data_8AKC # _model_server_result.job_id X6nCNEL2QEY5rNoSpvynBQ _model_server_result.datetime_utc '2024-11-15 20:25:33' _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 8akc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":402}' # _entry.id 8AKC # _exptl.entry_id 8AKC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _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 2 _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 8AKC _cell.length_a 91.071 _cell.length_b 91.071 _cell.length_c 143.588 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AKC _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,V 1 1 B,M,N,O,P,Q,R,S,T,U,W 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 N N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 O ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? # _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 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 8AKC _atom_sites.fract_transf_matrix[1][1] 0.01098 _atom_sites.fract_transf_matrix[1][2] 0.00634 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012679 _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] 0.006964 _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 C 2 AR6 A 1 401 500 AR6 AR6 . D 3 ZN A 1 402 501 ZN ZN . E 4 PEG A 1 403 503 PEG PEG . F 4 PEG A 1 404 503 PEG PEG . G 5 SO4 A 1 405 3 SO4 SO4 . H 5 SO4 A 1 406 4 SO4 SO4 . I 5 SO4 A 1 407 6 SO4 SO4 . J 6 GV9 A 1 408 1 GV9 GV9 . K 7 CL A 1 409 1 CL CL . L 7 CL A 1 410 2 CL CL . M 4 PEG B 1 401 502 PEG PEG . N 2 AR6 B 1 402 500 AR6 AR6 . O 3 ZN B 1 403 501 ZN ZN . P 4 PEG B 1 404 502 PEG PEG . Q 5 SO4 B 1 405 1 SO4 SO4 . R 5 SO4 B 1 406 2 SO4 SO4 . S 5 SO4 B 1 407 5 SO4 SO4 . T 6 GV9 B 1 408 2 GV9 GV9 . U 7 CL B 1 409 3 CL CL . V 8 HOH A 1 501 45 HOH HOH . V 8 HOH A 2 502 114 HOH HOH . V 8 HOH A 3 503 32 HOH HOH . V 8 HOH A 4 504 48 HOH HOH . V 8 HOH A 5 505 89 HOH HOH . V 8 HOH A 6 506 30 HOH HOH . V 8 HOH A 7 507 110 HOH HOH . V 8 HOH A 8 508 28 HOH HOH . V 8 HOH A 9 509 21 HOH HOH . V 8 HOH A 10 510 10 HOH HOH . V 8 HOH A 11 511 72 HOH HOH . V 8 HOH A 12 512 113 HOH HOH . V 8 HOH A 13 513 54 HOH HOH . V 8 HOH A 14 514 27 HOH HOH . V 8 HOH A 15 515 33 HOH HOH . V 8 HOH A 16 516 112 HOH HOH . V 8 HOH A 17 517 74 HOH HOH . V 8 HOH A 18 518 93 HOH HOH . V 8 HOH A 19 519 59 HOH HOH . V 8 HOH A 20 520 14 HOH HOH . V 8 HOH A 21 521 41 HOH HOH . V 8 HOH A 22 522 35 HOH HOH . V 8 HOH A 23 523 29 HOH HOH . V 8 HOH A 24 524 90 HOH HOH . V 8 HOH A 25 525 92 HOH HOH . V 8 HOH A 26 526 18 HOH HOH . V 8 HOH A 27 527 36 HOH HOH . V 8 HOH A 28 528 67 HOH HOH . V 8 HOH A 29 529 119 HOH HOH . V 8 HOH A 30 530 7 HOH HOH . V 8 HOH A 31 531 56 HOH HOH . V 8 HOH A 32 532 121 HOH HOH . V 8 HOH A 33 533 61 HOH HOH . V 8 HOH A 34 534 19 HOH HOH . V 8 HOH A 35 535 62 HOH HOH . V 8 HOH A 36 536 52 HOH HOH . V 8 HOH A 37 537 94 HOH HOH . V 8 HOH A 38 538 105 HOH HOH . V 8 HOH A 39 539 2 HOH HOH . V 8 HOH A 40 540 60 HOH HOH . V 8 HOH A 41 541 51 HOH HOH . V 8 HOH A 42 542 96 HOH HOH . V 8 HOH A 43 543 122 HOH HOH . V 8 HOH A 44 544 81 HOH HOH . V 8 HOH A 45 545 79 HOH HOH . V 8 HOH A 46 546 39 HOH HOH . V 8 HOH A 47 547 101 HOH HOH . V 8 HOH A 48 548 57 HOH HOH . V 8 HOH A 49 549 117 HOH HOH . V 8 HOH A 50 550 37 HOH HOH . V 8 HOH A 51 551 106 HOH HOH . V 8 HOH A 52 552 25 HOH HOH . V 8 HOH A 53 553 80 HOH HOH . V 8 HOH A 54 554 103 HOH HOH . V 8 HOH A 55 555 1 HOH HOH . V 8 HOH A 56 556 50 HOH HOH . V 8 HOH A 57 557 16 HOH HOH . V 8 HOH A 58 558 98 HOH HOH . V 8 HOH A 59 559 9 HOH HOH . V 8 HOH A 60 560 108 HOH HOH . V 8 HOH A 61 561 116 HOH HOH . V 8 HOH A 62 562 47 HOH HOH . V 8 HOH A 63 563 87 HOH HOH . V 8 HOH A 64 564 70 HOH HOH . V 8 HOH A 65 565 118 HOH HOH . W 8 HOH B 1 501 46 HOH HOH . W 8 HOH B 2 502 109 HOH HOH . W 8 HOH B 3 503 49 HOH HOH . W 8 HOH B 4 504 88 HOH HOH . W 8 HOH B 5 505 75 HOH HOH . W 8 HOH B 6 506 73 HOH HOH . W 8 HOH B 7 507 53 HOH HOH . W 8 HOH B 8 508 104 HOH HOH . W 8 HOH B 9 509 58 HOH HOH . W 8 HOH B 10 510 38 HOH HOH . W 8 HOH B 11 511 31 HOH HOH . W 8 HOH B 12 512 120 HOH HOH . W 8 HOH B 13 513 111 HOH HOH . W 8 HOH B 14 514 65 HOH HOH . W 8 HOH B 15 515 12 HOH HOH . W 8 HOH B 16 516 82 HOH HOH . W 8 HOH B 17 517 11 HOH HOH . W 8 HOH B 18 518 42 HOH HOH . W 8 HOH B 19 519 85 HOH HOH . W 8 HOH B 20 520 26 HOH HOH . W 8 HOH B 21 521 99 HOH HOH . W 8 HOH B 22 522 55 HOH HOH . W 8 HOH B 23 523 69 HOH HOH . W 8 HOH B 24 524 44 HOH HOH . W 8 HOH B 25 525 40 HOH HOH . W 8 HOH B 26 526 23 HOH HOH . W 8 HOH B 27 527 63 HOH HOH . W 8 HOH B 28 528 68 HOH HOH . W 8 HOH B 29 529 13 HOH HOH . W 8 HOH B 30 530 15 HOH HOH . W 8 HOH B 31 531 3 HOH HOH . W 8 HOH B 32 532 86 HOH HOH . W 8 HOH B 33 533 20 HOH HOH . W 8 HOH B 34 534 102 HOH HOH . W 8 HOH B 35 535 100 HOH HOH . W 8 HOH B 36 536 43 HOH HOH . W 8 HOH B 37 537 22 HOH HOH . W 8 HOH B 38 538 17 HOH HOH . W 8 HOH B 39 539 95 HOH HOH . W 8 HOH B 40 540 6 HOH HOH . W 8 HOH B 41 541 107 HOH HOH . W 8 HOH B 42 542 77 HOH HOH . W 8 HOH B 43 543 115 HOH HOH . W 8 HOH B 44 544 64 HOH HOH . W 8 HOH B 45 545 84 HOH HOH . W 8 HOH B 46 546 8 HOH HOH . W 8 HOH B 47 547 66 HOH HOH . W 8 HOH B 48 548 24 HOH HOH . W 8 HOH B 49 549 4 HOH HOH . W 8 HOH B 50 550 78 HOH HOH . W 8 HOH B 51 551 5 HOH HOH . W 8 HOH B 52 552 91 HOH HOH . W 8 HOH B 53 553 71 HOH HOH . W 8 HOH B 54 554 34 HOH HOH . W 8 HOH B 55 555 97 HOH HOH . W 8 HOH B 56 556 76 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 . . . N 2 -19.167 24.668 36.996 1 31.87 ? N1 AR6 402 B 1 HETATM 2 C C2 AR6 . . . N 2 -19.34 25.43 38.081 1 33.99 ? C2 AR6 402 B 1 HETATM 3 N N3 AR6 . . . N 2 -20.458 25.714 38.742 1 29.81 ? N3 AR6 402 B 1 HETATM 4 C C4 AR6 . . . N 2 -21.504 25.08 38.199 1 31.72 ? C4 AR6 402 B 1 HETATM 5 C C5 AR6 . . . N 2 -21.496 24.268 37.096 1 30.78 ? C5 AR6 402 B 1 HETATM 6 C C6 AR6 . . . N 2 -20.247 24.041 36.474 1 32.93 ? C6 AR6 402 B 1 HETATM 7 N N6 AR6 . . . N 2 -20.087 23.253 35.422 1 33.34 ? N6 AR6 402 B 1 HETATM 8 N N7 AR6 . . . N 2 -22.772 23.8 36.843 1 30.62 ? N7 AR6 402 B 1 HETATM 9 C C8 AR6 . . . N 2 -23.524 24.331 37.779 1 38.01 ? C8 AR6 402 B 1 HETATM 10 N N9 AR6 . . . N 2 -22.806 25.138 38.61 1 37.04 ? N9 AR6 402 B 1 HETATM 11 P PA AR6 . . . N 2 -27.122 24.075 43.823 1 34.81 ? PA AR6 402 B 1 HETATM 12 P PB AR6 . . . N 2 -25.988 22.341 45.858 1 32.66 ? PB AR6 402 B 1 HETATM 13 C C1' AR6 . . . N 2 -23.228 25.837 39.779 1 33.73 ? C1' AR6 402 B 1 HETATM 14 O O1A AR6 . . . N 2 -27.851 24.887 44.859 1 40.23 ? O1A AR6 402 B 1 HETATM 15 O O1B AR6 . . . N 2 -25.246 21.049 45.753 1 38.43 ? O1B AR6 402 B 1 HETATM 16 C C1D AR6 . . . N 2 -30.655 20.675 47.54 1 38.62 ? C1D AR6 402 B 1 HETATM 17 O O1D AR6 . . . N 2 -31.75 20.785 48.366 1 45.59 ? O1D AR6 402 B 1 HETATM 18 C C2' AR6 . . . N 2 -24.494 26.675 39.73 1 28.64 ? C2' AR6 402 B 1 HETATM 19 O O2' AR6 . . . N 2 -24.185 28.015 39.412 1 29.73 ? O2' AR6 402 B 1 HETATM 20 O O2A AR6 . . . N 2 -27.794 23.872 42.506 1 35.3 ? O2A AR6 402 B 1 HETATM 21 O O2B AR6 . . . N 2 -25.222 23.531 46.325 1 35.09 ? O2B AR6 402 B 1 HETATM 22 C C2D AR6 . . . N 2 -30.088 19.256 47.659 1 39.11 ? C2D AR6 402 B 1 HETATM 23 O O2D AR6 . . . N 2 -30.351 18.637 48.898 1 35.1 ? O2D AR6 402 B 1 HETATM 24 C C3' AR6 . . . N 2 -25.009 26.568 41.176 1 28.69 ? C3' AR6 402 B 1 HETATM 25 O O3' AR6 . . . N 2 -24.662 27.754 41.874 1 30.32 ? O3' AR6 402 B 1 HETATM 26 O O3A AR6 . . . N 2 -26.696 22.656 44.442 1 36.4 ? O3A AR6 402 B 1 HETATM 27 C C3D AR6 . . . N 2 -28.596 19.474 47.496 1 38.37 ? C3D AR6 402 B 1 HETATM 28 O O3D AR6 . . . N 2 -27.854 18.371 48.01 1 42.64 ? O3D AR6 402 B 1 HETATM 29 C C4' AR6 . . . N 2 -24.251 25.381 41.788 1 30.17 ? C4' AR6 402 B 1 HETATM 30 O O4' AR6 . . . N 2 -23.442 24.835 40.733 1 32.46 ? O4' AR6 402 B 1 HETATM 31 C C4D AR6 . . . N 2 -28.449 20.767 48.306 1 39.77 ? C4D AR6 402 B 1 HETATM 32 O O4D AR6 . . . N 2 -29.619 21.551 47.967 1 39.79 ? O4D AR6 402 B 1 HETATM 33 C C5' AR6 . . . N 2 -25.077 24.267 42.329 1 32.19 ? C5' AR6 402 B 1 HETATM 34 O O5' AR6 . . . N 2 -25.731 24.748 43.538 1 36.47 ? O5' AR6 402 B 1 HETATM 35 C C5D AR6 . . . N 2 -27.226 21.6 48.057 1 40 ? C5D AR6 402 B 1 HETATM 36 O O5D AR6 . . . N 2 -27.304 22.153 46.725 1 36.55 ? O5D AR6 402 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 924 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 36 #