data_2ZVJ # _model_server_result.job_id jE-NaRCqsOoah217TTzO9w _model_server_result.datetime_utc '2025-01-02 16:01:34' _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 2zvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 2ZVJ # _exptl.entry_id 2ZVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _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 120 _cell.entry_id 2ZVJ _cell.length_a 50.448 _cell.length_b 50.448 _cell.length_c 167.626 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZVJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 143 A ASP 141 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc2 A OD2 ASP 171 A ASP 169 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc3 A OD1 ASN 172 A ASN 170 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc4 B MG MG . A MG 300 1_555 D O9 KOM . A KOM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc5 B MG MG . A MG 300 1_555 D O10 KOM . A KOM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc6 B MG MG . A MG 300 1_555 E O HOH . A HOH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? # _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 308 n n N HN1 SAM sing 309 n n N HN2 SAM sing 310 n n CA C SAM sing 311 n n CA CB SAM sing 312 n n CA HA SAM sing 313 n n C O SAM doub 314 n n C OXT SAM sing 315 n n CB CG SAM sing 316 n n CB HB1 SAM sing 317 n n CB HB2 SAM sing 318 n n CG SD SAM sing 319 n n CG HG1 SAM sing 320 n n CG HG2 SAM sing 321 n n SD CE SAM sing 322 n n SD C5' SAM sing 323 n n CE HE1 SAM sing 324 n n CE HE2 SAM sing 325 n n CE HE3 SAM sing 326 n n C5' C4' SAM sing 327 n n C5' "H5'1" SAM sing 328 n n C5' "H5'2" SAM sing 329 n n C4' O4' SAM sing 330 n n C4' C3' SAM sing 331 n n C4' H4' SAM sing 332 n n O4' C1' SAM sing 333 n n C3' O3' SAM sing 334 n n C3' C2' SAM sing 335 n n C3' H3' SAM sing 336 n n O3' HO3' SAM sing 337 n n C2' O2' SAM sing 338 n n C2' C1' SAM sing 339 n n C2' H2' SAM sing 340 n n O2' HO2' SAM sing 341 n n C1' N9 SAM sing 342 n n C1' H1' SAM sing 343 n n N9 C8 SAM sing 344 n y N9 C4 SAM sing 345 n y C8 N7 SAM doub 346 n y C8 H8 SAM sing 347 n n N7 C5 SAM sing 348 n y C5 C6 SAM sing 349 n y C5 C4 SAM doub 350 n y C6 N6 SAM sing 351 n n C6 N1 SAM doub 352 n y N6 HN61 SAM sing 353 n n N6 HN62 SAM sing 354 n n N1 C2 SAM sing 355 n y C2 N3 SAM doub 356 n y C2 H2 SAM sing 357 n n N3 C4 SAM sing 358 n y # _atom_sites.entry_id 2ZVJ _atom_sites.fract_transf_matrix[1][1] 0.019822 _atom_sites.fract_transf_matrix[1][2] 0.011444 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022889 _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] 0.005966 _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 B 2 MG A 1 300 300 MG MG . C 3 SAM A 1 301 301 SAM SAM . D 4 KOM A 1 302 302 KOM KOM . E 5 HOH A 1 303 303 HOH HOH . E 5 HOH A 2 304 304 HOH HOH . E 5 HOH A 3 305 305 HOH HOH . E 5 HOH A 4 306 306 HOH HOH . E 5 HOH A 5 307 307 HOH HOH . E 5 HOH A 6 308 308 HOH HOH . E 5 HOH A 7 309 309 HOH HOH . E 5 HOH A 8 310 310 HOH HOH . E 5 HOH A 9 311 311 HOH HOH . E 5 HOH A 10 312 312 HOH HOH . E 5 HOH A 11 313 313 HOH HOH . E 5 HOH A 12 314 314 HOH HOH . E 5 HOH A 13 315 315 HOH HOH . E 5 HOH A 14 316 316 HOH HOH . E 5 HOH A 15 317 317 HOH HOH . E 5 HOH A 16 318 318 HOH HOH . E 5 HOH A 17 319 319 HOH HOH . E 5 HOH A 18 320 320 HOH HOH . E 5 HOH A 19 321 321 HOH HOH . E 5 HOH A 20 322 322 HOH HOH . E 5 HOH A 21 323 323 HOH HOH . E 5 HOH A 22 324 324 HOH HOH . E 5 HOH A 23 325 325 HOH HOH . E 5 HOH A 24 326 326 HOH HOH . E 5 HOH A 25 327 327 HOH HOH . E 5 HOH A 26 328 328 HOH HOH . E 5 HOH A 27 329 329 HOH HOH . E 5 HOH A 28 330 330 HOH HOH . E 5 HOH A 29 331 331 HOH HOH . E 5 HOH A 30 332 332 HOH HOH . E 5 HOH A 31 333 333 HOH HOH . E 5 HOH A 32 334 334 HOH HOH . E 5 HOH A 33 335 335 HOH HOH . E 5 HOH A 34 336 336 HOH HOH . E 5 HOH A 35 337 337 HOH HOH . E 5 HOH A 36 338 338 HOH HOH . E 5 HOH A 37 339 339 HOH HOH . E 5 HOH A 38 340 340 HOH HOH . E 5 HOH A 39 341 341 HOH HOH . E 5 HOH A 40 342 342 HOH HOH . E 5 HOH A 41 343 343 HOH HOH . E 5 HOH A 42 344 344 HOH HOH . E 5 HOH A 43 345 345 HOH HOH . E 5 HOH A 44 346 346 HOH HOH . E 5 HOH A 45 347 347 HOH HOH . E 5 HOH A 46 348 348 HOH HOH . E 5 HOH A 47 349 349 HOH HOH . E 5 HOH A 48 350 350 HOH HOH . E 5 HOH A 49 351 351 HOH HOH . E 5 HOH A 50 352 352 HOH HOH . E 5 HOH A 51 353 353 HOH HOH . E 5 HOH A 52 354 354 HOH HOH . E 5 HOH A 53 355 355 HOH HOH . E 5 HOH A 54 356 356 HOH HOH . E 5 HOH A 55 357 357 HOH HOH . E 5 HOH A 56 358 358 HOH HOH . E 5 HOH A 57 359 359 HOH HOH . E 5 HOH A 58 360 360 HOH HOH . E 5 HOH A 59 361 361 HOH HOH . E 5 HOH A 60 362 362 HOH HOH . E 5 HOH A 61 363 363 HOH HOH . E 5 HOH A 62 364 364 HOH HOH . E 5 HOH A 63 365 365 HOH HOH . E 5 HOH A 64 366 366 HOH HOH . E 5 HOH A 65 367 367 HOH HOH . E 5 HOH A 66 368 368 HOH HOH . E 5 HOH A 67 369 369 HOH HOH . E 5 HOH A 68 370 370 HOH HOH . E 5 HOH A 69 371 371 HOH HOH . E 5 HOH A 70 372 372 HOH HOH . E 5 HOH A 71 373 373 HOH HOH . E 5 HOH A 72 374 374 HOH HOH . E 5 HOH A 73 375 375 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 SAM . . . C 3 -19.953 6.49 -15.852 1 32.02 ? N SAM 301 A 1 HETATM 2 C CA SAM . . . C 3 -18.914 7.192 -15.057 1 33.43 ? CA SAM 301 A 1 HETATM 3 C C SAM . . . C 3 -19.183 8.692 -15.024 1 33.16 ? C SAM 301 A 1 HETATM 4 O O SAM . . . C 3 -19.786 9.196 -15.972 1 33.46 ? O SAM 301 A 1 HETATM 5 O OXT SAM . . . C 3 -18.774 9.405 -14.102 1 32.52 ? OXT SAM 301 A 1 HETATM 6 C CB SAM . . . C 3 -17.535 6.977 -15.674 1 33.03 ? CB SAM 301 A 1 HETATM 7 C CG SAM . . . C 3 -17.193 5.495 -15.792 1 35.87 ? CG SAM 301 A 1 HETATM 8 S SD SAM . . . C 3 -15.492 5.249 -16.348 1 36.25 ? SD SAM 301 A 1 HETATM 9 C CE SAM . . . C 3 -15.692 5.601 -18.128 1 39.44 ? CE SAM 301 A 1 HETATM 10 C C5' SAM . . . C 3 -15.527 3.446 -16.584 1 34.6 ? C5' SAM 301 A 1 HETATM 11 C C4' SAM . . . C 3 -15.457 2.645 -15.296 1 35.96 ? C4' SAM 301 A 1 HETATM 12 O O4' SAM . . . C 3 -15.935 1.328 -15.522 1 37.08 ? O4' SAM 301 A 1 HETATM 13 C C3' SAM . . . C 3 -14.067 2.512 -14.689 1 36.45 ? C3' SAM 301 A 1 HETATM 14 O O3' SAM . . . C 3 -14.118 3.074 -13.396 1 37.08 ? O3' SAM 301 A 1 HETATM 15 C C2' SAM . . . C 3 -13.833 0.995 -14.64 1 37.25 ? C2' SAM 301 A 1 HETATM 16 O O2' SAM . . . C 3 -13.21 0.539 -13.468 1 37.46 ? O2' SAM 301 A 1 HETATM 17 C C1' SAM . . . C 3 -15.247 0.434 -14.679 1 34.55 ? C1' SAM 301 A 1 HETATM 18 N N9 SAM . . . C 3 -15.376 -0.825 -15.375 1 33.69 ? N9 SAM 301 A 1 HETATM 19 C C8 SAM . . . C 3 -14.753 -1.201 -16.548 1 32.51 ? C8 SAM 301 A 1 HETATM 20 N N7 SAM . . . C 3 -15.215 -2.432 -16.853 1 33.02 ? N7 SAM 301 A 1 HETATM 21 C C5 SAM . . . C 3 -16.109 -2.849 -15.922 1 31.82 ? C5 SAM 301 A 1 HETATM 22 C C6 SAM . . . C 3 -16.864 -4 -15.777 1 33.34 ? C6 SAM 301 A 1 HETATM 23 N N6 SAM . . . C 3 -16.781 -5.029 -16.637 1 33.65 ? N6 SAM 301 A 1 HETATM 24 N N1 SAM . . . C 3 -17.708 -4.095 -14.691 1 33.81 ? N1 SAM 301 A 1 HETATM 25 C C2 SAM . . . C 3 -17.802 -3.07 -13.765 1 32.79 ? C2 SAM 301 A 1 HETATM 26 N N3 SAM . . . C 3 -17.053 -1.931 -13.928 1 31.67 ? N3 SAM 301 A 1 HETATM 27 C C4 SAM . . . C 3 -16.227 -1.828 -14.986 1 33.45 ? C4 SAM 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #