data_8IY2 # _model_server_result.job_id TQqsPqZQSkNbxOTmnYt_Uw _model_server_result.datetime_utc '2024-11-27 17:00:22' _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 8iy2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":205}' # _entry.id 8IY2 # _exptl.entry_id 8IY2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _entity.pdbx_number_of_molecules 22 _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 8IY2 _cell.length_a 103.427 _cell.length_b 103.427 _cell.length_c 101.487 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IY2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 ? hexameric 6 author_defined_assembly 3 ? hexameric 6 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,I,J,K,L,M,N,TA 1 1 A,G,H,I,J,K,L,M,N,TA 1 2 A,G,H,I,J,K,L,M,N,TA 1 4 A,G,H,I,J,K,L,M,N,TA 1 6 A,G,H,I,J,K,L,M,N,TA 1 8 A,G,H,I,J,K,L,M,N,TA 1 10 B,O,P,Q,R,S,T,U,UA 2 1 B,O,P,Q,R,S,T,U,UA 2 2 B,O,P,Q,R,S,T,U,UA 2 4 B,O,P,Q,R,S,T,U,UA 2 7 B,O,P,Q,R,S,T,U,UA 2 9 B,O,P,Q,R,S,T,U,UA 2 11 C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 1 C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 3 C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,VA,WA 3 5 E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 1 E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 3 E,F,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,XA 4 5 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -51.7135 -89.570409 0 4 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.7135 -89.570409 0 6 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 101.487 7 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 101.487 9 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 10 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 101.487 11 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 K N N ? 3 L N N ? 3 N N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 U N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N ? 3 JA N N ? 3 KA N N ? 3 LA N N ? 3 PA N N ? 3 QA N N ? 3 RA N N ? 3 SA N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id 3AM _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "3'-AMP" # 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 O1P P 3AM doub 1 n n P O2P 3AM sing 2 n n P O3P 3AM sing 3 n n P O3' 3AM sing 4 n n O2' C2' 3AM sing 5 n n C2' C3' 3AM sing 6 n n C2' C1' 3AM sing 7 n n C3' O3' 3AM sing 8 n n C3' C4' 3AM sing 9 n n C1' O4' 3AM sing 10 n n C1' N9 3AM sing 11 n n O4' C4' 3AM sing 12 n n C4' C5' 3AM sing 13 n n C5' O5' 3AM sing 14 n n N9 C8 3AM sing 15 n y N9 C4 3AM sing 16 n y C8 N7 3AM doub 17 n y N7 C5 3AM sing 18 n y C5 C6 3AM doub 19 n y C5 C4 3AM sing 20 n y C6 N6 3AM sing 21 n n C6 N1 3AM sing 22 n y C4 N3 3AM doub 23 n y N3 C2 3AM sing 24 n y C2 N1 3AM doub 25 n y O2P HO2P 3AM sing 26 n n O3P HO3P 3AM sing 27 n n O2' HO2' 3AM sing 28 n n C2' H2' 3AM sing 29 n n C3' H3' 3AM sing 30 n n C1' H1' 3AM sing 31 n n C4' H4' 3AM sing 32 n n C5' H5' 3AM sing 33 n n C5' "H5'A" 3AM sing 34 n n O5' HO5' 3AM sing 35 n n C8 H8 3AM sing 36 n n N6 HN6 3AM sing 37 n n N6 HN6A 3AM sing 38 n n C2 H2 3AM sing 39 n n # _atom_sites.entry_id 8IY2 _atom_sites.fract_transf_matrix[1][1] 0.009669 _atom_sites.fract_transf_matrix[1][2] 0.005582 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011164 _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] 0.009853 _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 G 2 EDO A 1 201 201 EDO EDO . H 2 EDO A 1 202 302 EDO EDO . I 2 EDO A 1 203 301 EDO EDO . J 3 3AM A 1 204 102 3AM AAA . K 3 3AM A 1 205 102 3AM AAA . L 3 3AM A 1 206 102 3AM AAA . M 4 3GP A 1 207 101 3GP 4BW . N 3 3AM A 1 208 101 3AM 4BW . O 2 EDO B 1 201 201 EDO EDO . P 2 EDO B 1 202 302 EDO EDO . Q 3 3AM B 1 203 102 3AM AAA . R 3 3AM B 1 204 102 3AM AAA . S 3 3AM B 1 205 102 3AM AAA . T 4 3GP B 1 206 101 3GP 4BW . U 3 3AM B 1 207 101 3AM 4BW . V 2 EDO C 1 201 201 EDO EDO . W 2 EDO C 1 202 302 EDO EDO . X 3 3AM C 1 203 101 3AM AAA . Y 3 3AM C 1 204 101 3AM AAA . Z 3 3AM C 1 205 101 3AM AAA . AA 4 3GP C 1 206 101 3GP 4BW . BA 2 EDO D 1 201 201 EDO EDO . CA 2 EDO D 1 202 302 EDO EDO . DA 3 3AM D 1 203 102 3AM AAA . EA 3 3AM D 1 204 102 3AM AAA . FA 3 3AM D 1 205 102 3AM AAA . GA 3 3AM D 1 206 101 3AM 4BW . HA 2 EDO E 1 201 201 EDO EDO . IA 2 EDO E 1 202 302 EDO EDO . JA 3 3AM E 1 203 102 3AM AAA . KA 3 3AM E 1 204 102 3AM AAA . LA 3 3AM E 1 205 102 3AM AAA . MA 4 3GP E 1 206 101 3GP 4BW . NA 2 EDO F 1 201 201 EDO EDO . OA 2 EDO F 1 202 302 EDO EDO . PA 3 3AM F 1 203 101 3AM AAA . QA 3 3AM F 1 204 101 3AM AAA . RA 3 3AM F 1 205 101 3AM AAA . SA 3 3AM F 1 206 101 3AM 4BW . TA 5 HOH A 1 301 1 HOH HOH . TA 5 HOH A 2 302 3 HOH HOH . TA 5 HOH A 3 303 25 HOH HOH . TA 5 HOH A 4 304 4 HOH HOH . TA 5 HOH A 5 305 5 HOH HOH . TA 5 HOH A 6 306 8 HOH HOH . TA 5 HOH A 7 307 7 HOH HOH . TA 5 HOH A 8 308 17 HOH HOH . TA 5 HOH A 9 309 12 HOH HOH . TA 5 HOH A 10 310 18 HOH HOH . TA 5 HOH A 11 311 20 HOH HOH . TA 5 HOH A 12 312 19 HOH HOH . TA 5 HOH A 13 313 16 HOH HOH . UA 5 HOH B 1 301 21 HOH HOH . UA 5 HOH B 2 302 27 HOH HOH . UA 5 HOH B 3 303 15 HOH HOH . UA 5 HOH B 4 304 26 HOH HOH . VA 5 HOH C 1 301 14 HOH HOH . WA 5 HOH D 1 301 6 HOH HOH . WA 5 HOH D 2 302 13 HOH HOH . WA 5 HOH D 3 303 11 HOH HOH . WA 5 HOH D 4 304 23 HOH HOH . WA 5 HOH D 5 305 24 HOH HOH . WA 5 HOH D 6 306 9 HOH HOH . XA 5 HOH F 1 301 2 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 P P 3AM . . . LA 3 -3.357 -61.088 -5.228 0.33 52.03 ? P 3AM 205 E 1 HETATM 2 O O2P 3AM . . . LA 3 -2.987 -61.582 -6.585 0.33 52.05 ? O2P 3AM 205 E 1 HETATM 3 O O3P 3AM . . . LA 3 -4.802 -60.912 -4.906 0.33 52.84 ? O3P 3AM 205 E 1 HETATM 4 O O2' 3AM . . . LA 3 -1.42 -61.279 -1.657 0.33 52.57 ? O2' 3AM 205 E 1 HETATM 5 C C2' 3AM . . . LA 3 -0.771 -62.155 -2.555 0.33 52.06 ? C2' 3AM 205 E 1 HETATM 6 C C3' 3AM . . . LA 3 -1.209 -61.996 -4.011 0.33 51.88 ? C3' 3AM 205 E 1 HETATM 7 O O3' 3AM . . . LA 3 -2.626 -61.966 -4.099 0.33 52.02 ? O3' 3AM 205 E 1 HETATM 8 C C1' 3AM . . . LA 3 -1.109 -63.627 -2.306 0.33 52.24 ? C1' 3AM 205 E 1 HETATM 9 O O4' 3AM . . . LA 3 -1.158 -64.263 -3.583 0.33 52.14 ? O4' 3AM 205 E 1 HETATM 10 C C4' 3AM . . . LA 3 -0.709 -63.317 -4.573 0.33 51.98 ? C4' 3AM 205 E 1 HETATM 11 C C5' 3AM . . . LA 3 0.796 -63.388 -4.631 0.33 52.13 ? C5' 3AM 205 E 1 HETATM 12 O O5' 3AM . . . LA 3 1.316 -62.415 -5.555 0.33 51.91 ? O5' 3AM 205 E 1 HETATM 13 N N9 3AM . . . LA 3 -0.132 -64.331 -1.477 0.33 52.19 ? N9 3AM 205 E 1 HETATM 14 C C8 3AM . . . LA 3 1.224 -64.128 -1.437 0.33 52.3 ? C8 3AM 205 E 1 HETATM 15 N N7 3AM . . . LA 3 1.851 -64.915 -0.597 0.33 52.07 ? N7 3AM 205 E 1 HETATM 16 C C5 3AM . . . LA 3 0.838 -65.685 -0.043 0.33 52.46 ? C5 3AM 205 E 1 HETATM 17 C C6 3AM . . . LA 3 0.856 -66.708 0.922 0.33 53.38 ? C6 3AM 205 E 1 HETATM 18 N N6 3AM . . . LA 3 1.966 -67.144 1.516 0.33 54.72 ? N6 3AM 205 E 1 HETATM 19 C C4 3AM . . . LA 3 -0.389 -65.335 -0.576 0.33 52.45 ? C4 3AM 205 E 1 HETATM 20 N N3 3AM . . . LA 3 -1.578 -65.879 -0.262 0.33 52.63 ? N3 3AM 205 E 1 HETATM 21 C C2 3AM . . . LA 3 -1.441 -66.832 0.654 0.33 53.03 ? C2 3AM 205 E 1 HETATM 22 N N1 3AM . . . LA 3 -0.329 -67.274 1.254 0.33 53.58 ? N1 3AM 205 E 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #