data_3ABU # _model_server_result.job_id afbqXTq_T0vd42frK02hNw _model_server_result.datetime_utc '2025-01-03 04:19:03' _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 3abu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3ABU # _exptl.entry_id 3ABU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1043.837 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate' _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 3ABU _cell.length_a 183.7 _cell.length_b 183.7 _cell.length_c 109.25 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ABU _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C43 H48 F N9 O17 P2' _chem_comp.formula_weight 1043.837 _chem_comp.id 12F _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(1R,3R,3AS)-1-HYDROXY-10,11-DIMETHYL-4,6-DIOXO-3-(3-FLUORO-2-BENZYLOXYPHENYL)-2,3,5,6-TETRAHYDRO-1H-BENZO[G] PYRROLO[2,1-E]PTERIDIN-8(4H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE' # 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 C01 C02 12F doub 1 n y C01 C06 12F sing 2 n y C01 C07 12F sing 3 n n O01 C07 12F sing 4 n n O01 CAO 12F sing 5 n n C02 C03 12F sing 6 n y C03 C04 12F doub 7 n y C04 C05 12F sing 8 n y C05 C06 12F doub 9 n y C1' C2' 12F sing 10 n n C1' O4' 12F sing 11 n n C1' NBS 12F sing 12 n n C2' O2' 12F sing 13 n n C2' C3' 12F sing 14 n n C3' O3' 12F sing 15 n n C3' C4' 12F sing 16 n n C4' O4' 12F sing 17 n n C4' C5' 12F sing 18 n n C5' O5' 12F sing 19 n n O5' PCR 12F sing 20 n n CAL CAM 12F doub 21 n y CAL CAN 12F sing 22 n y CAM CAO 12F sing 23 n y CAM CBL 12F sing 24 n n CAN CAP 12F doub 25 n y CAO CAQ 12F doub 26 n y CAP CAQ 12F sing 27 n y CAQ FBR 12F sing 28 n n CAR CAU 12F doub 29 n y CAR NBS 12F sing 30 n y CAR NBT 12F sing 31 n y CAS NBT 12F doub 32 n y CAS NBU 12F sing 33 n y CAT CAU 12F sing 34 n y CAT NBU 12F doub 35 n y CAT NBV 12F sing 36 n n CAU NBW 12F sing 37 n y CAV NBS 12F sing 38 n y CAV NBW 12F doub 39 n y CAW CAX 12F sing 40 n n CAW OCK 12F sing 41 n n CAX CAY 12F sing 42 n n CAX OCL 12F sing 43 n n CAY CAZ 12F sing 44 n n CAY OCM 12F sing 45 n n CAZ CBA 12F sing 46 n n CAZ OCN 12F sing 47 n n CBA NBX 12F sing 48 n n CBB CBE 12F sing 49 n n CBB NBX 12F sing 50 n n CBB NBY 12F doub 51 n n CBC NBY 12F sing 52 n n CBC NBZ 12F sing 53 n n CBC OCO 12F doub 54 n n CBD CBE 12F sing 55 n n CBD NBZ 12F sing 56 n n CBD OCP 12F doub 57 n n CBE CBL 12F sing 58 n n CBE NCA 12F sing 59 n n CBF CBG 12F doub 60 n y CBF CBH 12F sing 61 n y CBF NBX 12F sing 62 n n CBG CBI 12F sing 63 n y CBG NCA 12F sing 64 n n CBH CBP 12F doub 65 n y CBI CBJ 12F doub 66 n y CBJ CBK 12F sing 67 n n CBJ CBP 12F sing 68 n y CBL CBM 12F sing 69 n n CBM CBN 12F sing 70 n n CBN NCA 12F sing 71 n n CBN OCQ 12F sing 72 n n CBO CBP 12F sing 73 n n OCF PCR 12F sing 74 n n OCG PCR 12F doub 75 n n OCH PCR 12F sing 76 n n OCH PCS 12F sing 77 n n OCI PCS 12F doub 78 n n OCJ PCS 12F sing 79 n n OCK PCS 12F sing 80 n n C02 H02 12F sing 81 n n C03 H03 12F sing 82 n n C04 H04 12F sing 83 n n C05 H05 12F sing 84 n n C06 H06 12F sing 85 n n C07 H07 12F sing 86 n n C07 H07A 12F sing 87 n n C1' H1' 12F sing 88 n n C2' H2' 12F sing 89 n n O2' HO2' 12F sing 90 n n C3' H3' 12F sing 91 n n O3' HO3' 12F sing 92 n n C4' H4' 12F sing 93 n n C5' H5' 12F sing 94 n n C5' "H5'A" 12F sing 95 n n CAL HAL 12F sing 96 n n CAN HAN 12F sing 97 n n CAP HAP 12F sing 98 n n CAS HAS 12F sing 99 n n CAV HAV 12F sing 100 n n CAW HAW 12F sing 101 n n CAW HAWA 12F sing 102 n n CAX HAX 12F sing 103 n n CAY HAY 12F sing 104 n n CAZ HAZ 12F sing 105 n n CBA HBA 12F sing 106 n n CBA HBAA 12F sing 107 n n CBH HBH 12F sing 108 n n CBI HBI 12F sing 109 n n CBK HBK 12F sing 110 n n CBK HBKA 12F sing 111 n n CBK HBKB 12F sing 112 n n CBL HBL 12F sing 113 n n CBM HBM 12F sing 114 n n CBM HBMA 12F sing 115 n n CBO HBO 12F sing 116 n n CBO HBOA 12F sing 117 n n CBO HBOB 12F sing 118 n n NBV HNBV 12F sing 119 n n NBV HNBA 12F sing 120 n n NBZ HNBZ 12F sing 121 n n OCL HOCL 12F sing 122 n n OCM HOCM 12F sing 123 n n OCN HOCN 12F sing 124 n n OCF HOCF 12F sing 125 n n OCJ HOCJ 12F sing 126 n n OCQ HOCQ 12F sing 127 n n CBN HCBN 12F sing 128 n n # _atom_sites.entry_id 3ABU _atom_sites.fract_transf_matrix[1][1] 0.005444 _atom_sites.fract_transf_matrix[1][2] 0.003143 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006286 _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] 0.009153 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 12F _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 12F _pdbx_nonpoly_scheme.auth_mon_id UNK _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C C01 12F . . . B 2 33.733 53.423 42.267 1 31.5 ? C01 12F 1 A 1 HETATM 2 O O01 12F . . . B 2 33.115 51.716 40.443 1 32.26 ? O01 12F 1 A 1 HETATM 3 C C02 12F . . . B 2 32.579 53.588 43.027 1 31.85 ? C02 12F 1 A 1 HETATM 4 C C03 12F . . . B 2 32.681 54.012 44.347 1 31.48 ? C03 12F 1 A 1 HETATM 5 C C04 12F . . . B 2 33.927 54.27 44.911 1 30.25 ? C04 12F 1 A 1 HETATM 6 C C05 12F . . . B 2 35.077 54.104 44.149 1 30.86 ? C05 12F 1 A 1 HETATM 7 C C06 12F . . . B 2 34.978 53.684 42.826 1 30.91 ? C06 12F 1 A 1 HETATM 8 C C07 12F . . . B 2 33.652 52.909 40.827 1 30.89 ? C07 12F 1 A 1 HETATM 9 C C1' 12F . . . B 2 21.461 38.15 31.908 1 33.04 ? C1' 12F 1 A 1 HETATM 10 C C2' 12F . . . B 2 21.483 39.668 32.078 1 31.92 ? C2' 12F 1 A 1 HETATM 11 O O2' 12F . . . B 2 20.74 40.274 31.017 1 30.29 ? O2' 12F 1 A 1 HETATM 12 C C3' 12F . . . B 2 22.981 39.906 31.882 1 32.14 ? C3' 12F 1 A 1 HETATM 13 O O3' 12F . . . B 2 23.29 39.993 30.488 1 31.08 ? O3' 12F 1 A 1 HETATM 14 C C4' 12F . . . B 2 23.605 38.642 32.484 1 31.67 ? C4' 12F 1 A 1 HETATM 15 O O4' 12F . . . B 2 22.516 37.755 32.796 1 32.61 ? O4' 12F 1 A 1 HETATM 16 C C5' 12F . . . B 2 24.359 38.964 33.775 1 30.77 ? C5' 12F 1 A 1 HETATM 17 O O5' 12F . . . B 2 25.472 39.825 33.526 1 30.03 ? O5' 12F 1 A 1 HETATM 18 C CAL 12F . . . B 2 30.912 49.423 42.226 1 31.62 ? CAL 12F 1 A 1 HETATM 19 C CAM 12F . . . B 2 31.332 50.402 41.33 1 31.14 ? CAM 12F 1 A 1 HETATM 20 C CAN 12F . . . B 2 31.777 48.885 43.173 1 31.46 ? CAN 12F 1 A 1 HETATM 21 C CAO 12F . . . B 2 32.65 50.857 41.391 1 31.51 ? CAO 12F 1 A 1 HETATM 22 C CAP 12F . . . B 2 33.09 49.334 43.227 1 31.46 ? CAP 12F 1 A 1 HETATM 23 C CAQ 12F . . . B 2 33.519 50.314 42.338 1 32.06 ? CAQ 12F 1 A 1 HETATM 24 C CAR 12F . . . B 2 19.602 36.487 31.835 1 35.78 ? CAR 12F 1 A 1 HETATM 25 C CAS 12F . . . B 2 19.188 34.451 30.4 1 32.5 ? CAS 12F 1 A 1 HETATM 26 C CAT 12F . . . B 2 17.635 35.166 32.263 1 37.03 ? CAT 12F 1 A 1 HETATM 27 C CAU 12F . . . B 2 18.429 36.272 32.547 1 37.03 ? CAU 12F 1 A 1 HETATM 28 C CAV 12F . . . B 2 19.389 38.034 33.323 1 35.46 ? CAV 12F 1 A 1 HETATM 29 C CAW 12F . . . B 2 28.746 42.307 36.843 1 31.65 ? CAW 12F 1 A 1 HETATM 30 C CAX 12F . . . B 2 29.305 43.698 36.534 1 33.53 ? CAX 12F 1 A 1 HETATM 31 C CAY 12F . . . B 2 29.004 44.616 37.721 1 34.27 ? CAY 12F 1 A 1 HETATM 32 C CAZ 12F . . . B 2 29.356 46.089 37.495 1 33.77 ? CAZ 12F 1 A 1 HETATM 33 C CBA 12F . . . B 2 28.876 46.857 38.728 1 31.93 ? CBA 12F 1 A 1 HETATM 34 C CBB 12F . . . B 2 30.308 48.898 38.838 1 27.21 ? CBB 12F 1 A 1 HETATM 35 C CBC 12F . . . B 2 32.689 48.638 38.359 1 25.81 ? CBC 12F 1 A 1 HETATM 36 C CBD 12F . . . B 2 31.745 50.879 38.226 1 26.98 ? CBD 12F 1 A 1 HETATM 37 C CBE 12F . . . B 2 30.426 50.423 38.855 1 27.55 ? CBE 12F 1 A 1 HETATM 38 C CBF 12F . . . B 2 27.968 49.152 38.325 1 28.36 ? CBF 12F 1 A 1 HETATM 39 C CBG 12F . . . B 2 28.117 50.532 38.264 1 27.77 ? CBG 12F 1 A 1 HETATM 40 C CBH 12F . . . B 2 26.719 48.579 38.099 1 28.22 ? CBH 12F 1 A 1 HETATM 41 C CBI 12F . . . B 2 26.989 51.312 38.03 1 28.74 ? CBI 12F 1 A 1 HETATM 42 C CBJ 12F . . . B 2 25.735 50.748 37.821 1 28.08 ? CBJ 12F 1 A 1 HETATM 43 C CBK 12F . . . B 2 24.53 51.671 37.622 1 27.45 ? CBK 12F 1 A 1 HETATM 44 C CBL 12F . . . B 2 30.292 50.885 40.311 1 29.14 ? CBL 12F 1 A 1 HETATM 45 C CBM 12F . . . B 2 30.209 52.395 40.11 1 28.04 ? CBM 12F 1 A 1 HETATM 46 C CBN 12F . . . B 2 29.145 52.392 39.01 1 28.87 ? CBN 12F 1 A 1 HETATM 47 C CBO 12F . . . B 2 24.398 48.745 37.511 1 24.19 ? CBO 12F 1 A 1 HETATM 48 C CBP 12F . . . B 2 25.603 49.363 37.832 1 27.23 ? CBP 12F 1 A 1 HETATM 49 F FBR 12F . . . B 2 34.823 50.654 42.365 1 33.46 ? FBR 12F 1 A 1 HETATM 50 N NBS 12F . . . B 2 20.168 37.578 32.343 1 35.08 ? NBS 12F 1 A 1 HETATM 51 N NBT 12F . . . B 2 19.993 35.626 30.803 1 33.25 ? NBT 12F 1 A 1 HETATM 52 N NBU 12F . . . B 2 17.983 34.274 31.241 1 32.69 ? NBU 12F 1 A 1 HETATM 53 N NBV 12F . . . B 2 16.539 34.953 32.986 1 37.84 ? NBV 12F 1 A 1 HETATM 54 N NBW 12F . . . B 2 18.328 37.24 33.453 1 35.4 ? NBW 12F 1 A 1 HETATM 55 N NBX 12F . . . B 2 29.046 48.327 38.67 1 29.3 ? NBX 12F 1 A 1 HETATM 56 N NBY 12F . . . B 2 31.437 48.091 38.662 1 25.78 ? NBY 12F 1 A 1 HETATM 57 N NBZ 12F . . . B 2 32.84 50.011 38.135 1 25.41 ? NBZ 12F 1 A 1 HETATM 58 N NCA 12F . . . B 2 29.302 51.145 38.237 1 28.44 ? NCA 12F 1 A 1 HETATM 59 O OCF 12F . . . B 2 26.692 42.012 33.904 1 28.89 ? OCF 12F 1 A 1 HETATM 60 O OCG 12F . . . B 2 24.44 41.567 35.005 1 28.05 ? OCG 12F 1 A 1 HETATM 61 O OCH 12F . . . B 2 26.477 40.373 35.772 1 31.01 ? OCH 12F 1 A 1 HETATM 62 O OCI 12F . . . B 2 28.4 39.347 36.985 1 34.95 ? OCI 12F 1 A 1 HETATM 63 O OCJ 12F . . . B 2 28.354 39.344 34.446 1 35.3 ? OCJ 12F 1 A 1 HETATM 64 O OCK 12F . . . B 2 28.775 41.465 35.69 1 32.54 ? OCK 12F 1 A 1 HETATM 65 O OCL 12F . . . B 2 28.697 44.201 35.34 1 33.41 ? OCL 12F 1 A 1 HETATM 66 O OCM 12F . . . B 2 29.703 44.141 38.874 1 36.2 ? OCM 12F 1 A 1 HETATM 67 O OCN 12F . . . B 2 28.688 46.588 36.333 1 32.79 ? OCN 12F 1 A 1 HETATM 68 O OCO 12F . . . B 2 33.666 47.897 38.281 1 27.17 ? OCO 12F 1 A 1 HETATM 69 O OCP 12F . . . B 2 31.911 52.067 37.957 1 25.51 ? OCP 12F 1 A 1 HETATM 70 O OCQ 12F . . . B 2 29.358 53.503 38.135 1 30.88 ? OCQ 12F 1 A 1 HETATM 71 P PCR 12F . . . B 2 25.741 41.06 34.52 1 28.69 ? PCR 12F 1 A 1 HETATM 72 P PCS 12F . . . B 2 28.048 40.029 35.722 1 32.3 ? PCS 12F 1 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 72 #