data_4RB4 # _model_server_result.job_id wEmldT6TCbKVhaHDUYByeg _model_server_result.datetime_utc '2024-12-21 13:20:17' _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 4rb4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"KA","auth_seq_id":503}' # _entry.id 4RB4 # _exptl.entry_id 4RB4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 619.368 _entity.id 3 _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,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate' _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.26 _cell.angle_gamma 90 _cell.entry_id 4RB4 _cell.length_a 88.292 _cell.length_b 313.196 _cell.length_c 164.695 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RB4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 N N N ? 3 P N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 AA N N ? 3 CA N N ? 3 EA N N ? 3 HA N N ? 3 KA N N ? 3 MA 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 342 K CYS 342 1_555 M FE FE . K FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc2 B SG CYS 339 L CYS 339 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc3 B SG CYS 358 L CYS 358 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc4 B SG CYS 370 L CYS 370 1_555 O FE FE . L FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc5 C SG CYS 339 C CYS 339 1_555 Q FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc6 C SG CYS 342 C CYS 342 1_555 Q FE FE . C FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc7 D SG CYS 339 D CYS 339 1_555 T FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc8 D SG CYS 358 D CYS 358 1_555 T FE FE . D FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc9 E SG CYS 358 E CYS 358 1_555 V FE FE . E FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc10 F SG CYS 339 H CYS 339 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 F SG CYS 342 H CYS 342 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc12 F SG CYS 358 H CYS 358 1_555 X FE FE . H FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc13 G SG CYS 339 B CYS 339 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc14 G SG CYS 342 B CYS 342 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc15 G SG CYS 358 B CYS 358 1_555 Z FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc16 H SG CYS 339 F CYS 339 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc17 H SG CYS 342 F CYS 342 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc18 H SG CYS 358 F CYS 358 1_555 BA FE FE . F FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc19 I SG CYS 342 G CYS 342 1_555 DA FE FE . G FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc20 J SG CYS 358 I CYS 358 1_555 FA FE FE . I FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc21 J SG CYS 370 I CYS 370 1_555 FA FE FE . I FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc22 K SG CYS 339 J CYS 339 1_555 IA FE FE . J FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc23 L SG CYS 339 A CYS 339 1_555 LA FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc24 L SG CYS 358 A CYS 358 1_555 LA FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? # _chem_comp.formula 'C17 H27 N5 O16 P2' _chem_comp.formula_weight 619.368 _chem_comp.id AQH _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,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate' _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 O2' C2D AQH sing 13 n n N1 C2 AQH doub 14 n y N1 C6 AQH sing 15 n y C2 N3 AQH sing 16 n y N6 C6 AQH sing 17 n n C6 C5 AQH doub 18 n y N3 C4 AQH doub 19 n y C5 C4 AQH sing 20 n y C5 N7 AQH sing 21 n y C4 N9 AQH sing 22 n y N7 C8 AQH doub 23 n y O3D C3D AQH sing 24 n n N9 C1D AQH sing 25 n n N9 C8 AQH sing 26 n y C1D C2D AQH sing 27 n n C1D O4D AQH sing 28 n n C2D C3D AQH sing 29 n n C3D C4D AQH sing 30 n n O4D C4D AQH sing 31 n n C4D C5D AQH sing 32 n n O2A PA AQH doub 33 n n C5D O5D AQH sing 34 n n O1B PB AQH doub 35 n n O5D PA AQH sing 36 n n O2B PA AQH sing 37 n n O2B PB AQH sing 38 n n PA O1A AQH sing 39 n n PB O3B AQH sing 40 n n PB O3A AQH sing 41 n n O3B C1' AQH sing 42 n n C1' O5' AQH sing 43 n n C1' C2' AQH sing 44 n n O5' C5' AQH sing 45 n n O6' C6' AQH sing 46 n n O C2' AQH sing 47 n n C2' C3' AQH sing 48 n n C5' C6' AQH sing 49 n n C5' C4' AQH sing 50 n n C6' C7' AQH sing 51 n n C3' C4' AQH sing 52 n n C3' O3' AQH sing 53 n n C4' O4' AQH sing 54 n n O7' C7' AQH sing 55 n n C7' H1 AQH sing 56 n n C7' H2 AQH sing 57 n n O7' H3 AQH sing 58 n n C6' H4 AQH sing 59 n n O6' H5 AQH sing 60 n n C5' H6 AQH sing 61 n n C4' H7 AQH sing 62 n n O4' H8 AQH sing 63 n n C3' H9 AQH sing 64 n n O3' H10 AQH sing 65 n n C2' H11 AQH sing 66 n n O2' H12 AQH sing 67 n n C1' H13 AQH sing 68 n n C1D H14 AQH sing 69 n n O1A H15 AQH sing 70 n n O3A H16 AQH sing 71 n n C2 H17 AQH sing 72 n n C2D H18 AQH sing 73 n n C3D H19 AQH sing 74 n n O3D H20 AQH sing 75 n n C4D H21 AQH sing 76 n n C5D H22 AQH sing 77 n n C5D H23 AQH sing 78 n n N6 H24 AQH sing 79 n n N6 H25 AQH sing 80 n n C8 H26 AQH sing 81 n n O H27 AQH sing 82 n n # _atom_sites.entry_id 4RB4 _atom_sites.fract_transf_matrix[1][1] 0.011326 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002255 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003193 _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] 0.006191 _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 M 2 FE K 1 501 1397 FE FE . N 3 AQH K 1 502 3001 AQH APH . O 2 FE L 1 501 1396 FE FE . P 3 AQH L 1 502 3002 AQH APH . Q 2 FE C 1 501 1399 FE FE . R 4 EDO C 1 502 1400 EDO EDO . S 3 AQH C 1 503 3001 AQH APH . T 2 FE D 1 501 1392 FE FE . U 3 AQH D 1 502 3001 AQH APH . V 2 FE E 1 501 1400 FE FE . W 3 AQH E 1 502 3001 AQH APH . X 2 FE H 1 501 1396 FE FE . Y 3 AQH H 1 502 3001 AQH APH . Z 2 FE B 1 501 1392 FE FE . AA 3 AQH B 1 502 3001 AQH APH . BA 2 FE F 1 501 1396 FE FE . CA 3 AQH F 1 502 3001 AQH APH . DA 2 FE G 1 501 1400 FE FE . EA 3 AQH G 1 502 3001 AQH APH . FA 2 FE I 1 501 1400 FE FE . GA 4 EDO I 1 502 1401 EDO EDO . HA 3 AQH I 1 503 3001 AQH APH . IA 2 FE J 1 501 1393 FE FE . JA 4 EDO J 1 502 1394 EDO EDO . KA 3 AQH J 1 503 3001 AQH APH . LA 2 FE A 1 501 1392 FE FE . MA 3 AQH A 1 502 3001 AQH APH . # 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 PA AQH . . . KA 3 -9.63 58.965 -36.367 0.91 150 ? PA AQH 503 J 1 HETATM 2 P PB AQH . . . KA 3 -9.15 56.289 -37.048 0.91 150 ? PB AQH 503 J 1 HETATM 3 C C7' AQH . . . KA 3 -5.279 56.24 -42.556 0.91 150 ? C7' AQH 503 J 1 HETATM 4 O O7' AQH . . . KA 3 -4.335 55.311 -43.089 0.91 150 ? O7' AQH 503 J 1 HETATM 5 C C6' AQH . . . KA 3 -4.841 56.989 -41.268 0.91 150 ? C6' AQH 503 J 1 HETATM 6 O O6' AQH . . . KA 3 -3.816 57.929 -41.606 0.91 150 ? O6' AQH 503 J 1 HETATM 7 C C5' AQH . . . KA 3 -5.974 57.742 -40.492 0.91 150 ? C5' AQH 503 J 1 HETATM 8 O O5' AQH . . . KA 3 -6.79 56.712 -39.793 0.91 150 ? O5' AQH 503 J 1 HETATM 9 C C4' AQH . . . KA 3 -6.906 58.632 -41.358 0.91 150 ? C4' AQH 503 J 1 HETATM 10 O O4' AQH . . . KA 3 -6.081 59.57 -42.024 0.91 150 ? O4' AQH 503 J 1 HETATM 11 C C3' AQH . . . KA 3 -7.95 59.325 -40.453 0.91 150 ? C3' AQH 503 J 1 HETATM 12 O O3' AQH . . . KA 3 -8.789 60.182 -41.222 0.91 150 ? O3' AQH 503 J 1 HETATM 13 C C2' AQH . . . KA 3 -8.804 58.199 -39.812 0.91 150 ? C2' AQH 503 J 1 HETATM 14 O O2' AQH . . . KA 3 -7.108 62.245 -31.652 0.91 150 ? O2' AQH 503 J 1 HETATM 15 C C1' AQH . . . KA 3 -7.886 57.276 -39 0.91 150 ? C1' AQH 503 J 1 HETATM 16 C C1D AQH . . . KA 3 -9.395 62.978 -32.35 0.91 150 ? C1D AQH 503 J 1 HETATM 17 N N1 AQH . . . KA 3 -12.464 66.564 -30.069 0.91 150 ? N1 AQH 503 J 1 HETATM 18 O O1A AQH . . . KA 3 -8.784 60.002 -36.812 0.91 150 1 O1A AQH 503 J 1 HETATM 19 O O3A AQH . . . KA 3 -10.622 56.018 -37.004 0.91 150 ? O3A AQH 503 J 1 HETATM 20 C C2 AQH . . . KA 3 -11.211 66.754 -30.619 0.91 150 ? C2 AQH 503 J 1 HETATM 21 C C2D AQH . . . KA 3 -8.511 61.99 -31.587 0.91 150 ? C2D AQH 503 J 1 HETATM 22 O O2A AQH . . . KA 3 -10.903 59.083 -37.076 0.91 150 ? O2A AQH 503 J 1 HETATM 23 O O1B AQH . . . KA 3 -8.448 55.377 -36.193 0.91 150 1 O1B AQH 503 J 1 HETATM 24 C C3D AQH . . . KA 3 -8.951 60.665 -32.145 0.91 150 ? C3D AQH 503 J 1 HETATM 25 N N3 AQH . . . KA 3 -10.575 65.652 -31.174 0.91 150 ? N3 AQH 503 J 1 HETATM 26 O O2B AQH . . . KA 3 -8.859 57.66 -36.548 0.91 150 ? O2B AQH 503 J 1 HETATM 27 O O3B AQH . . . KA 3 -8.489 56.253 -38.526 0.91 150 ? O3B AQH 503 J 1 HETATM 28 O O3D AQH . . . KA 3 -7.938 59.647 -32.097 0.91 150 ? O3D AQH 503 J 1 HETATM 29 C C4 AQH . . . KA 3 -11.129 64.367 -31.208 0.91 150 ? C4 AQH 503 J 1 HETATM 30 C C4D AQH . . . KA 3 -9.243 61.003 -33.549 0.91 150 ? C4D AQH 503 J 1 HETATM 31 O O4D AQH . . . KA 3 -9.539 62.41 -33.642 0.91 150 ? O4D AQH 503 J 1 HETATM 32 C C5 AQH . . . KA 3 -12.439 64.14 -30.639 0.91 150 ? C5 AQH 503 J 1 HETATM 33 C C5D AQH . . . KA 3 -10.36 60.064 -33.972 0.91 150 ? C5D AQH 503 J 1 HETATM 34 O O5D AQH . . . KA 3 -9.797 58.992 -34.815 0.91 150 ? O5D AQH 503 J 1 HETATM 35 C C6 AQH . . . KA 3 -13.088 65.287 -30.067 0.91 150 ? C6 AQH 503 J 1 HETATM 36 N N6 AQH . . . KA 3 -14.299 65.125 -29.532 0.91 150 ? N6 AQH 503 J 1 HETATM 37 N N7 AQH . . . KA 3 -12.721 62.864 -30.8 0.91 150 ? N7 AQH 503 J 1 HETATM 38 C C8 AQH . . . KA 3 -11.706 62.284 -31.415 0.91 150 ? C8 AQH 503 J 1 HETATM 39 N N9 AQH . . . KA 3 -10.727 63.198 -31.668 0.91 150 ? N9 AQH 503 J 1 HETATM 40 O O AQH . . . KA 3 -9.09 56.974 -40.697 0.91 150 ? O AQH 503 J 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #