data_5SVM # _model_server_result.job_id qbZEM9UcEgbJVc6YCN_erA _model_server_result.datetime_utc '2024-11-05 21:24:08' _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":"I","auth_seq_id":407}' # _entry.id 5SVM # _exptl.entry_id 5SVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 I N N ? 6 O 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 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 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 C1 O1 EDO sing 185 n n C1 C2 EDO sing 186 n n C1 H11 EDO sing 187 n n C1 H12 EDO sing 188 n n O1 HO1 EDO sing 189 n n C2 O2 EDO sing 190 n n C2 H21 EDO sing 191 n n C2 H22 EDO sing 192 n n O2 HO2 EDO sing 193 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 C C1 EDO . . . I 6 35.147 10.786 21.331 1 74.72 ? C1 EDO 407 A 1 HETATM 2 O O1 EDO . . . I 6 34.963 9.931 20.189 1 90.45 ? O1 EDO 407 A 1 HETATM 3 C C2 EDO . . . I 6 33.783 11.482 21.641 1 59.16 ? C2 EDO 407 A 1 HETATM 4 O O2 EDO . . . I 6 32.735 10.653 21.239 1 87.21 ? O2 EDO 407 A 1 HETATM 5 H H11 EDO . . . I 6 35.831 11.472 21.127 1 89.67 ? H11 EDO 407 A 1 HETATM 6 H H12 EDO . . . I 6 35.425 10.267 22.084 1 89.67 ? H12 EDO 407 A 1 HETATM 7 H HO1 EDO . . . I 6 34.11 9.597 20.193 1 108.54 ? HO1 EDO 407 A 1 HETATM 8 H H21 EDO . . . I 6 33.73 12.353 21.138 1 70.99 ? H21 EDO 407 A 1 HETATM 9 H H22 EDO . . . I 6 33.715 11.651 22.596 1 70.99 ? H22 EDO 407 A 1 HETATM 10 H HO2 EDO . . . I 6 32.424 10.934 20.468 1 104.65 ? HO2 EDO 407 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #