data_8K6E # _model_server_result.job_id HPcDdBU4B07-7AoMH-LpTQ _model_server_result.datetime_utc '2025-02-24 10:54:26' _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 8k6e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 8K6E # _exptl.entry_id 8K6E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _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 90 _cell.entry_id 8K6E _cell.length_a 215.317 _cell.length_b 55.152 _cell.length_c 80.907 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8K6E _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id NH1 _struct_conn.ptnr1_label_comp_id ARG _struct_conn.ptnr1_label_seq_id 42 _struct_conn.ptnr1_auth_asym_id C _struct_conn.ptnr1_auth_comp_id ARG _struct_conn.ptnr1_auth_seq_id 42 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id O1D _struct_conn.ptnr2_label_comp_id AR6 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id AR6 _struct_conn.ptnr2_auth_seq_id 101 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.302 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 N1 C2 AR6 doub 63 n y N1 C6 AR6 sing 64 n y C2 N3 AR6 sing 65 n y N3 C4 AR6 doub 66 n y C4 C5 AR6 sing 67 n y C4 N9 AR6 sing 68 n y C5 C6 AR6 doub 69 n y C5 N7 AR6 sing 70 n y C6 N6 AR6 sing 71 n n N7 C8 AR6 doub 72 n y C8 N9 AR6 sing 73 n y N9 C1' AR6 sing 74 n n PA O1A AR6 sing 75 n n PA O2A AR6 doub 76 n n PA O3A AR6 sing 77 n n PA O5' AR6 sing 78 n n PB O1B AR6 sing 79 n n PB O2B AR6 doub 80 n n PB O3A AR6 sing 81 n n PB O5D AR6 sing 82 n n C1' C2' AR6 sing 83 n n C1' O4' AR6 sing 84 n n C1D O1D AR6 sing 85 n n C1D C2D AR6 sing 86 n n C1D O4D AR6 sing 87 n n C2' O2' AR6 sing 88 n n C2' C3' AR6 sing 89 n n C2D O2D AR6 sing 90 n n C2D C3D AR6 sing 91 n n C3' O3' AR6 sing 92 n n C3' C4' AR6 sing 93 n n C3D O3D AR6 sing 94 n n C3D C4D AR6 sing 95 n n C4' O4' AR6 sing 96 n n C4' C5' AR6 sing 97 n n C4D O4D AR6 sing 98 n n C4D C5D AR6 sing 99 n n C5' O5' AR6 sing 100 n n C5D O5D AR6 sing 101 n n C2 H2 AR6 sing 102 n n N6 HN6 AR6 sing 103 n n N6 HN6A AR6 sing 104 n n C8 H8 AR6 sing 105 n n C1' H1' AR6 sing 106 n n C1D H1D AR6 sing 107 n n C2' H2' AR6 sing 108 n n O2' HO2' AR6 sing 109 n n C2D H2D AR6 sing 110 n n O2D HO2D AR6 sing 111 n n C3' H3' AR6 sing 112 n n O3' HO3' AR6 sing 113 n n C3D H3D AR6 sing 114 n n O3D HO3D AR6 sing 115 n n C4' H4' AR6 sing 116 n n C4D H4D AR6 sing 117 n n C5' H5' AR6 sing 118 n n C5' "H5'A" AR6 sing 119 n n C5D H5D AR6 sing 120 n n C5D H5DA AR6 sing 121 n n O1A H1A AR6 sing 122 n n O1B H1B AR6 sing 123 n n O1D HD1 AR6 sing 124 n n # _atom_sites.entry_id 8K6E _atom_sites.fract_transf_matrix[1][1] 0.004644 _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] 0.018132 _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] 0.01236 _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 D 4 ANP A 1 401 401 ANP ANP . E 5 AR6 C 1 101 101 AR6 AR6 . F 6 HOH A 1 501 29 HOH HOH . F 6 HOH A 2 502 11 HOH HOH . F 6 HOH A 3 503 25 HOH HOH . F 6 HOH A 4 504 68 HOH HOH . F 6 HOH A 5 505 17 HOH HOH . F 6 HOH A 6 506 27 HOH HOH . F 6 HOH A 7 507 21 HOH HOH . F 6 HOH A 8 508 75 HOH HOH . F 6 HOH A 9 509 51 HOH HOH . F 6 HOH A 10 510 34 HOH HOH . F 6 HOH A 11 511 31 HOH HOH . F 6 HOH A 12 512 82 HOH HOH . F 6 HOH A 13 513 23 HOH HOH . F 6 HOH A 14 514 59 HOH HOH . F 6 HOH A 15 515 73 HOH HOH . F 6 HOH A 16 516 61 HOH HOH . F 6 HOH A 17 517 49 HOH HOH . F 6 HOH A 18 518 53 HOH HOH . F 6 HOH A 19 519 74 HOH HOH . F 6 HOH A 20 520 52 HOH HOH . F 6 HOH A 21 521 13 HOH HOH . F 6 HOH A 22 522 46 HOH HOH . F 6 HOH A 23 523 93 HOH HOH . F 6 HOH A 24 524 58 HOH HOH . F 6 HOH A 25 525 55 HOH HOH . F 6 HOH A 26 526 54 HOH HOH . F 6 HOH A 27 527 78 HOH HOH . F 6 HOH A 28 528 43 HOH HOH . F 6 HOH A 29 529 94 HOH HOH . F 6 HOH A 30 530 77 HOH HOH . F 6 HOH A 31 531 64 HOH HOH . F 6 HOH A 32 532 87 HOH HOH . F 6 HOH A 33 533 19 HOH HOH . F 6 HOH A 34 534 88 HOH HOH . F 6 HOH A 35 535 38 HOH HOH . F 6 HOH A 36 536 95 HOH HOH . F 6 HOH A 37 537 98 HOH HOH . F 6 HOH A 38 538 72 HOH HOH . F 6 HOH A 39 539 99 HOH HOH . G 6 HOH B 1 401 26 HOH HOH . G 6 HOH B 2 402 89 HOH HOH . G 6 HOH B 3 403 20 HOH HOH . G 6 HOH B 4 404 83 HOH HOH . G 6 HOH B 5 405 67 HOH HOH . G 6 HOH B 6 406 14 HOH HOH . G 6 HOH B 7 407 37 HOH HOH . G 6 HOH B 8 408 69 HOH HOH . G 6 HOH B 9 409 47 HOH HOH . G 6 HOH B 10 410 36 HOH HOH . G 6 HOH B 11 411 15 HOH HOH . G 6 HOH B 12 412 33 HOH HOH . G 6 HOH B 13 413 84 HOH HOH . G 6 HOH B 14 414 12 HOH HOH . G 6 HOH B 15 415 39 HOH HOH . G 6 HOH B 16 416 8 HOH HOH . G 6 HOH B 17 417 80 HOH HOH . G 6 HOH B 18 418 70 HOH HOH . G 6 HOH B 19 419 48 HOH HOH . G 6 HOH B 20 420 85 HOH HOH . G 6 HOH B 21 421 92 HOH HOH . G 6 HOH B 22 422 60 HOH HOH . G 6 HOH B 23 423 91 HOH HOH . G 6 HOH B 24 424 16 HOH HOH . G 6 HOH B 25 425 62 HOH HOH . G 6 HOH B 26 426 35 HOH HOH . G 6 HOH B 27 427 44 HOH HOH . G 6 HOH B 28 428 30 HOH HOH . G 6 HOH B 29 429 86 HOH HOH . G 6 HOH B 30 430 42 HOH HOH . G 6 HOH B 31 431 65 HOH HOH . G 6 HOH B 32 432 57 HOH HOH . G 6 HOH B 33 433 97 HOH HOH . G 6 HOH B 34 434 81 HOH HOH . G 6 HOH B 35 435 41 HOH HOH . G 6 HOH B 36 436 56 HOH HOH . G 6 HOH B 37 437 40 HOH HOH . H 6 HOH C 1 201 100 HOH HOH . H 6 HOH C 2 202 66 HOH HOH . H 6 HOH C 3 203 101 HOH HOH . H 6 HOH C 4 204 9 HOH HOH . H 6 HOH C 5 205 32 HOH HOH . H 6 HOH C 6 206 102 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 P PB AR6 . . . E 5 36.877 5.348 62.014 1 32.42 ? PB AR6 101 C 1 HETATM 2 O O1B AR6 . . . E 5 35.492 5.327 62.53 1 39.31 ? O1B AR6 101 C 1 HETATM 3 C C1D AR6 . . . E 5 40.828 8.59 62.836 1 57.02 ? C1D AR6 101 C 1 HETATM 4 O O1D AR6 . . . E 5 41.266 9.612 63.427 1 66.44 ? O1D AR6 101 C 1 HETATM 5 O O2B AR6 . . . E 5 36.72 5.367 60.511 1 44.76 ? O2B AR6 101 C 1 HETATM 6 C C2D AR6 . . . E 5 41.282 8.757 61.363 1 59.89 ? C2D AR6 101 C 1 HETATM 7 O O2D AR6 . . . E 5 41.639 10.163 60.896 1 64.8 ? O2D AR6 101 C 1 HETATM 8 O O3A AR6 . . . E 5 37.854 4.051 62.368 1 39.66 ? O3A AR6 101 C 1 HETATM 9 C C3D AR6 . . . E 5 40.238 8.341 60.662 1 59.04 ? C3D AR6 101 C 1 HETATM 10 O O3D AR6 . . . E 5 39.973 8.982 59.376 1 60.5 ? O3D AR6 101 C 1 HETATM 11 C C4D AR6 . . . E 5 38.888 8.565 61.592 1 49.14 ? C4D AR6 101 C 1 HETATM 12 O O4D AR6 . . . E 5 39.238 8.46 62.809 1 54.49 ? O4D AR6 101 C 1 HETATM 13 C C5D AR6 . . . E 5 38.127 7.338 61.085 1 51.61 ? C5D AR6 101 C 1 HETATM 14 O O5D AR6 . . . E 5 37.595 6.793 62.241 1 45.72 ? O5D AR6 101 C 1 HETATM 15 H H1D AR6 . . . E 5 41.184 7.638 63.345 1 68.43 ? H1D AR6 101 C 1 HETATM 16 H H2D AR6 . . . E 5 42.198 8.141 61.259 1 71.86 ? H2D AR6 101 C 1 HETATM 17 H HO2D AR6 . . . E 5 41.937 10.106 59.959 1 77.76 ? HO2D AR6 101 C 1 HETATM 18 H H3D AR6 . . . E 5 40.489 7.289 60.478 1 70.85 ? H3D AR6 101 C 1 HETATM 19 H HO3D AR6 . . . E 5 39.19 8.599 58.992 1 72.6 ? HO3D AR6 101 C 1 HETATM 20 H H4D AR6 . . . E 5 38.382 9.524 61.555 1 58.97 ? H4D AR6 101 C 1 HETATM 21 H H5D AR6 . . . E 5 37.332 7.628 60.388 1 61.93 ? H5D AR6 101 C 1 HETATM 22 H H5DA AR6 . . . E 5 38.805 6.629 60.594 1 61.93 ? H5DA AR6 101 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #