data_5SVM # _model_server_result.job_id gASawprtwGmwf-We9RvtgQ _model_server_result.datetime_utc '2024-11-05 21:22:11' _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 5svm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 5SVM # _exptl.entry_id 5SVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 553.273 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)" _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 5SVM _cell.length_a 172.64 _cell.length_b 172.64 _cell.length_c 172.64 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,P 1 1,2,4 B,J,K,L,M,N,O,Q 2 1,3,5 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 86.32 86.32 0 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 86.32 0 -86.32 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc2 F OAC 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? metalc ? metalc3 G NA NA . A NA 405 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc4 G NA NA . A NA 405 1_555 P O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc5 G NA NA . A NA 405 1_555 P O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 G NA NA . A NA 405 1_555 P O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 B OD2 ASP 157 B ASP 158 1_555 N NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc8 N NA NA . B NA 405 1_555 Q O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc9 N NA NA . B NA 405 1_555 Q O HOH . B HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? # _chem_comp.formula 'C11 H18 N5 O13 P3 S' _chem_comp.formula_weight 553.273 _chem_comp.id 6AT _chem_comp.mon_nstd_flag . _chem_comp.name "2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-methylthio-adenosine-5'-triphosphate" # 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 CAA S2 6AT sing 1 n n S2 C2 6AT sing 2 n n N1 C2 6AT doub 3 n y N1 C6 6AT sing 4 n y C2 N3 6AT sing 5 n y N6 C6 6AT sing 6 n n C6 C5 6AT doub 7 n y N3 C4 6AT doub 8 n y C5 C4 6AT sing 9 n y C5 N7 6AT sing 10 n y C4 N9 6AT sing 11 n y N7 C8 6AT doub 12 n y N9 C8 6AT sing 13 n y N9 C1' 6AT sing 14 n n O4' C1' 6AT sing 15 n n O4' C4' 6AT sing 16 n n C1' C2' 6AT sing 17 n n C4' C5' 6AT sing 18 n n C4' C3' 6AT sing 19 n n O5' C5' 6AT sing 20 n n O5' PBF 6AT sing 21 n n C2' O2' 6AT sing 22 n n C2' C3' 6AT sing 23 n n OAD PBF 6AT doub 24 n n C3' O3' 6AT sing 25 n n PBF OAT 6AT sing 26 n n PBF OAJ 6AT sing 27 n n OAK PBG 6AT doub 28 n n OAT PBG 6AT sing 29 n n PBG OAE 6AT sing 30 n n PBG OAS 6AT sing 31 n n OAS PBE 6AT sing 32 n n OAH PBE 6AT doub 33 n n PBE OAC 6AT sing 34 n n PBE OAI 6AT sing 35 n n OAI H1 6AT sing 36 n n OAC H2 6AT sing 37 n n OAE H3 6AT sing 38 n n OAJ H4 6AT sing 39 n n C5' H5 6AT sing 40 n n C5' H6 6AT sing 41 n n C4' H7 6AT sing 42 n n C3' H8 6AT sing 43 n n O3' H9 6AT sing 44 n n C2' H10 6AT sing 45 n n O2' H11 6AT sing 46 n n C1' H12 6AT sing 47 n n C8 H13 6AT sing 48 n n CAA H14 6AT sing 49 n n CAA H15 6AT sing 50 n n CAA H16 6AT sing 51 n n N6 H17 6AT sing 52 n n N6 H18 6AT sing 53 n n # _atom_sites.entry_id 5SVM _atom_sites.fract_transf_matrix[1][1] 0.005792 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005792 _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] 0.005792 _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 C 2 NAG A 1 401 500 NAG NAG . D 2 NAG A 1 402 501 NAG NAG . E 2 NAG A 1 403 502 NAG NAG . F 3 6AT A 1 404 1 6AT LIG . G 4 NA A 1 405 4 NA NA . H 5 TRS A 1 406 1 TRS TRS . I 6 EDO A 1 407 1 EDO EDO . J 7 ATP B 1 401 402 ATP ATP . K 2 NAG B 1 402 500 NAG NAG . L 2 NAG B 1 403 501 NAG NAG . M 2 NAG B 1 404 502 NAG NAG . N 4 NA B 1 405 3 NA NA . O 6 EDO B 1 406 2 EDO EDO . P 8 HOH A 1 501 20 HOH HOH . P 8 HOH A 2 502 40 HOH HOH . P 8 HOH A 3 503 52 HOH HOH . P 8 HOH A 4 504 3 HOH HOH . P 8 HOH A 5 505 44 HOH HOH . P 8 HOH A 6 506 6 HOH HOH . P 8 HOH A 7 507 1 HOH HOH . P 8 HOH A 8 508 5 HOH HOH . P 8 HOH A 9 509 4 HOH HOH . P 8 HOH A 10 510 11 HOH HOH . P 8 HOH A 11 511 43 HOH HOH . P 8 HOH A 12 512 14 HOH HOH . P 8 HOH A 13 513 26 HOH HOH . P 8 HOH A 14 514 49 HOH HOH . P 8 HOH A 15 515 54 HOH HOH . P 8 HOH A 16 516 15 HOH HOH . P 8 HOH A 17 517 45 HOH HOH . P 8 HOH A 18 518 42 HOH HOH . P 8 HOH A 19 519 2 HOH HOH . Q 8 HOH B 1 501 29 HOH HOH . Q 8 HOH B 2 502 22 HOH HOH . Q 8 HOH B 3 503 48 HOH HOH . Q 8 HOH B 4 504 37 HOH HOH . Q 8 HOH B 5 505 36 HOH HOH . Q 8 HOH B 6 506 23 HOH HOH . Q 8 HOH B 7 507 33 HOH HOH . Q 8 HOH B 8 508 51 HOH HOH . Q 8 HOH B 9 509 19 HOH HOH . Q 8 HOH B 10 510 50 HOH HOH . Q 8 HOH B 11 511 28 HOH HOH . Q 8 HOH B 12 512 32 HOH HOH . Q 8 HOH B 13 513 16 HOH HOH . Q 8 HOH B 14 514 35 HOH HOH . Q 8 HOH B 15 515 53 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 O OAI 6AT . . . F 3 32.737 3.296 18.573 1 72.15 -1 OAI 6AT 404 A 1 HETATM 2 P PBE 6AT . . . F 3 32.804 3.512 20.068 1 66.8 ? PBE 6AT 404 A 1 HETATM 3 O OAH 6AT . . . F 3 31.518 4.118 20.535 1 78.47 ? OAH 6AT 404 A 1 HETATM 4 O OAC 6AT . . . F 3 32.999 2.187 20.766 1 87.22 -1 OAC 6AT 404 A 1 HETATM 5 O OAS 6AT . . . F 3 34.067 4.531 20.4 1 64.8 ? OAS 6AT 404 A 1 HETATM 6 P PBG 6AT . . . F 3 35.18 4.953 19.276 1 64.07 ? PBG 6AT 404 A 1 HETATM 7 O OAK 6AT . . . F 3 34.525 5.782 18.198 1 66.77 ? OAK 6AT 404 A 1 HETATM 8 O OAE 6AT . . . F 3 35.834 3.699 18.693 1 65.56 -1 OAE 6AT 404 A 1 HETATM 9 O OAT 6AT . . . F 3 36.388 5.875 20.026 1 58.93 ? OAT 6AT 404 A 1 HETATM 10 P PBF 6AT . . . F 3 35.999 7.005 21.23 1 67.02 ? PBF 6AT 404 A 1 HETATM 11 O OAJ 6AT . . . F 3 34.6 7.471 21 1 72.14 -1 OAJ 6AT 404 A 1 HETATM 12 O OAD 6AT . . . F 3 36.981 8.15 21.15 1 70.58 ? OAD 6AT 404 A 1 HETATM 13 O O5' 6AT . . . F 3 36.102 6.294 22.692 1 76.92 ? O5' 6AT 404 A 1 HETATM 14 C C5' 6AT . . . F 3 37.354 5.798 23.092 1 77.78 ? C5' 6AT 404 A 1 HETATM 15 C C4' 6AT . . . F 3 37.21 4.389 23.584 1 72.58 ? C4' 6AT 404 A 1 HETATM 16 O O4' 6AT . . . F 3 36.337 4.414 24.97 1 75.82 ? O4' 6AT 404 A 1 HETATM 17 C C3' 6AT . . . F 3 36.554 3.638 22.695 1 77.97 ? C3' 6AT 404 A 1 HETATM 18 O O3' 6AT . . . F 3 37.16 2.271 22.615 1 73.43 ? O3' 6AT 404 A 1 HETATM 19 C C2' 6AT . . . F 3 35.109 3.556 23.21 1 70.76 ? C2' 6AT 404 A 1 HETATM 20 O O2' 6AT . . . F 3 34.573 2.364 22.937 1 74.79 ? O2' 6AT 404 A 1 HETATM 21 C C1' 6AT . . . F 3 35.243 3.735 24.773 1 83.36 ? C1' 6AT 404 A 1 HETATM 22 N N9 6AT . . . F 3 34.087 4.471 25.327 1 81.22 ? N9 6AT 404 A 1 HETATM 23 C C8 6AT . . . F 3 33.569 5.621 24.877 1 75.41 ? C8 6AT 404 A 1 HETATM 24 N N7 6AT . . . F 3 32.534 5.943 25.669 1 76.31 ? N7 6AT 404 A 1 HETATM 25 C C5 6AT . . . F 3 32.419 5.004 26.596 1 69.06 ? C5 6AT 404 A 1 HETATM 26 C C4 6AT . . . F 3 33.386 4.09 26.383 1 69.03 ? C4 6AT 404 A 1 HETATM 27 N N3 6AT . . . F 3 33.516 2.894 27.279 1 59.99 ? N3 6AT 404 A 1 HETATM 28 C C2 6AT . . . F 3 32.585 2.721 28.394 1 68.4 ? C2 6AT 404 A 1 HETATM 29 S S2 6AT . . . F 3 32.764 1.282 29.455 1 77.93 ? S2 6AT 404 A 1 HETATM 30 C CAA 6AT . . . F 3 34.057 0.222 28.753 1 92.54 ? CAA 6AT 404 A 1 HETATM 31 N N1 6AT . . . F 3 31.544 3.693 28.63 1 69.19 ? N1 6AT 404 A 1 HETATM 32 C C6 6AT . . . F 3 31.431 4.825 27.776 1 66.74 ? C6 6AT 404 A 1 HETATM 33 N N6 6AT . . . F 3 30.375 5.823 28.006 1 66.57 ? N6 6AT 404 A 1 HETATM 34 H H5 6AT . . . F 3 37.961 5.814 22.335 1 93.33 ? H5 6AT 404 A 1 HETATM 35 H H6 6AT . . . F 3 37.71 6.353 23.803 1 93.33 ? H6 6AT 404 A 1 HETATM 36 H H7 6AT . . . F 3 38.083 4.003 23.756 1 87.09 ? H7 6AT 404 A 1 HETATM 37 H H8 6AT . . . F 3 36.57 4.066 21.824 1 93.57 ? H8 6AT 404 A 1 HETATM 38 H H9 6AT . . . F 3 36.698 1.784 22.093 1 88.11 ? H9 6AT 404 A 1 HETATM 39 H H10 6AT . . . F 3 34.573 4.271 22.832 1 84.91 ? H10 6AT 404 A 1 HETATM 40 H H11 6AT . . . F 3 34.827 2.11 22.166 1 89.75 ? H11 6AT 404 A 1 HETATM 41 H H12 6AT . . . F 3 35.318 2.865 25.196 1 100.03 ? H12 6AT 404 A 1 HETATM 42 H H13 6AT . . . F 3 33.869 6.108 24.144 1 90.5 ? H13 6AT 404 A 1 HETATM 43 H H14 6AT . . . F 3 33.882 0.082 27.809 1 111.05 ? H14 6AT 404 A 1 HETATM 44 H H15 6AT . . . F 3 34.061 -0.633 29.212 1 111.05 ? H15 6AT 404 A 1 HETATM 45 H H16 6AT . . . F 3 34.921 0.651 28.862 1 111.05 ? H16 6AT 404 A 1 HETATM 46 H H17 6AT . . . F 3 30.583 6.643 28.161 1 79.88 ? H17 6AT 404 A 1 HETATM 47 H H18 6AT . . . F 3 29.548 5.586 27.984 1 79.88 ? H18 6AT 404 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 47 #