n n C5T C6T Z5A doub 372 n n C5T C7T Z5A sing 373 n n C6T H6T Z5A sing 374 n n C7T H7T1 Z5A sing 375 n n C7T H7T2 Z5A sing 376 n n C7T H7T3 Z5A sing 377 n n C5' O5' Z5A sing 378 n n C5' C4' Z5A sing 379 n n C5' "H5'1" Z5A sing 380 n n C5' "H5'2" Z5A sing 381 n n O5' PA Z5A sing 382 n n C4' O4' Z5A sing 383 n n C4' C3' Z5A sing 384 n n C4' H4' Z5A sing 385 n n O4' C1' Z5A sing 386 n n C3' C2' Z5A sing 387 n n C3' NA3 Z5A sing 388 n n C3' H3' Z5A sing 389 n n C2' C1' Z5A sing 390 n n C2' "H2'1" Z5A sing 391 n n C2' "H2'2" Z5A sing 392 n n C1' H1' Z5A sing 393 n n NA3 N3B Z5A doub 394 n n N3B N3C Z5A doub 395 n n PA O1P Z5A doub 396 n n PA O2P Z5A sing 397 n n PA OPA Z5A sing 398 n n OPA PB Z5A sing 399 n n PB O3P Z5A doub 400 n n PB O4P Z5A sing 401 n n PB OPB Z5A sing 402 n n OPB PC Z5A sing 403 n n PC O5P Z5A doub 404 n n PC O6P Z5A sing 405 n n PC OPC Z5A sing 406 n n OPC PD Z5A sing 407 n n PD O7P Z5A doub 408 n n PD O8P Z5A sing 409 n n PD OPD Z5A sing 410 n n OPD PE Z5A sing 411 n n PE O9P Z5A doub 412 n n PE OAP Z5A sing 413 n n PE O5B Z5A sing 414 n n O5B C5B Z5A sing 415 n n C5B C4B Z5A sing 416 n n C5B H5A1 Z5A sing 417 n n C5B H5A2 Z5A sing 418 n n C4B O4B Z5A sing 419 n n C4B C3B Z5A sing 420 n n C4B H4B Z5A sing 421 n n O4B C1B Z5A sing 422 n n C3B O3' Z5A sing 423 n n C3B C2B Z5A sing 424 n n C3B H3B Z5A sing 425 n n O3' "HO'3" Z5A sing 426 n n C2B O2' Z5A sing 427 n n C2B C1B Z5A sing 428 n n C2B H2' Z5A sing 429 n n O2' "HO'2" Z5A sing 430 n n C1B N9A Z5A sing 431 n n C1B H1B Z5A sing 432 n n N9A C8A Z5A sing 433 n y N9A C4A Z5A sing 434 n y C8A N7A Z5A doub 435 n y C8A H8A Z5A sing 436 n n N7A C5A Z5A sing 437 n y C5A C6A Z5A sing 438 n y C5A C4A Z5A doub 439 n y C6A N6A Z5A sing 440 n n C6A N1A Z5A doub 441 n y N6A H6A1 Z5A sing 442 n n N6A H6A2 Z5A sing 443 n n N1A C2A Z5A sing 444 n y C2A N3A Z5A doub 445 n y C2A H2A Z5A sing 446 n n N3A C4A Z5A sing 447 n y # _atom_sites.entry_id 5TMP _atom_sites.fract_transf_matrix[1][1] 0.006575 _atom_sites.fract_transf_matrix[1][2] 0.003796 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007592 _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] 0.013227 _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 Z5A A 1 214 214 Z5A Z5A . C 3 HOH A 1 1001 1001 HOH HOH . C 3 HOH A 2 1002 1002 HOH HOH . C 3 HOH A 3 1003 1003 HOH HOH . C 3 HOH A 4 1004 1004 HOH HOH . C 3 HOH A 5 1005 1005 HOH HOH . C 3 HOH A 6 1006 1006 HOH HOH . C 3 HOH A 7 1007 1007 HOH HOH . C 3 HOH A 8 1008 1008 HOH HOH . C 3 HOH A 9 1009 1009 HOH HOH . C 3 HOH A 10 1010 1010 HOH HOH . C 3 HOH A 11 1011 1011 HOH HOH . C 3 HOH A 12 1012 1012 HOH HOH . C 3 HOH A 13 1013 1013 HOH HOH . C 3 HOH A 14 1014 1014 HOH HOH . C 3 HOH A 15 1015 1015 HOH HOH . C 3 HOH A 16 1016 1016 HOH HOH . C 3 HOH A 17 1017 1017 HOH HOH . C 3 HOH A 18 1018 1018 HOH HOH . C 3 HOH A 19 1019 1019 HOH HOH . C 3 HOH A 20 1020 1020 HOH HOH . C 3 HOH A 21 1021 1021 HOH HOH . C 3 HOH A 22 1022 1022 HOH HOH . C 3 HOH A 23 1023 1023 HOH HOH . C 3 HOH A 24 1024 1024 HOH HOH . C 3 HOH A 25 1025 1025 HOH HOH . C 3 HOH A 26 1026 1026 HOH HOH . C 3 HOH A 27 1027 1027 HOH HOH . C 3 HOH A 28 1028 1028 HOH HOH . C 3 HOH A 29 1029 1029 HOH HOH . C 3 HOH A 30 1030 1030 HOH HOH . C 3 HOH A 31 1031 1031 HOH HOH . C 3 HOH A 32 1032 1032 HOH HOH . C 3 HOH A 33 1033 1033 HOH HOH . C 3 HOH A 34 1034 1034 HOH HOH . C 3 HOH A 35 1035 1035 HOH HOH . C 3 HOH A 36 1036 1036 HOH HOH . C 3 HOH A 37 1037 1037 HOH HOH . C 3 HOH A 38 1038 1038 HOH HOH . C 3 HOH A 39 1039 1039 HOH HOH . C 3 HOH A 40 1040 1040 HOH HOH . C 3 HOH A 41 1041 1041 HOH HOH . C 3 HOH A 42 1042 1042 HOH HOH . C 3 HOH A 43 1043 1043 HOH HOH . C 3 HOH A 44 1044 1044 HOH HOH . C 3 HOH A 45 1045 1045 HOH HOH . C 3 HOH A 46 1046 1046 HOH HOH . C 3 HOH A 47 1047 1047 HOH HOH . C 3 HOH A 48 1048 1048 HOH HOH . C 3 HOH A 49 1049 1049 HOH HOH . C 3 HOH A 50 1050 1050 HOH HOH . C 3 HOH A 51 1052 1052 HOH HOH . C 3 HOH A 52 1053 1053 HOH HOH . C 3 HOH A 53 1054 1054 HOH HOH . C 3 HOH A 54 1055 1055 HOH HOH . C 3 HOH A 55 1056 1056 HOH HOH . C 3 HOH A 56 1057 1057 HOH HOH . C 3 HOH A 57 1058 1058 HOH HOH . C 3 HOH A 58 1059 1059 HOH HOH . C 3 HOH A 59 1060 1060 HOH HOH . C 3 HOH A 60 1061 1061 HOH HOH . C 3 HOH A 61 1062 1062 HOH HOH . C 3 HOH A 62 1063 1063 HOH HOH . C 3 HOH A 63 1064 1064 HOH HOH . C 3 HOH A 64 1065 1065 HOH HOH . C 3 HOH A 65 1066 1066 HOH HOH . C 3 HOH A 66 1067 1067 HOH HOH . C 3 HOH A 67 1068 1068 HOH HOH . C 3 HOH A 68 1069 1069 HOH HOH . C 3 HOH A 69 1070 1070 HOH HOH . C 3 HOH A 70 1071 1071 HOH HOH . C 3 HOH A 71 1072 1072 HOH HOH . C 3 HOH A 72 1073 1073 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 N1T Z5A . . . B 2 24.83 100.609 17.625 1 9.63 ? N1T Z5A 214 A 1 HETATM 2 C C2T Z5A . . . B 2 25.802 99.777 18.164 1 5.53 ? C2T Z5A 214 A 1 HETATM 3 O O2T Z5A . . . B 2 25.746 99.387 19.331 1 13.17 ? O2T Z5A 214 A 1 HETATM 4 N N3T Z5A . . . B 2 26.793 99.34 17.253 1 7.62 ? N3T Z5A 214 A 1 HETATM 5 C C4T Z5A . . . B 2 26.689 99.479 15.847 1 7.22 ? C4T Z5A 214 A 1 HETATM 6 O O4T Z5A . . . B 2 27.485 98.925 15.098 1 13.21 ? O4T Z5A 214 A 1 HETATM 7 C C5T Z5A . . . B 2 25.649 100.333 15.366 1 7.04 ? C5T Z5A 214 A 1 HETATM 8 C C6T Z5A . . . B 2 24.785 100.899 16.253 1 10.78 ? C6T Z5A 214 A 1 HETATM 9 C C7T Z5A . . . B 2 25.569 100.633 13.847 1 6.54 ? C7T Z5A 214 A 1 HETATM 10 C C5' Z5A . . . B 2 20.579 102.588 17.728 1 23.42 ? C5' Z5A 214 A 1 HETATM 11 O O5' Z5A . . . B 2 21.239 103.306 16.735 1 29.28 ? O5' Z5A 214 A 1 HETATM 12 C C4' Z5A . . . B 2 21.704 101.929 18.496 1 24.53 ? C4' Z5A 214 A 1 HETATM 13 O O4' Z5A . . . B 2 22.595 101.16 17.642 1 24.16 ? O4' Z5A 214 A 1 HETATM 14 C C3' Z5A . . . B 2 22.549 102.739 19.451 1 18.44 ? C3' Z5A 214 A 1 HETATM 15 C C2' Z5A . . . B 2 23.911 102.308 19.059 1 19.16 ? C2' Z5A 214 A 1 HETATM 16 C C1' Z5A . . . B 2 23.732 100.97 18.487 1 14.46 ? C1' Z5A 214 A 1 HETATM 17 N NA3 Z5A . . . B 2 22.343 102.242 20.814 1 32.18 ? NA3 Z5A 214 A 1 HETATM 18 N N3B Z5A . . . B 2 22.799 102.919 21.737 1 31.63 ? N3B Z5A 214 A 1 HETATM 19 N N3C Z5A . . . B 2 23.151 103.425 22.675 1 37.53 ? N3C Z5A 214 A 1 HETATM 20 P PA Z5A . . . B 2 20.517 104.138 15.609 1 30.59 ? PA Z5A 214 A 1 HETATM 21 O O1P Z5A . . . B 2 19.516 103.313 14.879 1 37.03 ? O1P Z5A 214 A 1 HETATM 22 O O2P Z5A . . . B 2 21.372 105.078 14.831 1 30.75 ? O2P Z5A 214 A 1 HETATM 23 O OPA Z5A . . . B 2 19.824 104.962 16.609 1 36.51 ? OPA Z5A 214 A 1 HETATM 24 P PB Z5A . . . B 2 18.659 105.945 16.628 1 47.24 ? PB Z5A 214 A 1 HETATM 25 O O3P Z5A . A . B 2 19.054 107.048 17.54 0.5 39.87 ? O3P Z5A 214 A 1 HETATM 26 O O3P Z5A . B . B 2 17.713 105.622 15.51 0.5 43.26 ? O3P Z5A 214 A 1 HETATM 27 O O4P Z5A . A . B 2 17.359 105.207 16.769 0.5 39.16 ? O4P Z5A 214 A 1 HETATM 28 O O4P Z5A . B . B 2 18.209 105.907 18.045 0.5 47.66 ? O4P Z5A 214 A 1 HETATM 29 O OPB Z5A . A . B 2 18.614 106.579 15.18 0.5 37.19 ? OPB Z5A 214 A 1 HETATM 30 O OPB Z5A . B . B 2 19.335 107.367 16.325 0.5 42.89 ? OPB Z5A 214 A 1 HETATM 31 P PC Z5A . A . B 2 17.882 107.737 14.5 0.5 35.8 ? PC Z5A 214 A 1 HETATM 32 P PC Z5A . B . B 2 19.155 108.858 16.789 0.5 42.43 ? PC Z5A 214 A 1 HETATM 33 O O5P Z5A . A . B 2 17.819 107.504 13.053 0.5 35.44 ? O5P Z5A 214 A 1 HETATM 34 O O5P Z5A . B . B 2 17.909 109.376 16.182 0.5 39.04 ? O5P Z5A 214 A 1 HETATM 35 O O6P Z5A . A . B 2 16.653 107.987 15.321 0.5 32.85 ? O6P Z5A 214 A 1 HETATM 36 O O6P Z5A . B . B 2 19.363 108.858 18.247 0.5 42.71 ? O6P Z5A 214 A 1 HETATM 37 O OPC Z5A . A . B 2 18.842 108.931 14.794 0.5 31.16 ? OPC Z5A 214 A 1 HETATM 38 O OPC Z5A . B . B 2 20.311 109.793 16.335 0.5 44.97 ? OPC Z5A 214 A 1 HETATM 39 P PD Z5A . A . B 2 18.809 110.486 14.686 0.5 26.77 ? PD Z5A 214 A 1 HETATM 40 P PD Z5A . B . B 2 20.894 111.177 16.775 0.5 44.69 ? PD Z5A 214 A 1 HETATM 41 O O7P Z5A . A . B 2 17.396 110.89 14.758 0.5 24.63 ? O7P Z5A 214 A 1 HETATM 42 O O7P Z5A . B . B 2 20.524 111.298 18.182 0.5 45.81 ? O7P Z5A 214 A 1 HETATM 43 O O8P Z5A . A . B 2 19.584 110.724 13.464 0.5 26.34 ? O8P Z5A 214 A 1 HETATM 44 O O8P Z5A . B . B 2 22.32 111.34 16.399 0.5 48.38 ? O8P Z5A 214 A 1 HETATM 45 O OPD Z5A . A . B 2 19.514 111.172 15.947 0.5 26.83 ? OPD Z5A 214 A 1 HETATM 46 O OPD Z5A . B . B 2 19.925 112.094 15.859 0.5 44.51 ? OPD Z5A 214 A 1 HETATM 47 P PE Z5A . A . B 2 19.613 112.657 16.644 0.5 29.81 ? PE Z5A 214 A 1 HETATM 48 P PE Z5A . B . B 2 18.536 112.932 15.987 0.5 40.81 ? PE Z5A 214 A 1 HETATM 49 O O9P Z5A . A . B 2 20.636 112.566 17.696 0.5 25.36 ? O9P Z5A 214 A 1 HETATM 50 O O9P Z5A . B . B 2 18.772 114.246 15.33 0.5 42.45 ? O9P Z5A 214 A 1 HETATM 51 O OAP Z5A . A . B 2 19.739 113.702 15.592 0.5 27.55 ? OAP Z5A 214 A 1 HETATM 52 O OAP Z5A . B . B 2 17.421 112.075 15.524 0.5 41.76 ? OAP Z5A 214 A 1 HETATM 53 O O5B Z5A . A . B 2 18.199 112.917 17.364 0.5 27.72 ? O5B Z5A 214 A 1 HETATM 54 O O5B Z5A . B . B 2 18.419 113.135 17.599 0.5 37.26 ? O5B Z5A 214 A 1 HETATM 55 C C5B Z5A . . . B 2 17.825 112.226 18.535 1 28.68 ? C5B Z5A 214 A 1 HETATM 56 C C4B Z5A . . . B 2 16.874 112.969 19.423 1 35.04 ? C4B Z5A 214 A 1 HETATM 57 O O4B Z5A . . . B 2 17.52 114.015 20.171 1 39.02 ? O4B Z5A 214 A 1 HETATM 58 C C3B Z5A . . . B 2 15.649 113.614 18.628 1 33.55 ? C3B Z5A 214 A 1 HETATM 59 O O3' Z5A . . . B 2 14.487 113.578 19.478 1 27.8 ? O3' Z5A 214 A 1 HETATM 60 C C2B Z5A . . . B 2 16.142 115.045 18.436 1 36.86 ? C2B Z5A 214 A 1 HETATM 61 O O2' Z5A . . . B 2 15.116 116.047 18.196 1 33.62 ? O2' Z5A 214 A 1 HETATM 62 C C1B Z5A . . . B 2 16.969 115.278 19.72 1 36.57 ? C1B Z5A 214 A 1 HETATM 63 N N9A Z5A . . . B 2 18.026 116.285 19.485 1 35.81 ? N9A Z5A 214 A 1 HETATM 64 C C8A Z5A . . . B 2 19.067 116.327 18.574 1 35.14 ? C8A Z5A 214 A 1 HETATM 65 N N7A Z5A . . . B 2 19.688 117.482 18.553 1 34.92 ? N7A Z5A 214 A 1 HETATM 66 C C5A Z5A . . . B 2 19.14 118.144 19.67 1 33.99 ? C5A Z5A 214 A 1 HETATM 67 C C6A Z5A . . . B 2 19.395 119.41 20.271 1 33.83 ? C6A Z5A 214 A 1 HETATM 68 N N6A Z5A . . . B 2 20.365 120.229 19.835 1 30.02 ? N6A Z5A 214 A 1 HETATM 69 N N1A Z5A . . . B 2 18.569 119.803 21.291 1 31 ? N1A Z5A 214 A 1 HETATM 70 C C2A Z5A . . . B 2 17.568 118.998 21.655 1 30.93 ? C2A Z5A 214 A 1 HETATM 71 N N3A Z5A . . . B 2 17.179 117.858 21.083 1 29.54 ? N3A Z5A 214 A 1 HETATM 72 C C4A Z5A . . . B 2 18.012 117.5 20.092 1 31.4 ? C4A Z5A 214 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 410 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 72 #