data_5CMS # _model_server_result.job_id DYSZXupNGXVucOohAbbO2w _model_server_result.datetime_utc '2024-10-15 11:21:25' _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 5cms # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":201}' # _entry.id 5CMS # _exptl.entry_id 5CMS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _entity.pdbx_number_of_molecules 18 _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 5CMS _cell.length_a 290.019 _cell.length_b 290.019 _cell.length_c 114.324 _cell.Z_PDB 108 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CMS _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 PISA monomeric 1 author_and_software_defined_assembly 9 PISA monomeric 1 author_and_software_defined_assembly 10 PISA monomeric 1 author_and_software_defined_assembly 11 PISA monomeric 1 author_and_software_defined_assembly 12 PISA monomeric 1 author_and_software_defined_assembly 13 PISA monomeric 1 author_and_software_defined_assembly 14 PISA monomeric 1 author_and_software_defined_assembly 15 PISA monomeric 1 author_and_software_defined_assembly 16 PISA monomeric 1 author_and_software_defined_assembly 17 PISA monomeric 1 author_and_software_defined_assembly 18 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,S,T,CB 1 1 B,U,V,DB 2 1 C,W,X,EB 3 1 D,Y,Z,FB 4 1 E,AA,BA,GB 5 1 F,CA,DA,HB 6 1 G,EA,FA,IB 7 1 H,GA,HA,JB 8 1 I,IA,JA,KB 9 1 J,KA,LA,LB 10 1 K,MA,NA,MB 11 1 L,OA,PA,NB 12 1 M,QA,RA,OB 13 1 N,SA,TA,PB 14 1 O,UA,VA,QB 15 1 P,WA,XA,RB 16 1 Q,YA,ZA,SB 17 1 R,AB,BB,TB 18 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 ? 2 S N N ? 2 U N N ? 2 W N N ? 2 Y N N ? 2 AA N N ? 2 CA N N ? 2 EA N N ? 2 GA N N ? 2 IA N N ? 2 KA N N ? 2 MA N N ? 2 OA N N ? 2 QA N N ? 2 SA N N ? 2 UA N N ? 2 WA N N ? 2 YA N N ? 2 AB N N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 5CMS _atom_sites.fract_transf_matrix[1][1] 0.003448 _atom_sites.fract_transf_matrix[1][2] 0.001991 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003981 _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] 0.008747 _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 S 2 APR R 1 401 401 APR APR . T 3 SO4 R 1 402 1 SO4 SO4 . U 2 APR A 1 201 402 APR APR . V 3 SO4 A 1 202 2 SO4 SO4 . W 2 APR B 1 201 419 APR APR . X 3 SO4 B 1 202 3 SO4 SO4 . Y 2 APR C 1 201 421 APR APR . Z 3 SO4 C 1 202 4 SO4 SO4 . AA 2 APR D 1 201 405 APR APR . BA 3 SO4 D 1 202 5 SO4 SO4 . CA 2 APR E 1 201 420 APR APR . DA 3 SO4 E 1 202 6 SO4 SO4 . EA 2 APR F 1 201 407 APR APR . FA 3 SO4 F 1 202 7 SO4 SO4 . GA 2 APR G 1 201 408 APR APR . HA 3 SO4 G 1 202 8 SO4 SO4 . IA 2 APR H 1 201 409 APR APR . JA 3 SO4 H 1 202 9 SO4 SO4 . KA 2 APR I 1 201 410 APR APR . LA 3 SO4 I 1 202 10 SO4 SO4 . MA 2 APR J 1 201 411 APR APR . NA 3 SO4 J 1 202 11 SO4 SO4 . OA 2 APR K 1 201 412 APR APR . PA 3 SO4 K 1 202 12 SO4 SO4 . QA 2 APR L 1 201 413 APR APR . RA 3 SO4 L 1 202 13 SO4 SO4 . SA 2 APR M 1 201 414 APR APR . TA 3 SO4 M 1 202 14 SO4 SO4 . UA 2 APR N 1 201 415 APR APR . VA 3 SO4 N 1 202 15 SO4 SO4 . WA 2 APR O 1 201 417 APR APR . XA 3 SO4 O 1 202 16 SO4 SO4 . YA 2 APR P 1 201 416 APR APR . ZA 3 SO4 P 1 202 17 SO4 SO4 . AB 2 APR Q 1 201 418 APR APR . BB 3 SO4 Q 1 202 18 SO4 SO4 . CB 4 HOH R 1 501 43 HOH HOH . CB 4 HOH R 2 502 61 HOH HOH . CB 4 HOH R 3 503 110 HOH HOH . CB 4 HOH R 4 504 111 HOH HOH . DB 4 HOH A 1 301 78 HOH HOH . DB 4 HOH A 2 302 90 HOH HOH . DB 4 HOH A 3 303 50 HOH HOH . DB 4 HOH A 4 304 73 HOH HOH . DB 4 HOH A 5 305 30 HOH HOH . EB 4 HOH B 1 301 53 HOH HOH . EB 4 HOH B 2 302 36 HOH HOH . EB 4 HOH B 3 303 13 HOH HOH . EB 4 HOH B 4 304 10 HOH HOH . EB 4 HOH B 5 305 1 HOH HOH . EB 4 HOH B 6 306 54 HOH HOH . EB 4 HOH B 7 307 83 HOH HOH . EB 4 HOH B 8 308 40 HOH HOH . EB 4 HOH B 9 309 35 HOH HOH . FB 4 HOH C 1 301 103 HOH HOH . FB 4 HOH C 2 302 75 HOH HOH . FB 4 HOH C 3 303 89 HOH HOH . FB 4 HOH C 4 304 20 HOH HOH . FB 4 HOH C 5 305 115 HOH HOH . FB 4 HOH C 6 306 5 HOH HOH . FB 4 HOH C 7 307 106 HOH HOH . FB 4 HOH C 8 308 70 HOH HOH . FB 4 HOH C 9 309 34 HOH HOH . FB 4 HOH C 10 310 60 HOH HOH . FB 4 HOH C 11 311 107 HOH HOH . FB 4 HOH C 12 312 7 HOH HOH . GB 4 HOH D 1 301 24 HOH HOH . GB 4 HOH D 2 302 41 HOH HOH . GB 4 HOH D 3 303 39 HOH HOH . GB 4 HOH D 4 304 77 HOH HOH . GB 4 HOH D 5 305 95 HOH HOH . GB 4 HOH D 6 306 59 HOH HOH . HB 4 HOH E 1 301 6 HOH HOH . HB 4 HOH E 2 302 88 HOH HOH . HB 4 HOH E 3 303 32 HOH HOH . HB 4 HOH E 4 304 98 HOH HOH . HB 4 HOH E 5 305 63 HOH HOH . HB 4 HOH E 6 306 74 HOH HOH . HB 4 HOH E 7 307 56 HOH HOH . HB 4 HOH E 8 308 15 HOH HOH . HB 4 HOH E 9 309 99 HOH HOH . HB 4 HOH E 10 310 82 HOH HOH . HB 4 HOH E 11 311 58 HOH HOH . HB 4 HOH E 12 312 28 HOH HOH . IB 4 HOH F 1 301 113 HOH HOH . IB 4 HOH F 2 302 76 HOH HOH . IB 4 HOH F 3 303 51 HOH HOH . IB 4 HOH F 4 304 72 HOH HOH . IB 4 HOH F 5 305 93 HOH HOH . IB 4 HOH F 6 306 92 HOH HOH . IB 4 HOH F 7 307 97 HOH HOH . IB 4 HOH F 8 308 31 HOH HOH . JB 4 HOH G 1 301 105 HOH HOH . JB 4 HOH G 2 302 49 HOH HOH . JB 4 HOH G 3 303 2 HOH HOH . JB 4 HOH G 4 304 38 HOH HOH . JB 4 HOH G 5 305 119 HOH HOH . JB 4 HOH G 6 306 52 HOH HOH . JB 4 HOH G 7 307 80 HOH HOH . KB 4 HOH H 1 301 87 HOH HOH . KB 4 HOH H 2 302 11 HOH HOH . KB 4 HOH H 3 303 21 HOH HOH . KB 4 HOH H 4 304 12 HOH HOH . KB 4 HOH H 5 305 109 HOH HOH . KB 4 HOH H 6 306 86 HOH HOH . LB 4 HOH I 1 301 114 HOH HOH . LB 4 HOH I 2 302 94 HOH HOH . LB 4 HOH I 3 303 64 HOH HOH . MB 4 HOH J 1 301 68 HOH HOH . MB 4 HOH J 2 302 4 HOH HOH . MB 4 HOH J 3 303 23 HOH HOH . MB 4 HOH J 4 304 44 HOH HOH . MB 4 HOH J 5 305 8 HOH HOH . MB 4 HOH J 6 306 47 HOH HOH . MB 4 HOH J 7 307 79 HOH HOH . NB 4 HOH K 1 301 3 HOH HOH . NB 4 HOH K 2 302 91 HOH HOH . NB 4 HOH K 3 303 22 HOH HOH . NB 4 HOH K 4 304 112 HOH HOH . NB 4 HOH K 5 305 29 HOH HOH . NB 4 HOH K 6 306 45 HOH HOH . NB 4 HOH K 7 307 14 HOH HOH . OB 4 HOH L 1 301 120 HOH HOH . OB 4 HOH L 2 302 71 HOH HOH . OB 4 HOH L 3 303 101 HOH HOH . OB 4 HOH L 4 304 81 HOH HOH . OB 4 HOH L 5 305 118 HOH HOH . OB 4 HOH L 6 306 27 HOH HOH . OB 4 HOH L 7 307 18 HOH HOH . PB 4 HOH M 1 301 66 HOH HOH . PB 4 HOH M 2 302 42 HOH HOH . PB 4 HOH M 3 303 37 HOH HOH . PB 4 HOH M 4 304 9 HOH HOH . PB 4 HOH M 5 305 67 HOH HOH . PB 4 HOH M 6 306 17 HOH HOH . PB 4 HOH M 7 307 102 HOH HOH . QB 4 HOH N 1 301 55 HOH HOH . QB 4 HOH N 2 302 33 HOH HOH . QB 4 HOH N 3 303 62 HOH HOH . QB 4 HOH N 4 304 57 HOH HOH . QB 4 HOH N 5 305 104 HOH HOH . QB 4 HOH N 6 306 121 HOH HOH . RB 4 HOH O 1 301 108 HOH HOH . RB 4 HOH O 2 302 116 HOH HOH . RB 4 HOH O 3 303 19 HOH HOH . SB 4 HOH P 1 301 84 HOH HOH . SB 4 HOH P 2 302 96 HOH HOH . SB 4 HOH P 3 303 16 HOH HOH . SB 4 HOH P 4 304 26 HOH HOH . SB 4 HOH P 5 305 46 HOH HOH . SB 4 HOH P 6 306 69 HOH HOH . TB 4 HOH Q 1 301 100 HOH HOH . TB 4 HOH Q 2 302 85 HOH HOH . TB 4 HOH Q 3 303 25 HOH HOH . TB 4 HOH Q 4 304 65 HOH HOH . TB 4 HOH Q 5 305 117 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 N N1 APR . . . W 2 -98.006 93.112 -34.378 1 41.54 ? N1 APR 201 B 1 HETATM 2 C C2 APR . . . W 2 -98.99 93.988 -34.004 1 41.09 ? C2 APR 201 B 1 HETATM 3 N N3 APR . . . W 2 -100.04 93.672 -33.206 1 38.96 ? N3 APR 201 B 1 HETATM 4 C C4 APR . . . W 2 -100.133 92.389 -32.722 1 42.33 ? C4 APR 201 B 1 HETATM 5 C C5 APR . . . W 2 -99.088 91.388 -33.098 1 43.4 ? C5 APR 201 B 1 HETATM 6 C C6 APR . . . W 2 -97.971 91.816 -33.972 1 39.37 ? C6 APR 201 B 1 HETATM 7 N N6 APR . . . W 2 -96.992 90.964 -34.346 1 37.62 ? N6 APR 201 B 1 HETATM 8 N N7 APR . . . W 2 -99.455 90.221 -32.496 1 48.41 ? N7 APR 201 B 1 HETATM 9 C C8 APR . . . W 2 -100.612 90.447 -31.781 1 44 ? C8 APR 201 B 1 HETATM 10 N N9 APR . . . W 2 -101.002 91.723 -31.923 1 40.36 ? N9 APR 201 B 1 HETATM 11 C C1' APR . . . W 2 -102.18 92.339 -31.304 1 43.22 ? C1' APR 201 B 1 HETATM 12 C C2' APR . . . W 2 -103.253 91.328 -30.939 1 43.62 ? C2' APR 201 B 1 HETATM 13 O O2' APR . . . W 2 -104.494 91.646 -31.617 1 48.34 ? O2' APR 201 B 1 HETATM 14 C C3' APR . . . W 2 -103.495 91.541 -29.47 1 43.22 ? C3' APR 201 B 1 HETATM 15 O O3' APR . . . W 2 -104.795 92.133 -29.326 1 37.18 ? O3' APR 201 B 1 HETATM 16 O O4' APR . . . W 2 -101.774 93.009 -30.095 1 46.18 ? O4' APR 201 B 1 HETATM 17 C C4' APR . . . W 2 -102.481 92.541 -28.943 1 41.29 ? C4' APR 201 B 1 HETATM 18 C C5' APR . . . W 2 -101.496 91.903 -27.981 1 39.5 ? C5' APR 201 B 1 HETATM 19 O O5' APR . . . W 2 -102.064 90.884 -27.157 1 36.61 ? O5' APR 201 B 1 HETATM 20 P PA APR . . . W 2 -101.037 89.682 -26.634 1 42.17 ? PA APR 201 B 1 HETATM 21 O O1A APR . . . W 2 -101.936 88.479 -26.304 1 46.28 ? O1A APR 201 B 1 HETATM 22 O O2A APR . . . W 2 -99.794 89.356 -27.47 1 33.33 ? O2A APR 201 B 1 HETATM 23 O O3A APR . . . W 2 -100.421 90.415 -25.269 1 40.01 ? O3A APR 201 B 1 HETATM 24 P PB APR . . . W 2 -101.353 90.639 -23.922 1 39.56 ? PB APR 201 B 1 HETATM 25 O O1B APR . . . W 2 -100.934 91.887 -23.117 1 36.21 ? O1B APR 201 B 1 HETATM 26 O O2B APR . . . W 2 -102.835 90.516 -24.347 1 38.15 ? O2B APR 201 B 1 HETATM 27 O O5D APR . . . W 2 -100.842 89.332 -23.067 1 40.39 ? O5D APR 201 B 1 HETATM 28 C C5D APR . . . W 2 -99.514 89.341 -22.43 1 46.6 ? C5D APR 201 B 1 HETATM 29 O O4D APR . . . W 2 -98.058 87.728 -21.058 1 60.73 ? O4D APR 201 B 1 HETATM 30 O O1D APR . . . W 2 -97.86 89.528 -19.242 1 74.44 ? O1D APR 201 B 1 HETATM 31 C C1D APR . . . W 2 -98.175 88.152 -19.632 1 68.85 ? C1D APR 201 B 1 HETATM 32 O O2D APR . . . W 2 -99.852 87.198 -18.221 1 68.71 ? O2D APR 201 B 1 HETATM 33 C C2D APR . . . W 2 -99.621 88.244 -19.197 1 62.08 ? C2D APR 201 B 1 HETATM 34 O O3D APR . . . W 2 -100.973 86.631 -20.375 1 42.43 ? O3D APR 201 B 1 HETATM 35 C C3D APR . . . W 2 -100.373 87.958 -20.481 1 58.26 ? C3D APR 201 B 1 HETATM 36 C C4D APR . . . W 2 -99.358 87.994 -21.654 1 55.57 ? C4D APR 201 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #