data_3JB1 # _model_server_result.job_id 9zElv6UEY2HAX8ccT2fEwg _model_server_result.datetime_utc '2024-12-18 14:27:53' _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 3jb1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1101}' # _entry.id 3JB1 # _exptl.entry_id 3JB1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 398.437 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 3JB1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? 300-MERIC 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 (1-60) A,B,C,D,E,F 2 1 A,B,C,D,E,F 3 (1-5) A,B,C,D,E,F 4 (1,2,6,10,23,24) A,B,C,D,E,F 5 P # 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] P 'transform to point frame' ? ? 0.587785 -0.809017 0 0.688191 0.5 0.525731 -0.425326 -0.309017 0.850651 -0.00003 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0 0 0 1 -0.00001 -0.00003 0 3 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 0.00002 -0.00005 0 4 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 0.00005 -0.00003 0 5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 0.00004 0 0 6 'point symmetry operation' ? ? -0.638196 0.262866 -0.723607 0.262866 -0.809017 -0.525731 -0.723607 -0.525731 0.447213 0.00004 -0.00005 0 7 'point symmetry operation' ? ? 0.052787 0.688191 -0.723607 -0.688191 -0.5 -0.525731 -0.723607 0.525731 0.447213 0.00003 -0.00002 0.00003 8 'point symmetry operation' ? ? 0.67082 0.16246 -0.723607 -0.688191 0.5 -0.525731 0.276393 0.850651 0.447214 0 0 0.00002 9 'point symmetry operation' ? ? 0.361803 -0.587785 -0.723607 0.262866 0.809017 -0.525731 0.894427 0 0.447214 0 0 -0.00002 10 'point symmetry operation' ? ? -0.447214 -0.525731 -0.723607 0.850651 0 -0.525731 0.276393 -0.850651 0.447214 0.00001 -0.00004 -0.00003 11 'point symmetry operation' ? ? -0.052787 0.688191 0.723607 0.688191 -0.5 0.525731 0.723607 0.525731 -0.447213 0.00004 -0.00005 0 12 'point symmetry operation' ? ? 0.638196 0.262866 0.723607 -0.262866 -0.809017 0.525731 0.723607 -0.525731 -0.447213 0.00001 -0.00004 -0.00003 13 'point symmetry operation' ? ? 0.447214 -0.525731 0.723607 -0.850651 0 0.525731 -0.276393 -0.850651 -0.447214 0 0 -0.00002 14 'point symmetry operation' ? ? -0.361803 -0.587785 0.723607 -0.262866 0.809017 0.525731 -0.894427 0 -0.447214 0 0 0.00002 15 'point symmetry operation' ? ? -0.67082 0.16246 0.723607 0.688191 0.5 0.525731 -0.276393 0.850651 -0.447214 0.00003 -0.00002 0.00003 16 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 0 0 0 17 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0.00004 0 0 18 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 0.00005 -0.00003 0 19 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 0.00002 -0.00005 0 20 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 -0.00001 -0.00003 0 21 'point symmetry operation' ? ? -0.138197 -0.951057 0.276393 0.425326 -0.309017 -0.850651 0.894427 0 0.447214 0 -0.00004 -0.00002 22 'point symmetry operation' ? ? -0.947214 -0.16246 0.276393 -0.16246 -0.5 -0.850651 0.276393 -0.850651 0.447214 0.00003 -0.00003 -0.00003 23 'point symmetry operation' ? ? -0.447214 0.850651 0.276393 -0.525731 0 -0.850651 -0.723607 -0.525731 0.447214 0.00005 -0.00001 0 24 'point symmetry operation' ? ? 0.67082 0.688191 0.276393 -0.16246 0.5 -0.850651 -0.723607 0.525731 0.447214 0.00002 0 0.00003 25 'point symmetry operation' ? ? 0.861803 -0.425326 0.276393 0.425326 0.309017 -0.850651 0.276393 0.850651 0.447214 0 -0.00002 0.00002 26 'point symmetry operation' ? ? -0.361803 0.587785 0.723607 0.262866 0.809017 -0.525731 -0.894427 0 -0.447214 0.00004 0 0.00002 27 'point symmetry operation' ? ? 0.447214 0.525731 0.723607 0.850651 0 -0.525731 -0.276393 0.850651 -0.447214 0.00002 -0.00004 0.00003 28 'point symmetry operation' ? ? 0.638196 -0.262866 0.723607 0.262866 -0.809017 -0.525731 0.723607 0.525731 -0.447213 0 -0.00005 0 29 'point symmetry operation' ? ? -0.052787 -0.688191 0.723607 -0.688191 -0.5 -0.525731 0.723607 -0.525731 -0.447213 0 -0.00002 -0.00003 30 'point symmetry operation' ? ? -0.67082 -0.16246 0.723607 -0.688191 0.5 -0.525731 -0.276393 -0.850651 -0.447214 0.00003 0 -0.00002 31 'point symmetry operation' ? ? -0.447214 0.525731 -0.723607 -0.850651 0 0.525731 0.276393 0.850651 0.447214 0.00004 0 0.00002 32 'point symmetry operation' ? ? 0.361803 0.587785 -0.723607 -0.262866 0.809017 0.525731 0.894427 0 0.447214 0.00003 0 -0.00002 33 'point symmetry operation' ? ? 0.67082 -0.16246 -0.723607 0.688191 0.5 0.525731 0.276393 -0.850651 0.447214 0 -0.00002 -0.00003 34 'point symmetry operation' ? ? 0.052787 -0.688191 -0.723607 0.688191 -0.5 0.525731 -0.723607 -0.525731 0.447213 0 -0.00005 0 35 'point symmetry operation' ? ? -0.638196 -0.262866 -0.723607 -0.262866 -0.809017 0.525731 -0.723607 0.525731 0.447213 0.00002 -0.00004 0.00003 36 'point symmetry operation' ? ? 0.947214 -0.16246 -0.276393 0.16246 -0.5 0.850651 -0.276393 -0.850651 -0.447214 0 -0.00004 -0.00002 37 'point symmetry operation' ? ? 0.138197 -0.951057 -0.276393 -0.425326 -0.309017 0.850651 -0.894427 0 -0.447214 0 -0.00002 0.00002 38 'point symmetry operation' ? ? -0.861803 -0.425326 -0.276393 -0.425326 0.309017 0.850651 -0.276393 0.850651 -0.447214 0.00002 0 0.00003 39 'point symmetry operation' ? ? -0.67082 0.688191 -0.276393 0.16246 0.5 0.850651 0.723607 0.525731 -0.447214 0.00005 -0.00001 0 40 'point symmetry operation' ? ? 0.447214 0.850651 -0.276393 0.525731 0 0.850651 0.723607 -0.525731 -0.447214 0.00003 -0.00003 -0.00003 41 'point symmetry operation' ? ? -0.138197 0.425326 0.894427 -0.951056 -0.309017 0 0.276393 -0.850651 0.447214 0.00003 -0.00002 -0.00003 42 'point symmetry operation' ? ? 0.361803 0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 0.447214 0.00002 0 0 43 'point symmetry operation' ? ? 0.361803 -0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 0.447214 0 -0.00001 0.00003 44 'point symmetry operation' ? ? -0.138197 -0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 0.447214 0 -0.00005 0.00002 45 'point symmetry operation' ? ? -0.447214 0 0.894427 0 -1 0 0.894427 0 0.447214 0.00003 -0.00005 -0.00002 46 'point symmetry operation' ? ? -0.447214 -0.850651 0.276393 0.525731 0 0.850651 -0.723607 0.525731 0.447214 0 -0.00003 0.00003 47 'point symmetry operation' ? ? -0.947214 0.16246 0.276393 0.16246 -0.5 0.850651 0.276393 0.850651 0.447214 0.00004 -0.00004 0.00002 48 'point symmetry operation' ? ? -0.138197 0.951057 0.276393 -0.425325 -0.309017 0.850651 0.894427 0 0.447214 0.00004 -0.00002 -0.00002 49 'point symmetry operation' ? ? 0.861803 0.425326 0.276393 -0.425325 0.309017 0.850651 0.276393 -0.850651 0.447214 0.00001 0 -0.00003 50 'point symmetry operation' ? ? 0.67082 -0.688191 0.276393 0.16246 0.5 0.850651 -0.723607 -0.525731 0.447214 -0.00001 -0.00001 0 51 'point symmetry operation' ? ? 0.947214 0.16246 -0.276393 -0.16246 -0.5 -0.850651 -0.276393 0.850651 -0.447214 0 -0.00003 0.00003 52 'point symmetry operation' ? ? 0.447214 -0.850651 -0.276393 -0.525731 0 -0.850651 0.723607 0.525731 -0.447214 -0.00001 -0.00001 0 53 'point symmetry operation' ? ? -0.67082 -0.688191 -0.276393 -0.16246 0.5 -0.850651 0.723607 -0.525731 -0.447214 0.00001 0 -0.00003 54 'point symmetry operation' ? ? -0.861803 0.425326 -0.276393 0.425326 0.309017 -0.850651 -0.276393 -0.850651 -0.447214 0.00004 -0.00002 -0.00002 55 'point symmetry operation' ? ? 0.138197 0.951057 -0.276393 0.425325 -0.309017 -0.850651 -0.894427 0 -0.447214 0.00004 -0.00004 0.00002 56 'point symmetry operation' ? ? -0.361803 0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 -0.447214 0.00003 -0.00002 -0.00003 57 'point symmetry operation' ? ? 0.138197 0.425326 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 -0.447214 0.00003 -0.00005 -0.00002 58 'point symmetry operation' ? ? 0.447214 0 -0.894427 0 -1 0 -0.894427 0 -0.447214 0 -0.00005 0.00002 59 'point symmetry operation' ? ? 0.138197 -0.425326 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 -0.447214 0 -0.00001 0.00003 60 'point symmetry operation' ? ? -0.361803 -0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 -0.447214 0.00002 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 SAM sing 275 n n N HN1 SAM sing 276 n n N HN2 SAM sing 277 n n CA C SAM sing 278 n n CA CB SAM sing 279 n n CA HA SAM sing 280 n n C O SAM doub 281 n n C OXT SAM sing 282 n n CB CG SAM sing 283 n n CB HB1 SAM sing 284 n n CB HB2 SAM sing 285 n n CG SD SAM sing 286 n n CG HG1 SAM sing 287 n n CG HG2 SAM sing 288 n n SD CE SAM sing 289 n n SD C5' SAM sing 290 n n CE HE1 SAM sing 291 n n CE HE2 SAM sing 292 n n CE HE3 SAM sing 293 n n C5' C4' SAM sing 294 n n C5' "H5'1" SAM sing 295 n n C5' "H5'2" SAM sing 296 n n C4' O4' SAM sing 297 n n C4' C3' SAM sing 298 n n C4' H4' SAM sing 299 n n O4' C1' SAM sing 300 n n C3' O3' SAM sing 301 n n C3' C2' SAM sing 302 n n C3' H3' SAM sing 303 n n O3' HO3' SAM sing 304 n n C2' O2' SAM sing 305 n n C2' C1' SAM sing 306 n n C2' H2' SAM sing 307 n n O2' HO2' SAM sing 308 n n C1' N9 SAM sing 309 n n C1' H1' SAM sing 310 n n N9 C8 SAM sing 311 n y N9 C4 SAM sing 312 n y C8 N7 SAM doub 313 n y C8 H8 SAM sing 314 n n N7 C5 SAM sing 315 n y C5 C6 SAM sing 316 n y C5 C4 SAM doub 317 n y C6 N6 SAM sing 318 n n C6 N1 SAM doub 319 n y N6 HN61 SAM sing 320 n n N6 HN62 SAM sing 321 n n N1 C2 SAM sing 322 n y C2 N3 SAM doub 323 n y C2 H2 SAM sing 324 n n N3 C4 SAM sing 325 n y # _atom_sites.entry_id 3JB1 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id SAM _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1101 _pdbx_nonpoly_scheme.auth_seq_num 0 _pdbx_nonpoly_scheme.pdb_mon_id SAM _pdbx_nonpoly_scheme.auth_mon_id SAM _pdbx_nonpoly_scheme.pdb_ins_code . # 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 SAM . . . F 4 -19.86 -47.236 325.169 1 290.91 ? N SAM 1101 A 1 HETATM 2 C CA SAM . . . F 4 -21.134 -46.786 324.616 1 309.39 ? CA SAM 1101 A 1 HETATM 3 C C SAM . . . F 4 -21.269 -47.178 323.15 1 316.85 ? C SAM 1101 A 1 HETATM 4 O O SAM . . . F 4 -20.632 -48.127 322.692 1 327.13 ? O SAM 1101 A 1 HETATM 5 O OXT SAM . . . F 4 -22.017 -46.556 322.394 1 302.41 ? OXT SAM 1101 A 1 HETATM 6 C CB SAM . . . F 4 -21.286 -45.278 324.768 1 305.31 ? CB SAM 1101 A 1 HETATM 7 C CG SAM . . . F 4 -22.584 -44.854 325.444 1 297.91 ? CG SAM 1101 A 1 HETATM 8 S SD SAM . . . F 4 -22.303 -43.951 326.987 1 372.45 ? SD SAM 1101 A 1 HETATM 9 C CE SAM . . . F 4 -20.615 -44.457 327.398 1 442.55 ? CE SAM 1101 A 1 HETATM 10 C C5' SAM . . . F 4 -23.237 -44.964 328.156 1 318.96 ? C5' SAM 1101 A 1 HETATM 11 C C4' SAM . . . F 4 -24.725 -44.675 328.062 1 331.08 ? C4' SAM 1101 A 1 HETATM 12 O O4' SAM . . . F 4 -25.408 -45.396 329.065 1 335.79 ? O4' SAM 1101 A 1 HETATM 13 C C3' SAM . . . F 4 -25.035 -43.202 328.261 1 341.53 ? C3' SAM 1101 A 1 HETATM 14 O O3' SAM . . . F 4 -25.418 -42.623 327.037 1 342.54 ? O3' SAM 1101 A 1 HETATM 15 C C2' SAM . . . F 4 -26.188 -43.166 329.24 1 346.87 ? C2' SAM 1101 A 1 HETATM 16 O O2' SAM . . . F 4 -27.366 -42.78 328.568 1 349.6 ? O2' SAM 1101 A 1 HETATM 17 C C1' SAM . . . F 4 -26.333 -44.588 329.756 1 329.73 ? C1' SAM 1101 A 1 HETATM 18 N N9 SAM . . . F 4 -25.968 -44.63 331.18 1 293.87 ? N9 SAM 1101 A 1 HETATM 19 C C8 SAM . . . F 4 -25.092 -43.788 331.81 1 277.98 ? C8 SAM 1101 A 1 HETATM 20 N N7 SAM . . . F 4 -25.016 -44.143 333.111 1 269.51 ? N7 SAM 1101 A 1 HETATM 21 C C5 SAM . . . F 4 -25.827 -45.201 333.316 1 265.15 ? C5 SAM 1101 A 1 HETATM 22 C C6 SAM . . . F 4 -26.113 -45.941 334.451 1 281.04 ? C6 SAM 1101 A 1 HETATM 23 N N6 SAM . . . F 4 -25.532 -45.633 335.609 1 268.79 ? N6 SAM 1101 A 1 HETATM 24 N N1 SAM . . . F 4 -27.004 -46.992 334.361 1 303.04 ? N1 SAM 1101 A 1 HETATM 25 C C2 SAM . . . F 4 -27.596 -47.295 333.148 1 291.18 ? C2 SAM 1101 A 1 HETATM 26 N N3 SAM . . . F 4 -27.306 -46.553 332.023 1 275.18 ? N3 SAM 1101 A 1 HETATM 27 C C4 SAM . . . F 4 -26.434 -45.521 332.109 1 272.91 ? C4 SAM 1101 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 434 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 27 #