data_5SVP # _model_server_result.job_id XqCR9RsGXBroIOj5UCQhSw _model_server_result.datetime_utc '2024-11-27 01:21:09' _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 5svp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 5SVP # _exptl.entry_id 5SVP _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 5SVP _cell.length_a 172.93 _cell.length_b 172.93 _cell.length_c 172.93 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVP _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 1 1,3,5 B,J,K,L,M,N,O 2 1,2,4 # 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_564 z,x+1,y-1 0 0 1 1 0 0 0 1 0 0 172.93 -172.93 3 'crystal symmetry operation' 7_564 -z+1/2,-x+1,y-1/2 0 0 -1 -1 0 0 0 1 0 86.465 172.93 -86.465 4 'crystal symmetry operation' 9_465 y-1,z+1,x 0 1 0 0 0 1 1 0 0 -172.93 172.93 0 5 'crystal symmetry operation' 10_655 -y+1,z+1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 172.93 86.465 86.465 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.509 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? # _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 5SVP _atom_sites.fract_transf_matrix[1][1] 0.005783 _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] 0.005783 _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] 0.005783 _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 . # 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 40.019 162.708 61.659 1 95.06 ? OAI 6AT 404 A 1 HETATM 2 P PBE 6AT . . . F 3 39.787 162.695 63.153 1 96.42 ? PBE 6AT 404 A 1 HETATM 3 O OAH 6AT . . . F 3 39.263 161.355 63.56 1 72.11 ? OAH 6AT 404 A 1 HETATM 4 O OAC 6AT . . . F 3 41.086 162.971 63.867 1 84.08 ? OAC 6AT 404 A 1 HETATM 5 O OAS 6AT . . . F 3 38.667 163.848 63.539 1 57.4 ? OAS 6AT 404 A 1 HETATM 6 P PBG 6AT . . . F 3 38.24 165.028 62.494 1 63.55 ? PBG 6AT 404 A 1 HETATM 7 O OAK 6AT . . . F 3 37.319 164.468 61.439 1 78.74 ? OAK 6AT 404 A 1 HETATM 8 O OAE 6AT . . . F 3 39.495 165.617 61.845 1 84.6 ? OAE 6AT 404 A 1 HETATM 9 O OAT 6AT . . . F 3 37.413 166.233 63.361 1 67.47 ? OAT 6AT 404 A 1 HETATM 10 P PBF 6AT . . . F 3 36.219 165.83 64.503 1 61.71 ? PBF 6AT 404 A 1 HETATM 11 O OAJ 6AT . . . F 3 35.775 164.428 64.258 1 68.49 ? OAJ 6AT 404 A 1 HETATM 12 O OAD 6AT . . . F 3 35.052 166.78 64.373 1 67.19 ? OAD 6AT 404 A 1 HETATM 13 O O5' 6AT . . . F 3 36.863 165.945 65.997 1 80.24 ? O5' 6AT 404 A 1 HETATM 14 C C5' 6AT . . . F 3 37.396 167.187 66.381 1 79.46 ? C5' 6AT 404 A 1 HETATM 15 C C4' 6AT . . . F 3 38.824 167.039 66.827 1 77.15 ? C4' 6AT 404 A 1 HETATM 16 O O4' 6AT . . . F 3 38.865 166.172 68.219 1 77.18 ? O4' 6AT 404 A 1 HETATM 17 C C3' 6AT . . . F 3 39.561 166.388 65.923 1 75.39 ? C3' 6AT 404 A 1 HETATM 18 O O3' 6AT . . . F 3 40.916 167.015 65.822 1 87.32 ? O3' 6AT 404 A 1 HETATM 19 C C2' 6AT . . . F 3 39.682 164.942 66.431 1 70.7 ? C2' 6AT 404 A 1 HETATM 20 O O2' 6AT . . . F 3 40.879 164.423 66.135 1 87.95 ? O2' 6AT 404 A 1 HETATM 21 C C1' 6AT . . . F 3 39.516 165.066 67.998 1 78.12 ? C1' 6AT 404 A 1 HETATM 22 N N9 6AT . . . F 3 38.753 163.925 68.545 1 80.48 ? N9 6AT 404 A 1 HETATM 23 C C8 6AT . . . F 3 37.582 163.44 68.109 1 76.24 ? C8 6AT 404 A 1 HETATM 24 N N7 6AT . . . F 3 37.252 162.406 68.901 1 78.8 ? N7 6AT 404 A 1 HETATM 25 C C5 6AT . . . F 3 38.203 162.259 69.812 1 66.23 ? C5 6AT 404 A 1 HETATM 26 C C4 6AT . . . F 3 39.133 163.207 69.588 1 71.42 ? C4 6AT 404 A 1 HETATM 27 N N3 6AT . . . F 3 40.347 163.304 70.462 1 68.17 ? N3 6AT 404 A 1 HETATM 28 C C2 6AT . . . F 3 40.527 162.366 71.568 1 72.09 ? C2 6AT 404 A 1 HETATM 29 S S2 6AT . . . F 3 42.004 162.534 72.578 1 85.15 ? S2 6AT 404 A 1 HETATM 30 C CAA 6AT . . . F 3 43.009 163.842 71.825 1 88.77 ? CAA 6AT 404 A 1 HETATM 31 N N1 6AT . . . F 3 39.539 161.342 71.82 1 73.13 ? N1 6AT 404 A 1 HETATM 32 C C6 6AT . . . F 3 38.386 161.26 70.986 1 64.13 ? C6 6AT 404 A 1 HETATM 33 N N6 6AT . . . F 3 37.371 160.224 71.226 1 69.22 ? N6 6AT 404 A 1 HETATM 34 H H5 6AT . . . F 3 37.36 167.795 65.626 1 95.36 ? H5 6AT 404 A 1 HETATM 35 H H6 6AT . . . F 3 36.869 167.551 67.11 1 95.36 ? H6 6AT 404 A 1 HETATM 36 H H7 6AT . . . F 3 39.212 167.914 66.985 1 92.58 ? H7 6AT 404 A 1 HETATM 37 H H8 6AT . . . F 3 39.116 166.4 65.06 1 90.46 ? H8 6AT 404 A 1 HETATM 38 H H9 6AT . . . F 3 41.406 166.553 65.304 1 104.78 ? H9 6AT 404 A 1 HETATM 39 H H10 6AT . . . F 3 38.971 164.396 66.06 1 84.84 ? H10 6AT 404 A 1 HETATM 40 H H11 6AT . . . F 3 41.077 164.608 65.329 1 105.54 ? H11 6AT 404 A 1 HETATM 41 H H12 6AT . . . F 3 40.39 165.112 68.416 1 93.74 ? H12 6AT 404 A 1 HETATM 42 H H13 6AT . . . F 3 37.09 163.759 67.388 1 91.49 ? H13 6AT 404 A 1 HETATM 43 H H14 6AT . . . F 3 43.103 163.669 70.875 1 106.52 ? H14 6AT 404 A 1 HETATM 44 H H15 6AT . . . F 3 43.886 163.857 72.239 1 106.52 ? H15 6AT 404 A 1 HETATM 45 H H16 6AT . . . F 3 42.576 164.7 71.956 1 106.52 ? H16 6AT 404 A 1 HETATM 46 H H17 6AT . . . F 3 36.556 160.448 71.385 1 83.07 ? H17 6AT 404 A 1 HETATM 47 H H18 6AT . . . F 3 37.593 159.393 71.208 1 83.07 ? H18 6AT 404 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 47 #