data_3OPY # _model_server_result.job_id 3Ef5RLmIRQktvVY2xLrBoQ _model_server_result.datetime_utc '2024-10-19 15:26:57' _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 3opy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":942}' # _entry.id 3OPY # _exptl.entry_id 3OPY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.85 _cell.angle_gamma 90 _cell.entry_id 3OPY _cell.length_a 161.658 _cell.length_b 188.303 _cell.length_c 231.56 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OPY _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,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC _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 ? 5 Z N N ? 5 MA N N ? 5 YA N N ? 5 KB N N # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3OPY _atom_sites.fract_transf_matrix[1][1] 0.006186 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000308 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005311 _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] 0.004324 _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 4 SO4 A 1 990 1 SO4 SO4 . N 4 SO4 A 1 991 2 SO4 SO4 . O 4 SO4 A 1 992 5 SO4 SO4 . P 4 SO4 A 1 993 6 SO4 SO4 . Q 4 SO4 A 1 994 7 SO4 SO4 . R 4 SO4 A 1 995 8 SO4 SO4 . S 4 SO4 A 1 996 14 SO4 SO4 . T 4 SO4 A 1 997 33 SO4 SO4 . U 4 SO4 A 1 998 36 SO4 SO4 . V 4 SO4 A 1 999 46 SO4 SO4 . W 4 SO4 A 1 1000 47 SO4 SO4 . X 4 SO4 A 1 1001 48 SO4 SO4 . Y 4 SO4 A 1 1002 49 SO4 SO4 . Z 5 ATP B 1 942 3 ATP ATP . AA 4 SO4 B 1 943 4 SO4 SO4 . BA 4 SO4 B 1 944 13 SO4 SO4 . CA 4 SO4 C 1 990 12 SO4 SO4 . DA 4 SO4 C 1 991 16 SO4 SO4 . EA 4 SO4 C 1 992 20 SO4 SO4 . FA 4 SO4 C 1 993 24 SO4 SO4 . GA 4 SO4 C 1 994 41 SO4 SO4 . HA 4 SO4 C 1 995 42 SO4 SO4 . IA 4 SO4 C 1 996 50 SO4 SO4 . JA 4 SO4 C 1 997 51 SO4 SO4 . KA 4 SO4 C 1 998 52 SO4 SO4 . LA 4 SO4 C 1 999 53 SO4 SO4 . MA 5 ATP D 1 942 2 ATP ATP . NA 4 SO4 D 1 943 15 SO4 SO4 . OA 4 SO4 D 1 944 19 SO4 SO4 . PA 4 SO4 D 1 945 21 SO4 SO4 . QA 4 SO4 E 1 990 9 SO4 SO4 . RA 4 SO4 E 1 991 29 SO4 SO4 . SA 4 SO4 E 1 992 32 SO4 SO4 . TA 4 SO4 E 1 993 37 SO4 SO4 . UA 4 SO4 E 1 994 44 SO4 SO4 . VA 4 SO4 E 1 995 54 SO4 SO4 . WA 4 SO4 E 1 996 55 SO4 SO4 . XA 4 SO4 E 1 997 56 SO4 SO4 . YA 5 ATP F 1 942 1 ATP ATP . ZA 4 SO4 F 1 943 25 SO4 SO4 . AB 4 SO4 F 1 944 35 SO4 SO4 . BB 4 SO4 F 1 945 43 SO4 SO4 . CB 4 SO4 G 1 990 17 SO4 SO4 . DB 4 SO4 G 1 991 22 SO4 SO4 . EB 4 SO4 G 1 992 26 SO4 SO4 . FB 4 SO4 G 1 993 39 SO4 SO4 . GB 4 SO4 G 1 994 40 SO4 SO4 . HB 4 SO4 G 1 995 58 SO4 SO4 . IB 4 SO4 G 1 996 59 SO4 SO4 . JB 4 SO4 G 1 997 60 SO4 SO4 . KB 5 ATP H 1 942 4 ATP ATP . LB 4 SO4 H 1 943 23 SO4 SO4 . MB 4 SO4 H 1 944 28 SO4 SO4 . NB 4 SO4 H 1 945 30 SO4 SO4 . OB 4 SO4 H 1 946 45 SO4 SO4 . PB 4 SO4 I 1 352 10 SO4 SO4 . QB 4 SO4 I 1 353 11 SO4 SO4 . RB 4 SO4 I 1 354 62 SO4 SO4 . SB 4 SO4 I 1 355 63 SO4 SO4 . TB 4 SO4 I 1 356 64 SO4 SO4 . UB 4 SO4 J 1 352 18 SO4 SO4 . VB 4 SO4 J 1 353 34 SO4 SO4 . WB 4 SO4 J 1 354 65 SO4 SO4 . XB 4 SO4 K 1 352 31 SO4 SO4 . YB 4 SO4 K 1 353 38 SO4 SO4 . ZB 4 SO4 K 1 354 69 SO4 SO4 . AC 4 SO4 L 1 352 71 SO4 SO4 . BC 4 SO4 L 1 353 72 SO4 SO4 . CC 4 SO4 L 1 354 73 SO4 SO4 . # 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 PG ATP . . . Z 5 6.641 -37.448 -15.213 1 57.13 ? PG ATP 942 B 1 HETATM 2 O O1G ATP . . . Z 5 6.704 -37.816 -16.715 1 55.07 ? O1G ATP 942 B 1 HETATM 3 O O2G ATP . . . Z 5 8.007 -37.557 -14.476 1 55.02 ? O2G ATP 942 B 1 HETATM 4 O O3G ATP . . . Z 5 5.523 -38.128 -14.34 1 55.38 ? O3G ATP 942 B 1 HETATM 5 P PB ATP . . . Z 5 5.257 -35.016 -15.897 1 50.74 ? PB ATP 942 B 1 HETATM 6 O O1B ATP . . . Z 5 4.719 -35.727 -17.181 1 51.31 ? O1B ATP 942 B 1 HETATM 7 O O2B ATP . . . Z 5 4.091 -34.624 -14.906 1 51.05 ? O2B ATP 942 B 1 HETATM 8 O O3B ATP . . . Z 5 6.291 -35.916 -15.147 1 55.14 ? O3B ATP 942 B 1 HETATM 9 P PA ATP . . . Z 5 6.906 -32.744 -15.423 1 42.77 ? PA ATP 942 B 1 HETATM 10 O O1A ATP . . . Z 5 7.797 -33.384 -14.295 1 43.07 ? O1A ATP 942 B 1 HETATM 11 O O2A ATP . . . Z 5 7.826 -31.936 -16.394 1 43.84 ? O2A ATP 942 B 1 HETATM 12 O O3A ATP . . . Z 5 6.159 -33.802 -16.334 1 47.88 ? O3A ATP 942 B 1 HETATM 13 O O5' ATP . . . Z 5 5.834 -31.705 -14.752 1 40.91 ? O5' ATP 942 B 1 HETATM 14 C C5' ATP . . . Z 5 5.386 -30.63 -15.595 1 37.19 ? C5' ATP 942 B 1 HETATM 15 C C4' ATP . . . Z 5 4.637 -29.631 -14.809 1 36.5 ? C4' ATP 942 B 1 HETATM 16 O O4' ATP . . . Z 5 3.602 -30.382 -14.245 1 35.54 ? O4' ATP 942 B 1 HETATM 17 C C3' ATP . . . Z 5 5.446 -29.239 -13.62 1 36.7 ? C3' ATP 942 B 1 HETATM 18 O O3' ATP . . . Z 5 6.473 -28.303 -13.831 1 38.42 ? O3' ATP 942 B 1 HETATM 19 C C2' ATP . . . Z 5 4.399 -28.792 -12.654 1 36.94 ? C2' ATP 942 B 1 HETATM 20 O O2' ATP . . . Z 5 4.118 -27.35 -12.807 1 37.36 ? O2' ATP 942 B 1 HETATM 21 C C1' ATP . . . Z 5 3.33 -29.918 -12.917 1 35.02 ? C1' ATP 942 B 1 HETATM 22 N N9 ATP . . . Z 5 3.498 -31.038 -11.988 1 34.62 ? N9 ATP 942 B 1 HETATM 23 C C8 ATP . . . Z 5 3.889 -32.322 -12.22 1 34.34 ? C8 ATP 942 B 1 HETATM 24 N N7 ATP . . . Z 5 3.96 -33.069 -11.116 1 35.22 ? N7 ATP 942 B 1 HETATM 25 C C5 ATP . . . Z 5 3.59 -32.211 -10.118 1 34.12 ? C5 ATP 942 B 1 HETATM 26 C C6 ATP . . . Z 5 3.425 -32.359 -8.706 1 35.15 ? C6 ATP 942 B 1 HETATM 27 N N6 ATP . . . Z 5 3.627 -33.549 -8.036 1 34.88 ? N6 ATP 942 B 1 HETATM 28 N N1 ATP . . . Z 5 3.023 -31.258 -7.957 1 35.08 ? N1 ATP 942 B 1 HETATM 29 C C2 ATP . . . Z 5 2.786 -30.07 -8.562 1 34.6 ? C2 ATP 942 B 1 HETATM 30 N N3 ATP . . . Z 5 2.888 -29.859 -9.9 1 35.14 ? N3 ATP 942 B 1 HETATM 31 C C4 ATP . . . Z 5 3.299 -30.953 -10.634 1 34.33 ? C4 ATP 942 B 1 # _model_server_stats.io_time_ms 134 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 85 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #