data_5CB6 # _model_server_result.job_id p4pMcpLOXfaaw22fohdfcA _model_server_result.datetime_utc '2024-11-16 19:57:07' _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 5cb6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":301}' # _entry.id 5CB6 # _exptl.entry_id 5CB6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.284 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-PHOSPHOSULFATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.72 _cell.angle_gamma 90 _cell.entry_id 5CB6 _cell.length_a 136.904 _cell.length_b 109.681 _cell.length_c 100.807 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CB6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 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,D,G,H,I,J,R,S,T,U,BA,EA 1 1 B,F,K,L,M,Y,Z,AA,CA,GA 2 1 C,N,O,P,Q,DA 3 1 C,N,O,P,Q,DA 3 2 E,V,W,X,FA 4 1 E,V,W,X,FA 4 3 # 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_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -136.904 0 0 3 'crystal symmetry operation' 2_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 1.266745 0 -100.799041 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 K N N ? 2 N N N ? 2 R N N ? 2 V N N ? 2 Y 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 OG1 THR 39 A THR 19 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc2 A OD2 ASP 62 A ASP 42 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc3 A O THR 173 A THR 153 1_555 J NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc4 A O GLU 176 A GLU 156 1_555 J NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? metalc ? metalc5 H O2G ANP . A ANP 302 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.783 ? metalc ? metalc6 I MG MG . A MG 303 1_555 BA O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc7 J NA NA . A NA 304 1_555 B O THR 173 B THR 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc8 J NA NA . A NA 304 1_555 B O GLU 176 B GLU 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? metalc ? metalc9 B OG1 THR 39 B THR 19 1_555 M MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc10 L O2G ANP . B ANP 302 1_555 M MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc11 M MG MG . B MG 303 1_555 CA O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc12 C OG1 THR 39 C THR 19 1_555 P MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc13 C OD2 ASP 60 C ASP 40 1_555 P MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc14 O O2G ANP . C ANP 302 1_555 P MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc15 O O3G ANP . C ANP 302 1_555 P MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc16 D OG1 THR 39 D THR 19 1_555 T MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc17 D OD2 ASP 62 D ASP 42 1_555 T MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc18 S O1G ANP . D ANP 302 1_555 T MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc19 S O2G ANP . D ANP 302 1_555 T MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc20 E OG1 THR 39 E THR 19 1_555 X MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? metalc ? metalc21 E OD2 ASP 62 E ASP 42 1_555 X MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc22 W O2G ANP . E ANP 302 1_555 X MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc23 X MG MG . E MG 303 1_555 FA O HOH . E HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc24 F OG1 THR 39 F THR 19 1_555 AA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc25 F OD2 ASP 62 F ASP 42 1_555 AA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc26 Z O2G ANP . F ANP 302 1_555 AA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc27 Z O1B ANP . F ANP 302 1_555 AA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc28 AA MG MG . F MG 303 1_555 GA O HOH . F HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? # _chem_comp.formula 'C10 H14 N5 O10 P S' _chem_comp.formula_weight 427.284 _chem_comp.id ADX _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-PHOSPHOSULFATE" _chem_comp.type 'rna linking' _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 SB O1B ADX doub 1 n n SB O2B ADX doub 2 n n SB O3B ADX sing 3 n n SB O3A ADX sing 4 n n O3B HOB3 ADX sing 5 n n PA O1A ADX doub 6 n n PA O2A ADX sing 7 n n PA O3A ADX sing 8 n n PA O5' ADX sing 9 n n O2A HOA2 ADX sing 10 n n O5' C5' ADX sing 11 n n C5' C4' ADX sing 12 n n C5' H5' ADX sing 13 n n C5' "H5''" ADX sing 14 n n C4' O4' ADX sing 15 n n C4' C3' ADX sing 16 n n C4' H4' ADX sing 17 n n O4' C1' ADX sing 18 n n C3' O3' ADX sing 19 n n C3' C2' ADX sing 20 n n C3' H3' ADX sing 21 n n O3' HO3' ADX sing 22 n n C2' O2' ADX sing 23 n n C2' C1' ADX sing 24 n n C2' H2' ADX sing 25 n n O2' HO2' ADX sing 26 n n C1' N9 ADX sing 27 n n C1' H1' ADX sing 28 n n N9 C8 ADX sing 29 n y N9 C4 ADX sing 30 n y C8 N7 ADX doub 31 n y C8 H8 ADX sing 32 n n N7 C5 ADX sing 33 n y C5 C6 ADX sing 34 n y C5 C4 ADX doub 35 n y C6 N6 ADX sing 36 n n C6 N1 ADX doub 37 n y N6 HN61 ADX sing 38 n n N6 HN62 ADX sing 39 n n N1 C2 ADX sing 40 n y C2 N3 ADX doub 41 n y C2 H2 ADX sing 42 n n N3 C4 ADX sing 43 n y # _atom_sites.entry_id 5CB6 _atom_sites.fract_transf_matrix[1][1] 0.007304 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000092 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009117 _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] 0.009921 _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 ADX A 1 301 301 ADX ADX . H 3 ANP A 1 302 302 ANP ANP . I 4 MG A 1 303 303 MG MG . J 5 NA A 1 304 304 NA NA . K 2 ADX B 1 301 301 ADX ADX . L 3 ANP B 1 302 302 ANP ANP . M 4 MG B 1 303 303 MG MG . N 2 ADX C 1 301 301 ADX ADX . O 3 ANP C 1 302 302 ANP ANP . P 4 MG C 1 303 303 MG MG . Q 6 CAC C 1 304 304 CAC CAC . R 2 ADX D 1 301 301 ADX ADX . S 3 ANP D 1 302 302 ANP ANP . T 4 MG D 1 303 303 MG MG . U 6 CAC D 1 304 304 CAC CAC . V 2 ADX E 1 301 301 ADX ADX . W 3 ANP E 1 302 302 ANP ANP . X 4 MG E 1 303 303 MG MG . Y 2 ADX F 1 301 301 ADX ADX . Z 3 ANP F 1 302 302 ANP ANP . AA 4 MG F 1 303 303 MG MG . BA 7 HOH A 1 401 401 HOH HOH . BA 7 HOH A 2 402 402 HOH HOH . BA 7 HOH A 3 403 403 HOH HOH . BA 7 HOH A 4 404 404 HOH HOH . BA 7 HOH A 5 405 405 HOH HOH . BA 7 HOH A 6 406 406 HOH HOH . BA 7 HOH A 7 407 407 HOH HOH . BA 7 HOH A 8 408 408 HOH HOH . BA 7 HOH A 9 409 409 HOH HOH . BA 7 HOH A 10 410 410 HOH HOH . BA 7 HOH A 11 411 411 HOH HOH . BA 7 HOH A 12 412 412 HOH HOH . BA 7 HOH A 13 413 413 HOH HOH . BA 7 HOH A 14 414 414 HOH HOH . BA 7 HOH A 15 415 415 HOH HOH . BA 7 HOH A 16 416 416 HOH HOH . BA 7 HOH A 17 417 417 HOH HOH . BA 7 HOH A 18 418 418 HOH HOH . BA 7 HOH A 19 419 419 HOH HOH . BA 7 HOH A 20 420 420 HOH HOH . BA 7 HOH A 21 421 421 HOH HOH . BA 7 HOH A 22 422 422 HOH HOH . BA 7 HOH A 23 423 423 HOH HOH . BA 7 HOH A 24 424 424 HOH HOH . BA 7 HOH A 25 425 425 HOH HOH . BA 7 HOH A 26 426 426 HOH HOH . CA 7 HOH B 1 401 402 HOH HOH . CA 7 HOH B 2 402 401 HOH HOH . CA 7 HOH B 3 403 403 HOH HOH . CA 7 HOH B 4 404 404 HOH HOH . CA 7 HOH B 5 405 405 HOH HOH . CA 7 HOH B 6 406 406 HOH HOH . CA 7 HOH B 7 407 407 HOH HOH . CA 7 HOH B 8 408 408 HOH HOH . CA 7 HOH B 9 409 409 HOH HOH . CA 7 HOH B 10 410 410 HOH HOH . CA 7 HOH B 11 411 411 HOH HOH . CA 7 HOH B 12 412 412 HOH HOH . CA 7 HOH B 13 413 413 HOH HOH . CA 7 HOH B 14 414 414 HOH HOH . DA 7 HOH C 1 401 401 HOH HOH . DA 7 HOH C 2 402 402 HOH HOH . DA 7 HOH C 3 403 403 HOH HOH . DA 7 HOH C 4 404 404 HOH HOH . DA 7 HOH C 5 405 405 HOH HOH . DA 7 HOH C 6 406 406 HOH HOH . DA 7 HOH C 7 407 407 HOH HOH . DA 7 HOH C 8 408 408 HOH HOH . DA 7 HOH C 9 409 409 HOH HOH . DA 7 HOH C 10 410 410 HOH HOH . DA 7 HOH C 11 411 411 HOH HOH . DA 7 HOH C 12 412 412 HOH HOH . DA 7 HOH C 13 413 413 HOH HOH . DA 7 HOH C 14 414 414 HOH HOH . DA 7 HOH C 15 415 415 HOH HOH . DA 7 HOH C 16 416 416 HOH HOH . DA 7 HOH C 17 417 417 HOH HOH . EA 7 HOH D 1 401 401 HOH HOH . EA 7 HOH D 2 402 402 HOH HOH . EA 7 HOH D 3 403 403 HOH HOH . EA 7 HOH D 4 404 404 HOH HOH . EA 7 HOH D 5 405 405 HOH HOH . EA 7 HOH D 6 406 406 HOH HOH . EA 7 HOH D 7 407 407 HOH HOH . EA 7 HOH D 8 408 408 HOH HOH . EA 7 HOH D 9 409 409 HOH HOH . EA 7 HOH D 10 410 410 HOH HOH . EA 7 HOH D 11 411 411 HOH HOH . FA 7 HOH E 1 401 401 HOH HOH . FA 7 HOH E 2 402 402 HOH HOH . FA 7 HOH E 3 403 403 HOH HOH . FA 7 HOH E 4 404 404 HOH HOH . FA 7 HOH E 5 405 405 HOH HOH . FA 7 HOH E 6 406 406 HOH HOH . FA 7 HOH E 7 407 407 HOH HOH . FA 7 HOH E 8 408 408 HOH HOH . GA 7 HOH F 1 401 401 HOH HOH . GA 7 HOH F 2 402 402 HOH HOH . GA 7 HOH F 3 403 403 HOH HOH . GA 7 HOH F 4 404 404 HOH HOH . GA 7 HOH F 5 405 405 HOH HOH . GA 7 HOH F 6 406 406 HOH HOH . GA 7 HOH F 7 407 407 HOH HOH . GA 7 HOH F 8 408 408 HOH HOH . GA 7 HOH F 9 409 409 HOH HOH . GA 7 HOH F 10 410 410 HOH HOH . GA 7 HOH F 11 411 411 HOH HOH . GA 7 HOH F 12 412 412 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 S SB ADX . . . N 2 -72.034 -13.408 13.531 1 37.41 ? SB ADX 301 C 1 HETATM 2 O O1B ADX . . . N 2 -71.84 -13.223 12.092 1 34.21 ? O1B ADX 301 C 1 HETATM 3 O O2B ADX . . . N 2 -72.622 -14.748 13.737 1 32.62 ? O2B ADX 301 C 1 HETATM 4 O O3B ADX . . . N 2 -72.909 -12.342 14.112 1 29.46 ? O3B ADX 301 C 1 HETATM 5 P PA ADX . . . N 2 -69.581 -14.259 14.025 1 45.09 ? PA ADX 301 C 1 HETATM 6 O O1A ADX . . . N 2 -69.343 -14.46 12.562 1 34.6 ? O1A ADX 301 C 1 HETATM 7 O O2A ADX . . . N 2 -69.794 -15.578 14.723 1 39.79 ? O2A ADX 301 C 1 HETATM 8 O O3A ADX . . . N 2 -70.741 -13.256 14.228 1 41.87 ? O3A ADX 301 C 1 HETATM 9 O O5' ADX . . . N 2 -68.359 -13.44 14.585 1 36.15 ? O5' ADX 301 C 1 HETATM 10 C C5' ADX . . . N 2 -68.311 -13.126 15.937 1 43.08 ? C5' ADX 301 C 1 HETATM 11 C C4' ADX . . . N 2 -67.018 -12.986 16.49 1 43.94 ? C4' ADX 301 C 1 HETATM 12 O O4' ADX . . . N 2 -66.457 -11.844 15.771 1 42.99 ? O4' ADX 301 C 1 HETATM 13 C C3' ADX . . . N 2 -67.124 -12.61 17.904 1 47.88 ? C3' ADX 301 C 1 HETATM 14 O O3' ADX . . . N 2 -66.869 -13.663 18.721 1 49.02 ? O3' ADX 301 C 1 HETATM 15 C C2' ADX . . . N 2 -66.077 -11.599 18.06 1 50.78 ? C2' ADX 301 C 1 HETATM 16 O O2' ADX . . . N 2 -64.923 -12.231 18.342 1 51.81 ? O2' ADX 301 C 1 HETATM 17 C C1' ADX . . . N 2 -65.959 -10.934 16.718 1 48.11 ? C1' ADX 301 C 1 HETATM 18 N N9 ADX . . . N 2 -66.584 -9.631 16.688 1 45.7 ? N9 ADX 301 C 1 HETATM 19 C C8 ADX . . . N 2 -65.992 -8.469 16.327 1 42.15 ? C8 ADX 301 C 1 HETATM 20 N N7 ADX . . . N 2 -66.873 -7.465 16.469 1 39.28 ? N7 ADX 301 C 1 HETATM 21 C C5 ADX . . . N 2 -68.043 -7.989 16.92 1 36.7 ? C5 ADX 301 C 1 HETATM 22 C C6 ADX . . . N 2 -69.292 -7.42 17.229 1 38.69 ? C6 ADX 301 C 1 HETATM 23 N N6 ADX . . . N 2 -69.524 -5.999 17.015 1 33.07 ? N6 ADX 301 C 1 HETATM 24 N N1 ADX . . . N 2 -70.288 -8.215 17.674 1 40.12 ? N1 ADX 301 C 1 HETATM 25 C C2 ADX . . . N 2 -70.071 -9.538 17.803 1 43.48 ? C2 ADX 301 C 1 HETATM 26 N N3 ADX . . . N 2 -68.894 -10.12 17.516 1 30.81 ? N3 ADX 301 C 1 HETATM 27 C C4 ADX . . . N 2 -67.861 -9.373 17.069 1 35.71 ? C4 ADX 301 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #