data_3JB3 # _model_server_result.job_id -YRiw7EEYB-HYrd4RvQSoA _model_server_result.datetime_utc '2024-11-15 06:04:21' _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 3jb3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1101}' # _entry.id 3JB3 # _exptl.entry_id 3JB3 _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 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 3JB3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JB3 _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,G,H,I,J 1 (1-60) A,B,C,D,E,F,G,H,I,J 2 1 A,B,C,D,E,F,G,H,I,J 3 (1-5) A,B,C,D,E,F,G,H,I,J 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J 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 -0.00002 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 -0.00002 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 -0.951057 -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 -0.425326 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 0.425326 -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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 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 metalc ? metalc1 I O2B GTP . A GTP 1104 1_555 J MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc2 I O3G GTP . A GTP 1104 1_555 J MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? # _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 374 n n N HN1 SAM sing 375 n n N HN2 SAM sing 376 n n CA C SAM sing 377 n n CA CB SAM sing 378 n n CA HA SAM sing 379 n n C O SAM doub 380 n n C OXT SAM sing 381 n n CB CG SAM sing 382 n n CB HB1 SAM sing 383 n n CB HB2 SAM sing 384 n n CG SD SAM sing 385 n n CG HG1 SAM sing 386 n n CG HG2 SAM sing 387 n n SD CE SAM sing 388 n n SD C5' SAM sing 389 n n CE HE1 SAM sing 390 n n CE HE2 SAM sing 391 n n CE HE3 SAM sing 392 n n C5' C4' SAM sing 393 n n C5' "H5'1" SAM sing 394 n n C5' "H5'2" SAM sing 395 n n C4' O4' SAM sing 396 n n C4' C3' SAM sing 397 n n C4' H4' SAM sing 398 n n O4' C1' SAM sing 399 n n C3' O3' SAM sing 400 n n C3' C2' SAM sing 401 n n C3' H3' SAM sing 402 n n O3' HO3' SAM sing 403 n n C2' O2' SAM sing 404 n n C2' C1' SAM sing 405 n n C2' H2' SAM sing 406 n n O2' HO2' SAM sing 407 n n C1' N9 SAM sing 408 n n C1' H1' SAM sing 409 n n N9 C8 SAM sing 410 n y N9 C4 SAM sing 411 n y C8 N7 SAM doub 412 n y C8 H8 SAM sing 413 n n N7 C5 SAM sing 414 n y C5 C6 SAM sing 415 n y C5 C4 SAM doub 416 n y C6 N6 SAM sing 417 n n C6 N1 SAM doub 418 n y N6 HN61 SAM sing 419 n n N6 HN62 SAM sing 420 n n N1 C2 SAM sing 421 n y C2 N3 SAM doub 422 n y C2 H2 SAM sing 423 n n N3 C4 SAM sing 424 n y # _atom_sites.entry_id 3JB3 _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 # 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 F 4 SAM A 1 1101 0 SAM SAM . G 4 SAM A 1 1102 0 SAM SAM . H 5 ATP A 1 1103 701 ATP ATP . I 6 GTP A 1 1104 4034 GTP GTP . J 7 MG A 1 1105 1 MG MG . # 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 18.7 -42.101 312.244 1 310.16 ? N SAM 1101 A 1 HETATM 2 C CA SAM . . . F 4 19.836 -41.987 311.335 1 317.38 ? CA SAM 1101 A 1 HETATM 3 C C SAM . . . F 4 19.425 -41.447 309.965 1 294.81 ? C SAM 1101 A 1 HETATM 4 O O SAM . . . F 4 18.945 -42.184 309.103 1 271.89 ? O SAM 1101 A 1 HETATM 5 O OXT SAM . . . F 4 19.572 -40.255 309.686 1 290.52 ? OXT SAM 1101 A 1 HETATM 6 C CB SAM . . . F 4 20.541 -43.334 311.197 1 333.06 ? CB SAM 1101 A 1 HETATM 7 C CG SAM . . . F 4 19.603 -44.535 311.238 1 329.37 ? CG SAM 1101 A 1 HETATM 8 S SD SAM . . . F 4 20.353 -46.051 310.591 1 477.02 ? SD SAM 1101 A 1 HETATM 9 C CE SAM . . . F 4 19.148 -47.275 311.164 1 265.13 ? CE SAM 1101 A 1 HETATM 10 C C5' SAM . . . F 4 21.722 -46.331 311.745 1 272.65 ? C5' SAM 1101 A 1 HETATM 11 C C4' SAM . . . F 4 23.09 -46.096 311.113 1 255.84 ? C4' SAM 1101 A 1 HETATM 12 O O4' SAM . . . F 4 24.118 -46.284 312.067 1 231.77 ? O4' SAM 1101 A 1 HETATM 13 C C3' SAM . . . F 4 23.374 -47.068 309.974 1 260.84 ? C3' SAM 1101 A 1 HETATM 14 O O3' SAM . . . F 4 23.324 -46.395 308.737 1 267.25 ? O3' SAM 1101 A 1 HETATM 15 C C2' SAM . . . F 4 24.768 -47.606 310.249 1 250.57 ? C2' SAM 1101 A 1 HETATM 16 O O2' SAM . . . F 4 25.626 -47.473 309.137 1 241.45 ? O2' SAM 1101 A 1 HETATM 17 C C1' SAM . . . F 4 25.274 -46.772 311.415 1 239.72 ? C1' SAM 1101 A 1 HETATM 18 N N9 SAM . . . F 4 26.124 -47.592 312.3 1 223.78 ? N9 SAM 1101 A 1 HETATM 19 C C8 SAM . . . F 4 26.018 -48.943 312.498 1 235.32 ? C8 SAM 1101 A 1 HETATM 20 N N7 SAM . . . F 4 26.977 -49.324 313.369 1 232.77 ? N7 SAM 1101 A 1 HETATM 21 C C5 SAM . . . F 4 27.697 -48.239 313.727 1 199.51 ? C5 SAM 1101 A 1 HETATM 22 C C6 SAM . . . F 4 28.777 -48.076 314.587 1 231.52 ? C6 SAM 1101 A 1 HETATM 23 N N6 SAM . . . F 4 29.282 -49.125 315.232 1 226.31 ? N6 SAM 1101 A 1 HETATM 24 N N1 SAM . . . F 4 29.32 -46.82 314.763 1 237.45 ? N1 SAM 1101 A 1 HETATM 25 C C2 SAM . . . F 4 28.79 -45.736 314.092 1 230.78 ? C2 SAM 1101 A 1 HETATM 26 N N3 SAM . . . F 4 27.716 -45.908 313.241 1 215.38 ? N3 SAM 1101 A 1 HETATM 27 C C4 SAM . . . F 4 27.175 -47.141 313.062 1 177.69 ? C4 SAM 1101 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #