data_2OPB # _model_server_result.job_id QigYjJ6Uc6GlouChi4ky-A _model_server_result.datetime_utc '2024-11-24 08:02:01' _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 2opb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3001}' # _entry.id 2OPB # _exptl.entry_id 2OPB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 2OPB _cell.length_a 94.42 _cell.length_b 94.42 _cell.length_c 187.67 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OPB _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 1 A,B,C,D,E,F,G,H,I 3 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 ? 3 D N N ? 3 G 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 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 323 n n N HN1 SAH sing 324 n n N HN2 SAH sing 325 n n CA CB SAH sing 326 n n CA C SAH sing 327 n n CA HA SAH sing 328 n n CB CG SAH sing 329 n n CB HB1 SAH sing 330 n n CB HB2 SAH sing 331 n n CG SD SAH sing 332 n n CG HG1 SAH sing 333 n n CG HG2 SAH sing 334 n n SD C5' SAH sing 335 n n C O SAH doub 336 n n C OXT SAH sing 337 n n OXT HXT SAH sing 338 n n C5' C4' SAH sing 339 n n C5' "H5'1" SAH sing 340 n n C5' "H5'2" SAH sing 341 n n C4' O4' SAH sing 342 n n C4' C3' SAH sing 343 n n C4' H4' SAH sing 344 n n O4' C1' SAH sing 345 n n C3' O3' SAH sing 346 n n C3' C2' SAH sing 347 n n C3' H3' SAH sing 348 n n O3' HO3' SAH sing 349 n n C2' O2' SAH sing 350 n n C2' C1' SAH sing 351 n n C2' H2' SAH sing 352 n n O2' HO2' SAH sing 353 n n C1' N9 SAH sing 354 n n C1' H1' SAH sing 355 n n N9 C8 SAH sing 356 n y N9 C4 SAH sing 357 n y C8 N7 SAH doub 358 n y C8 H8 SAH sing 359 n n N7 C5 SAH sing 360 n y C5 C6 SAH sing 361 n y C5 C4 SAH doub 362 n y C6 N6 SAH sing 363 n n C6 N1 SAH doub 364 n y N6 HN61 SAH sing 365 n n N6 HN62 SAH sing 366 n n N1 C2 SAH sing 367 n y C2 N3 SAH doub 368 n y C2 H2 SAH sing 369 n n N3 C4 SAH sing 370 n y # _atom_sites.entry_id 2OPB _atom_sites.fract_transf_matrix[1][1] 0.010591 _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] 0.010591 _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] 0.005329 _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 F21 A 1 4001 4001 F21 F21 . D 3 SAH A 1 3001 3001 SAH SAH . E 4 PO4 B 1 290 1 PO4 PO4 . F 2 F21 B 1 4002 4002 F21 F21 . G 3 SAH B 1 3002 3002 SAH SAH . H 5 HOH A 1 4002 1001 HOH WAT . H 5 HOH A 2 4003 1002 HOH WAT . H 5 HOH A 3 4004 1003 HOH WAT . H 5 HOH A 4 4005 1004 HOH WAT . H 5 HOH A 5 4006 1006 HOH WAT . H 5 HOH A 6 4007 1008 HOH HOH . H 5 HOH A 7 4008 1009 HOH WAT . H 5 HOH A 8 4009 1016 HOH WAT . H 5 HOH A 9 4010 1017 HOH WAT . H 5 HOH A 10 4011 1018 HOH WAT . H 5 HOH A 11 4012 1025 HOH WAT . H 5 HOH A 12 4013 1027 HOH WAT . H 5 HOH A 13 4014 1029 HOH WAT . H 5 HOH A 14 4015 1030 HOH WAT . H 5 HOH A 15 4016 1031 HOH WAT . H 5 HOH A 16 4017 1033 HOH WAT . H 5 HOH A 17 4018 1036 HOH WAT . H 5 HOH A 18 4019 1037 HOH WAT . H 5 HOH A 19 4020 1038 HOH WAT . H 5 HOH A 20 4021 1039 HOH WAT . H 5 HOH A 21 4022 1040 HOH WAT . H 5 HOH A 22 4023 1041 HOH WAT . H 5 HOH A 23 4024 1042 HOH WAT . H 5 HOH A 24 4025 1044 HOH WAT . H 5 HOH A 25 4026 1045 HOH WAT . H 5 HOH A 26 4027 1047 HOH WAT . H 5 HOH A 27 4028 1050 HOH WAT . H 5 HOH A 28 4029 1052 HOH WAT . H 5 HOH A 29 4030 1055 HOH WAT . H 5 HOH A 30 4031 1056 HOH WAT . H 5 HOH A 31 4032 1057 HOH WAT . H 5 HOH A 32 4033 1061 HOH WAT . H 5 HOH A 33 4034 1064 HOH WAT . H 5 HOH A 34 4035 1066 HOH WAT . H 5 HOH A 35 4036 1067 HOH WAT . H 5 HOH A 36 4037 1070 HOH HOH . H 5 HOH A 37 4038 1071 HOH HOH . H 5 HOH A 38 4039 1072 HOH HOH . H 5 HOH A 39 4040 1073 HOH HOH . I 5 HOH B 1 4003 1005 HOH WAT . I 5 HOH B 2 4004 1007 HOH WAT . I 5 HOH B 3 4005 1010 HOH WAT . I 5 HOH B 4 4006 1011 HOH WAT . I 5 HOH B 5 4007 1012 HOH WAT . I 5 HOH B 6 4008 1013 HOH WAT . I 5 HOH B 7 4009 1014 HOH WAT . I 5 HOH B 8 4010 1015 HOH WAT . I 5 HOH B 9 4011 1019 HOH WAT . I 5 HOH B 10 4012 1020 HOH WAT . I 5 HOH B 11 4013 1021 HOH WAT . I 5 HOH B 12 4014 1022 HOH WAT . I 5 HOH B 13 4015 1023 HOH WAT . I 5 HOH B 14 4016 1024 HOH WAT . I 5 HOH B 15 4017 1026 HOH WAT . I 5 HOH B 16 4018 1028 HOH WAT . I 5 HOH B 17 4019 1032 HOH WAT . I 5 HOH B 18 4020 1034 HOH WAT . I 5 HOH B 19 4021 1035 HOH WAT . I 5 HOH B 20 4022 1043 HOH WAT . I 5 HOH B 21 4023 1046 HOH WAT . I 5 HOH B 22 4024 1048 HOH WAT . I 5 HOH B 23 4025 1049 HOH WAT . I 5 HOH B 24 4026 1051 HOH WAT . I 5 HOH B 25 4027 1053 HOH WAT . I 5 HOH B 26 4028 1054 HOH WAT . I 5 HOH B 27 4029 1058 HOH WAT . I 5 HOH B 28 4030 1059 HOH WAT . I 5 HOH B 29 4031 1060 HOH WAT . I 5 HOH B 30 4032 1062 HOH WAT . I 5 HOH B 31 4033 1063 HOH WAT . I 5 HOH B 32 4034 1065 HOH WAT . I 5 HOH B 33 4035 1068 HOH HOH . I 5 HOH B 34 4036 1069 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 N SAH . . . D 3 27.453 52.705 18.761 1 57.06 ? N SAH 3001 A 1 HETATM 2 C CA SAH . . . D 3 28.611 52.271 17.984 1 58.71 ? CA SAH 3001 A 1 HETATM 3 C CB SAH . . . D 3 29.794 51.929 18.929 1 60.81 ? CB SAH 3001 A 1 HETATM 4 C CG SAH . . . D 3 29.475 50.956 20.077 1 66.31 ? CG SAH 3001 A 1 HETATM 5 S SD SAH . . . D 3 30.93 50.53 21.074 1 74.9 ? SD SAH 3001 A 1 HETATM 6 C C SAH . . . D 3 28.219 51.082 17.089 1 58.4 ? C SAH 3001 A 1 HETATM 7 O O SAH . . . D 3 29.077 50.213 16.775 1 49.96 ? O SAH 3001 A 1 HETATM 8 O OXT SAH . . . D 3 27.029 51.065 16.692 1 58.62 ? OXT SAH 3001 A 1 HETATM 9 C C5' SAH . . . D 3 30.489 51.224 22.709 1 69.3 ? C5' SAH 3001 A 1 HETATM 10 C C4' SAH . . . D 3 30.709 52.716 22.754 1 70.79 ? C4' SAH 3001 A 1 HETATM 11 O O4' SAH . . . D 3 30.299 53.299 24.022 1 74.22 ? O4' SAH 3001 A 1 HETATM 12 C C3' SAH . . . D 3 32.122 53.22 22.479 1 70.21 ? C3' SAH 3001 A 1 HETATM 13 O O3' SAH . . . D 3 32.08 54.172 21.425 1 69.17 ? O3' SAH 3001 A 1 HETATM 14 C C2' SAH . . . D 3 32.548 53.83 23.814 1 71.85 ? C2' SAH 3001 A 1 HETATM 15 O O2' SAH . . . D 3 33.445 54.912 23.708 1 74.01 ? O2' SAH 3001 A 1 HETATM 16 C C1' SAH . . . D 3 31.214 54.322 24.364 1 73.82 ? C1' SAH 3001 A 1 HETATM 17 N N9 SAH . . . D 3 31.181 54.562 25.812 1 74.77 ? N9 SAH 3001 A 1 HETATM 18 C C8 SAH . . . D 3 32.122 54.173 26.815 1 76.58 ? C8 SAH 3001 A 1 HETATM 19 N N7 SAH . . . D 3 31.799 54.59 28.019 1 75.9 ? N7 SAH 3001 A 1 HETATM 20 C C5 SAH . . . D 3 30.609 55.271 27.812 1 74.39 ? C5 SAH 3001 A 1 HETATM 21 C C6 SAH . . . D 3 29.8 55.949 28.75 1 73.06 ? C6 SAH 3001 A 1 HETATM 22 N N6 SAH . . . D 3 30.086 56.044 30.043 1 74.33 ? N6 SAH 3001 A 1 HETATM 23 N N1 SAH . . . D 3 28.666 56.541 28.29 1 73.64 ? N1 SAH 3001 A 1 HETATM 24 C C2 SAH . . . D 3 28.386 56.452 26.964 1 76.68 ? C2 SAH 3001 A 1 HETATM 25 N N3 SAH . . . D 3 29.094 55.837 25.985 1 75.25 ? N3 SAH 3001 A 1 HETATM 26 C C4 SAH . . . D 3 30.208 55.26 26.485 1 74.49 ? C4 SAH 3001 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #