data_8K6V # _model_server_result.job_id MOyXTj4-qTSwMbuFSK8FNQ _model_server_result.datetime_utc '2025-02-24 11:26:35' _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 8k6v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8K6V # _exptl.entry_id 8K6V _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 8K6V _cell.length_a 215.964 _cell.length_b 55.044 _cell.length_c 79.747 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8K6V _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 # _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 8K6V _atom_sites.fract_transf_matrix[1][1] 0.00463 _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] 0.018167 _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] 0.01254 _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 B 1 401 383 AR6 AR6 . F 6 HOH A 1 501 33 HOH HOH . F 6 HOH A 2 502 26 HOH HOH . F 6 HOH A 3 503 46 HOH HOH . F 6 HOH A 4 504 115 HOH HOH . F 6 HOH A 5 505 89 HOH HOH . F 6 HOH A 6 506 5 HOH HOH . F 6 HOH A 7 507 12 HOH HOH . F 6 HOH A 8 508 107 HOH HOH . F 6 HOH A 9 509 97 HOH HOH . F 6 HOH A 10 510 37 HOH HOH . F 6 HOH A 11 511 1 HOH HOH . F 6 HOH A 12 512 54 HOH HOH . F 6 HOH A 13 513 11 HOH HOH . F 6 HOH A 14 514 74 HOH HOH . F 6 HOH A 15 515 56 HOH HOH . F 6 HOH A 16 516 92 HOH HOH . F 6 HOH A 17 517 95 HOH HOH . F 6 HOH A 18 518 31 HOH HOH . F 6 HOH A 19 519 38 HOH HOH . F 6 HOH A 20 520 24 HOH HOH . F 6 HOH A 21 521 20 HOH HOH . F 6 HOH A 22 522 66 HOH HOH . F 6 HOH A 23 523 91 HOH HOH . F 6 HOH A 24 524 65 HOH HOH . F 6 HOH A 25 525 111 HOH HOH . F 6 HOH A 26 526 41 HOH HOH . F 6 HOH A 27 527 57 HOH HOH . F 6 HOH A 28 528 61 HOH HOH . F 6 HOH A 29 529 96 HOH HOH . F 6 HOH A 30 530 67 HOH HOH . F 6 HOH A 31 531 122 HOH HOH . F 6 HOH A 32 532 121 HOH HOH . F 6 HOH A 33 533 51 HOH HOH . F 6 HOH A 34 534 87 HOH HOH . F 6 HOH A 35 535 49 HOH HOH . F 6 HOH A 36 536 129 HOH HOH . F 6 HOH A 37 537 119 HOH HOH . F 6 HOH A 38 538 22 HOH HOH . F 6 HOH A 39 539 72 HOH HOH . F 6 HOH A 40 540 53 HOH HOH . F 6 HOH A 41 541 130 HOH HOH . F 6 HOH A 42 542 70 HOH HOH . F 6 HOH A 43 543 60 HOH HOH . F 6 HOH A 44 544 100 HOH HOH . F 6 HOH A 45 545 125 HOH HOH . F 6 HOH A 46 546 124 HOH HOH . F 6 HOH A 47 547 79 HOH HOH . F 6 HOH A 48 548 64 HOH HOH . F 6 HOH A 49 549 68 HOH HOH . F 6 HOH A 50 550 55 HOH HOH . G 6 HOH B 1 501 36 HOH HOH . G 6 HOH B 2 502 39 HOH HOH . G 6 HOH B 3 503 52 HOH HOH . G 6 HOH B 4 504 86 HOH HOH . G 6 HOH B 5 505 8 HOH HOH . G 6 HOH B 6 506 93 HOH HOH . G 6 HOH B 7 507 28 HOH HOH . G 6 HOH B 8 508 114 HOH HOH . G 6 HOH B 9 509 16 HOH HOH . G 6 HOH B 10 510 45 HOH HOH . G 6 HOH B 11 511 29 HOH HOH . G 6 HOH B 12 512 15 HOH HOH . G 6 HOH B 13 513 25 HOH HOH . G 6 HOH B 14 514 88 HOH HOH . G 6 HOH B 15 515 18 HOH HOH . G 6 HOH B 16 516 98 HOH HOH . G 6 HOH B 17 517 27 HOH HOH . G 6 HOH B 18 518 32 HOH HOH . G 6 HOH B 19 519 21 HOH HOH . G 6 HOH B 20 520 102 HOH HOH . G 6 HOH B 21 521 90 HOH HOH . G 6 HOH B 22 522 2 HOH HOH . G 6 HOH B 23 523 99 HOH HOH . G 6 HOH B 24 524 109 HOH HOH . G 6 HOH B 25 525 82 HOH HOH . G 6 HOH B 26 526 63 HOH HOH . G 6 HOH B 27 527 40 HOH HOH . G 6 HOH B 28 528 113 HOH HOH . G 6 HOH B 29 529 69 HOH HOH . G 6 HOH B 30 530 83 HOH HOH . G 6 HOH B 31 531 110 HOH HOH . G 6 HOH B 32 532 78 HOH HOH . G 6 HOH B 33 533 84 HOH HOH . G 6 HOH B 34 534 30 HOH HOH . G 6 HOH B 35 535 4 HOH HOH . G 6 HOH B 36 536 81 HOH HOH . G 6 HOH B 37 537 17 HOH HOH . G 6 HOH B 38 538 42 HOH HOH . G 6 HOH B 39 539 106 HOH HOH . G 6 HOH B 40 540 104 HOH HOH . G 6 HOH B 41 541 103 HOH HOH . G 6 HOH B 42 542 101 HOH HOH . G 6 HOH B 43 543 123 HOH HOH . G 6 HOH B 44 544 50 HOH HOH . G 6 HOH B 45 545 112 HOH HOH . G 6 HOH B 46 546 10 HOH HOH . G 6 HOH B 47 547 19 HOH HOH . G 6 HOH B 48 548 43 HOH HOH . G 6 HOH B 49 549 127 HOH HOH . G 6 HOH B 50 550 73 HOH HOH . G 6 HOH B 51 551 118 HOH HOH . G 6 HOH B 52 552 76 HOH HOH . G 6 HOH B 53 553 35 HOH HOH . G 6 HOH B 54 554 71 HOH HOH . G 6 HOH B 55 555 48 HOH HOH . G 6 HOH B 56 556 75 HOH HOH . G 6 HOH B 57 557 62 HOH HOH . G 6 HOH B 58 558 105 HOH HOH . G 6 HOH B 59 559 108 HOH HOH . G 6 HOH B 60 560 126 HOH HOH . G 6 HOH B 61 561 7 HOH HOH . G 6 HOH B 62 562 44 HOH HOH . G 6 HOH B 63 563 80 HOH HOH . G 6 HOH B 64 564 77 HOH HOH . G 6 HOH B 65 565 58 HOH HOH . G 6 HOH B 66 566 128 HOH HOH . G 6 HOH B 67 567 34 HOH HOH . G 6 HOH B 68 568 47 HOH HOH . G 6 HOH B 69 569 120 HOH HOH . H 6 HOH C 1 101 116 HOH HOH . H 6 HOH C 2 102 6 HOH HOH . H 6 HOH C 3 103 117 HOH HOH . H 6 HOH C 4 104 23 HOH HOH . H 6 HOH C 5 105 9 HOH HOH . H 6 HOH C 6 106 59 HOH HOH . H 6 HOH C 7 107 13 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 N1 AR6 . . . E 5 38.443 17.337 60.178 1 94.15 ? N1 AR6 401 B 1 HETATM 2 C C2 AR6 . . . E 5 37.223 17.003 60.664 1 94.78 ? C2 AR6 401 B 1 HETATM 3 N N3 AR6 . . . E 5 36.846 15.7 60.704 1 97.12 ? N3 AR6 401 B 1 HETATM 4 C C4 AR6 . . . E 5 37.669 14.716 60.269 1 97.04 ? C4 AR6 401 B 1 HETATM 5 C C5 AR6 . . . E 5 38.882 15.047 59.789 1 97.86 ? C5 AR6 401 B 1 HETATM 6 C C6 AR6 . . . E 5 39.26 16.384 59.747 1 96.19 ? C6 AR6 401 B 1 HETATM 7 N N6 AR6 . . . E 5 40.497 16.947 59.276 1 95.61 ? N6 AR6 401 B 1 HETATM 8 N N7 AR6 . . . E 5 39.521 13.908 59.423 1 96.94 ? N7 AR6 401 B 1 HETATM 9 C C8 AR6 . . . E 5 38.723 12.861 59.665 1 94.45 ? C8 AR6 401 B 1 HETATM 10 N N9 AR6 . . . E 5 37.599 13.371 60.168 1 94.16 ? N9 AR6 401 B 1 HETATM 11 P PA AR6 . . . E 5 36.51 7.665 58.983 1 104.59 ? PA AR6 401 B 1 HETATM 12 P PB AR6 . . . E 5 37.256 6.112 61.34 1 57.64 ? PB AR6 401 B 1 HETATM 13 C C1' AR6 . . . E 5 36.307 12.906 60.68 1 92.84 ? C1' AR6 401 B 1 HETATM 14 O O1A AR6 . . . E 5 37.64 8.519 58.429 1 107.36 -1 O1A AR6 401 B 1 HETATM 15 O O1B AR6 . . . E 5 37.68 4.706 61.718 1 50.08 -1 O1B AR6 401 B 1 HETATM 16 C C1D AR6 . . . E 5 41.157 10.205 60.3 1 74.43 ? C1D AR6 401 B 1 HETATM 17 O O1D AR6 . . . E 5 42.119 9.199 60.561 1 74.72 ? O1D AR6 401 B 1 HETATM 18 C C2' AR6 . . . E 5 35.246 13.075 59.877 1 85.41 ? C2' AR6 401 B 1 HETATM 19 O O2' AR6 . . . E 5 34.562 14.329 60.117 1 75.76 ? O2' AR6 401 B 1 HETATM 20 O O2A AR6 . . . E 5 35.594 7.24 57.859 1 110.7 ? O2A AR6 401 B 1 HETATM 21 O O2B AR6 . . . E 5 35.847 6.295 61.878 1 59.29 ? O2B AR6 401 B 1 HETATM 22 C C2D AR6 . . . E 5 40.932 11.047 61.611 1 74.08 ? C2D AR6 401 B 1 HETATM 23 O O2D AR6 . . . E 5 42.098 11.224 62.296 1 70.72 ? O2D AR6 401 B 1 HETATM 24 C C3' AR6 . . . E 5 34.183 11.878 60.215 1 93.67 ? C3' AR6 401 B 1 HETATM 25 O O3' AR6 . . . E 5 33.222 12.305 61.199 1 95.07 ? O3' AR6 401 B 1 HETATM 26 O O3A AR6 . . . E 5 37.2 6.314 59.68 1 81.84 ? O3A AR6 401 B 1 HETATM 27 C C3D AR6 . . . E 5 40.007 10.167 62.405 1 71.56 ? C3D AR6 401 B 1 HETATM 28 O O3D AR6 . . . E 5 40.781 9.718 63.592 1 70.78 ? O3D AR6 401 B 1 HETATM 29 C C4' AR6 . . . E 5 34.906 10.803 60.679 1 99.02 ? C4' AR6 401 B 1 HETATM 30 O O4' AR6 . . . E 5 36.359 11.314 60.81 1 98.84 ? O4' AR6 401 B 1 HETATM 31 C C4D AR6 . . . E 5 39.724 9.116 61.603 1 71.56 ? C4D AR6 401 B 1 HETATM 32 O O4D AR6 . . . E 5 40.018 9.642 60.11 1 71.44 ? O4D AR6 401 B 1 HETATM 33 C C5' AR6 . . . E 5 34.797 9.608 59.711 1 99.91 ? C5' AR6 401 B 1 HETATM 34 O O5' AR6 . . . E 5 35.611 8.524 60.114 1 103.1 ? O5' AR6 401 B 1 HETATM 35 C C5D AR6 . . . E 5 38.307 8.613 61.716 1 66.53 ? C5D AR6 401 B 1 HETATM 36 O O5D AR6 . . . E 5 38.344 7.209 61.958 1 61.92 ? O5D AR6 401 B 1 HETATM 37 H H2 AR6 . . . E 5 36.644 17.665 60.964 1 132.13 ? H2 AR6 401 B 1 HETATM 38 H HN6 AR6 . . . E 5 40.523 17.764 59.01 1 133.96 ? HN6 AR6 401 B 1 HETATM 39 H HN6A AR6 . . . E 5 41.21 16.466 59.262 1 133.96 ? HN6A AR6 401 B 1 HETATM 40 H H8 AR6 . . . E 5 38.909 11.965 59.502 1 131.36 ? H8 AR6 401 B 1 HETATM 41 H H1' AR6 . . . E 5 36.129 13.302 61.548 1 127.85 ? H1' AR6 401 B 1 HETATM 42 H H1D AR6 . . . E 5 41.408 10.769 59.551 1 88.13 ? H1D AR6 401 B 1 HETATM 43 H H2' AR6 . . . E 5 35.525 13.017 58.95 1 112.11 ? H2' AR6 401 B 1 HETATM 44 H HO2' AR6 . . . E 5 33.729 14.184 60.201 1 91.57 ? HO2' AR6 401 B 1 HETATM 45 H H2D AR6 . . . E 5 40.51 11.895 61.408 1 87.35 ? H2D AR6 401 B 1 HETATM 46 H HO2D AR6 . . . E 5 42.206 10.581 62.842 1 80.04 ? HO2D AR6 401 B 1 HETATM 47 H H3' AR6 . . . E 5 33.723 11.624 59.401 1 129.53 ? H3' AR6 401 B 1 HETATM 48 H HO3' AR6 . . . E 5 32.446 12.046 60.967 1 132.36 ? HO3' AR6 401 B 1 HETATM 49 H H3D AR6 . . . E 5 39.201 10.643 62.66 1 81.83 ? H3D AR6 401 B 1 HETATM 50 H HO3D AR6 . . . E 5 40.858 10.363 64.141 1 79.9 ? HO3D AR6 401 B 1 HETATM 51 H H4' AR6 . . . E 5 34.574 10.547 61.554 1 140.77 ? H4' AR6 401 B 1 HETATM 52 H H4D AR6 . . . E 5 40.338 8.392 61.807 1 81.75 ? H4D AR6 401 B 1 HETATM 53 H H5' AR6 . . . E 5 35.07 9.896 58.824 1 142.63 ? H5' AR6 401 B 1 HETATM 54 H "H5'A" AR6 . . . E 5 33.874 9.314 59.675 1 142.63 ? "H5'A" AR6 401 B 1 HETATM 55 H H5D AR6 . . . E 5 37.832 8.79 60.888 1 70.97 ? H5D AR6 401 B 1 HETATM 56 H H5DA AR6 . . . E 5 37.859 9.061 62.451 1 70.97 ? H5DA AR6 401 B 1 HETATM 57 H HD1 AR6 . . . E 5 42.35 9.234 61.378 1 88.51 ? HD1 AR6 401 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 49 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 57 #