data_6A05 # _model_server_result.job_id k6u_CX_afk6d8QGF0bXuVQ _model_server_result.datetime_utc '2024-11-24 16:08:25' _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 6a05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":403}' # _entry.id 6A05 # _exptl.entry_id 6A05 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 674.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-amino-9-[(2R,3R,3aR,5S,7aS,9R,10R,10aR,12R,14aS)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" _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 6A05 _cell.length_a 49.405 _cell.length_b 64.741 _cell.length_c 100.953 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,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 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H24 N10 O13 P2' _chem_comp.formula_weight 674.411 _chem_comp.id 1YD _chem_comp.mon_nstd_flag . _chem_comp.name "2-amino-9-[(2R,3R,3aR,5S,7aS,9R,10R,10aR,12R,14aS)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" _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 O4' C1' 1YD sing 1 n n O4' C4' 1YD sing 2 n n C1' N9 1YD sing 3 n n C1' C2' 1YD sing 4 n n N3 C2 1YD doub 5 n y N3 C4 1YD sing 6 n y C2 N1 1YD sing 7 n y O2' C2' 1YD sing 8 n n C4 N9 1YD sing 9 n y C4 C5 1YD doub 10 n y N9 C8 1YD sing 11 n y N1 C6 1YD doub 12 n y C2' C3' 1YD sing 13 n n C5 C6 1YD sing 14 n y C5 N7 1YD sing 15 n y C8 N7 1YD doub 16 n y C4' C5' 1YD sing 17 n n C4' C3' 1YD sing 18 n n C6 N6 1YD sing 19 n n C5' O5' 1YD sing 20 n n C3' O3' 1YD sing 21 n n O5' PBS 1YD sing 22 n n OAE PBS 1YD doub 23 n n PBS OAI 1YD sing 24 n n PBS OAZ 1YD sing 25 n n O3' PBR 1YD sing 26 n n OAZ CBM 1YD sing 27 n n PBR OAH 1YD doub 28 n n PBR OAV 1YD sing 29 n n PBR OAD 1YD sing 30 n n OAV CAN 1YD sing 31 n n CBM CBK 1YD sing 32 n n CBM CBI 1YD sing 33 n n CAN CBK 1YD sing 34 n n CBK OAX 1YD sing 35 n n CBI OAG 1YD sing 36 n n CBI CBO 1YD sing 37 n n CAL NAR 1YD doub 38 n y CAL NBQ 1YD sing 39 n y NAR CBE 1YD sing 40 n y NBQ CBO 1YD sing 41 n n NBQ CBG 1YD sing 42 n y OAX CBO 1YD sing 43 n n CBE CBG 1YD doub 44 n y CBE CBC 1YD sing 45 n n OAC CBC 1YD doub 46 n n CBG NAS 1YD sing 47 n n CBC NAT 1YD sing 48 n n NAS CBA 1YD doub 49 n n NAT CBA 1YD sing 50 n n CBA NAA 1YD sing 51 n n NAT H1 1YD sing 52 n n NAA H2 1YD sing 53 n n NAA H3 1YD sing 54 n n CAL H4 1YD sing 55 n n CBO H5 1YD sing 56 n n CBI H6 1YD sing 57 n n OAG H7 1YD sing 58 n n CBK H8 1YD sing 59 n n CAN H9 1YD sing 60 n n CAN H10 1YD sing 61 n n OAD H11 1YD sing 62 n n CBM H12 1YD sing 63 n n OAI H13 1YD sing 64 n n C5' H14 1YD sing 65 n n C5' H15 1YD sing 66 n n C4' H16 1YD sing 67 n n C3' H17 1YD sing 68 n n C2' H18 1YD sing 69 n n O2' H19 1YD sing 70 n n C1' H20 1YD sing 71 n n C8 H21 1YD sing 72 n n C2 H22 1YD sing 73 n n N6 H23 1YD sing 74 n n N6 H24 1YD sing 75 n n # _atom_sites.entry_id 6A05 _atom_sites.fract_transf_matrix[1][1] 0.020241 _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] 0.015446 _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] 0.009906 _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 SO4 A 1 401 1 SO4 SO4 . D 2 SO4 A 1 402 2 SO4 SO4 . E 3 1YD A 1 403 401 1YD 1YD . F 2 SO4 B 1 401 3 SO4 SO4 . G 4 HOH A 1 501 42 HOH HOH . G 4 HOH A 2 502 41 HOH HOH . G 4 HOH A 3 503 2 HOH HOH . G 4 HOH A 4 504 31 HOH HOH . G 4 HOH A 5 505 3 HOH HOH . G 4 HOH A 6 506 26 HOH HOH . G 4 HOH A 7 507 34 HOH HOH . G 4 HOH A 8 508 8 HOH HOH . G 4 HOH A 9 509 1 HOH HOH . G 4 HOH A 10 510 20 HOH HOH . G 4 HOH A 11 511 13 HOH HOH . G 4 HOH A 12 512 22 HOH HOH . G 4 HOH A 13 513 6 HOH HOH . G 4 HOH A 14 514 17 HOH HOH . G 4 HOH A 15 515 14 HOH HOH . G 4 HOH A 16 516 15 HOH HOH . G 4 HOH A 17 517 35 HOH HOH . G 4 HOH A 18 518 29 HOH HOH . G 4 HOH A 19 519 24 HOH HOH . G 4 HOH A 20 520 33 HOH HOH . G 4 HOH A 21 521 28 HOH HOH . H 4 HOH B 1 501 16 HOH HOH . H 4 HOH B 2 502 43 HOH HOH . H 4 HOH B 3 503 36 HOH HOH . H 4 HOH B 4 504 38 HOH HOH . H 4 HOH B 5 505 10 HOH HOH . H 4 HOH B 6 506 27 HOH HOH . H 4 HOH B 7 507 45 HOH HOH . H 4 HOH B 8 508 5 HOH HOH . H 4 HOH B 9 509 44 HOH HOH . H 4 HOH B 10 510 12 HOH HOH . H 4 HOH B 11 511 30 HOH HOH . H 4 HOH B 12 512 39 HOH HOH . H 4 HOH B 13 513 32 HOH HOH . H 4 HOH B 14 514 23 HOH HOH . H 4 HOH B 15 515 37 HOH HOH . H 4 HOH B 16 516 9 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 O OAC 1YD . . . E 3 25.711 0.089 23.366 1 40.17 ? OAC 1YD 403 A 1 HETATM 2 C CBC 1YD . . . E 3 24.674 0.301 23.97 1 40.99 ? CBC 1YD 403 A 1 HETATM 3 N NAT 1YD . . . E 3 24.701 0.84 25.204 1 43.11 ? NAT 1YD 403 A 1 HETATM 4 C CBA 1YD . . . E 3 23.537 1.07 25.881 1 42.27 ? CBA 1YD 403 A 1 HETATM 5 N NAA 1YD . . . E 3 23.564 1.608 27.137 1 48.83 ? NAA 1YD 403 A 1 HETATM 6 N NAS 1YD . . . E 3 22.36 0.786 25.377 1 44.54 ? NAS 1YD 403 A 1 HETATM 7 C CBG 1YD . . . E 3 22.249 0.263 24.161 1 46.26 ? CBG 1YD 403 A 1 HETATM 8 C CBE 1YD . . . E 3 23.407 -0.002 23.409 1 43.81 ? CBE 1YD 403 A 1 HETATM 9 N NAR 1YD . . . E 3 22.99 -0.541 22.238 1 39.77 ? NAR 1YD 403 A 1 HETATM 10 C CAL 1YD . . . E 3 21.694 -0.61 22.246 1 35.59 ? CAL 1YD 403 A 1 HETATM 11 N NBQ 1YD . . . E 3 21.171 -0.116 23.407 1 46.52 ? NBQ 1YD 403 A 1 HETATM 12 C CBO 1YD . . . E 3 19.753 -0.026 23.832 1 38.62 ? CBO 1YD 403 A 1 HETATM 13 C CBI 1YD . . . E 3 19.035 1.307 23.498 1 43.14 ? CBI 1YD 403 A 1 HETATM 14 O OAG 1YD . . . E 3 18.362 1.785 24.649 1 38.87 ? OAG 1YD 403 A 1 HETATM 15 O OAX 1YD . . . E 3 19.003 -0.991 23.13 1 43.03 ? OAX 1YD 403 A 1 HETATM 16 C CBK 1YD . . . E 3 18.559 -0.316 21.952 1 46.24 ? CBK 1YD 403 A 1 HETATM 17 C CAN 1YD . . . E 3 17.709 -1.233 21.094 1 39.67 ? CAN 1YD 403 A 1 HETATM 18 O OAV 1YD . . . E 3 18.742 -2.024 20.501 1 45.09 ? OAV 1YD 403 A 1 HETATM 19 P PBR 1YD . . . E 3 18.97 -1.954 18.924 1 42.42 ? PBR 1YD 403 A 1 HETATM 20 O O3' 1YD . . . E 3 18.499 -0.47 18.539 1 44.85 ? O3' 1YD 403 A 1 HETATM 21 O OAH 1YD . . . E 3 20.397 -2.173 18.566 1 38.77 ? OAH 1YD 403 A 1 HETATM 22 O OAD 1YD . . . E 3 18.03 -3.101 18.316 1 48.89 ? OAD 1YD 403 A 1 HETATM 23 C CBM 1YD . . . E 3 17.911 0.934 22.521 1 42.36 ? CBM 1YD 403 A 1 HETATM 24 O OAZ 1YD . . . E 3 17.577 1.92 21.535 1 39.06 ? OAZ 1YD 403 A 1 HETATM 25 P PBS 1YD . . . E 3 18.232 3.352 21.136 1 41.95 ? PBS 1YD 403 A 1 HETATM 26 O OAI 1YD . . . E 3 19.554 3.777 21.938 1 43.89 ? OAI 1YD 403 A 1 HETATM 27 O OAE 1YD . . . E 3 17.185 4.405 21.138 1 43.63 ? OAE 1YD 403 A 1 HETATM 28 O O5' 1YD . . . E 3 18.62 3.174 19.604 1 43.74 ? O5' 1YD 403 A 1 HETATM 29 C C5' 1YD . . . E 3 17.803 2.342 18.786 1 41.7 ? C5' 1YD 403 A 1 HETATM 30 C C4' 1YD . . . E 3 18.876 1.712 17.916 1 45.25 ? C4' 1YD 403 A 1 HETATM 31 O O4' 1YD . . . E 3 19.276 2.529 16.815 1 30.29 ? O4' 1YD 403 A 1 HETATM 32 C C3' 1YD . . . E 3 18.594 0.326 17.364 1 35.42 ? C3' 1YD 403 A 1 HETATM 33 C C2' 1YD . . . E 3 19.881 0.25 16.539 1 43.24 ? C2' 1YD 403 A 1 HETATM 34 O O2' 1YD . . . E 3 19.567 -0.324 15.27 1 43.75 ? O2' 1YD 403 A 1 HETATM 35 C C1' 1YD . . . E 3 20.311 1.725 16.294 1 35.6 ? C1' 1YD 403 A 1 HETATM 36 N N9 1YD . . . E 3 21.572 2.038 16.97 1 38.94 ? N9 1YD 403 A 1 HETATM 37 C C8 1YD . . . E 3 21.783 2.758 18.123 1 41.72 ? C8 1YD 403 A 1 HETATM 38 N N7 1YD . . . E 3 23.042 2.823 18.412 1 37.91 ? N7 1YD 403 A 1 HETATM 39 C C5 1YD . . . E 3 23.721 2.143 17.456 1 44.04 ? C5 1YD 403 A 1 HETATM 40 C C4 1YD . . . E 3 22.794 1.639 16.522 1 40.95 ? C4 1YD 403 A 1 HETATM 41 N N3 1YD . . . E 3 23.214 0.934 15.47 1 40.4 ? N3 1YD 403 A 1 HETATM 42 C C2 1YD . . . E 3 24.501 0.702 15.318 1 40.4 ? C2 1YD 403 A 1 HETATM 43 N N1 1YD . . . E 3 25.406 1.15 16.173 1 40.97 ? N1 1YD 403 A 1 HETATM 44 C C6 1YD . . . E 3 25.069 1.87 17.241 1 38.59 ? C6 1YD 403 A 1 HETATM 45 N N6 1YD . . . E 3 26.004 2.343 18.13 1 47.63 ? N6 1YD 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 45 #