data_5PA7 # _model_server_result.job_id gYuSfzXRBmk9e25FHFSPWw _model_server_result.datetime_utc '2025-01-26 14:05:54' _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 5pa7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 5PA7 # _exptl.entry_id 5PA7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _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 5PA7 _cell.length_a 57.185 _cell.length_b 60.105 _cell.length_c 147.614 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PA7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,I 1 1 B,G,H,J 2 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 ? 2 C N N ? 2 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 A OD1 ASP 141 A ASP 141 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc2 A OD2 ASP 169 A ASP 169 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc3 A OD1 ASN 170 A ASN 170 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc4 A O VAL 183 A VAL 183 1_555 F NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc5 A O ARG 184 A ARG 184 1_555 F NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc6 A O SER 186 A SER 186 1_555 F NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc7 A O PHE 189 A PHE 189 1_555 F NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc8 D MG MG . A MG 301 1_555 E O12 7JX . A 7JX 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc9 D MG MG . A MG 301 1_555 I O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc10 F NA NA . A NA 303 1_555 I O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc11 F NA NA . A NA 303 1_555 I O HOH . A HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc12 B O VAL 183 B VAL 183 1_555 H NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc13 B O ARG 184 B ARG 184 1_555 H NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc14 B O SER 186 B SER 186 1_555 H NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc15 B O PHE 189 B PHE 189 1_555 H NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc16 H NA NA . B NA 302 1_555 J O HOH . B HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc17 H NA NA . B NA 302 1_555 J O HOH . B HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 296 n n N HN1 SAH sing 297 n n N HN2 SAH sing 298 n n CA CB SAH sing 299 n n CA C SAH sing 300 n n CA HA SAH sing 301 n n CB CG SAH sing 302 n n CB HB1 SAH sing 303 n n CB HB2 SAH sing 304 n n CG SD SAH sing 305 n n CG HG1 SAH sing 306 n n CG HG2 SAH sing 307 n n SD C5' SAH sing 308 n n C O SAH doub 309 n n C OXT SAH sing 310 n n OXT HXT SAH sing 311 n n C5' C4' SAH sing 312 n n C5' "H5'1" SAH sing 313 n n C5' "H5'2" SAH sing 314 n n C4' O4' SAH sing 315 n n C4' C3' SAH sing 316 n n C4' H4' SAH sing 317 n n O4' C1' SAH sing 318 n n C3' O3' SAH sing 319 n n C3' C2' SAH sing 320 n n C3' H3' SAH sing 321 n n O3' HO3' SAH sing 322 n n C2' O2' SAH sing 323 n n C2' C1' SAH sing 324 n n C2' H2' SAH sing 325 n n O2' HO2' SAH sing 326 n n C1' N9 SAH sing 327 n n C1' H1' SAH sing 328 n n N9 C8 SAH sing 329 n y N9 C4 SAH sing 330 n y C8 N7 SAH doub 331 n y C8 H8 SAH sing 332 n n N7 C5 SAH sing 333 n y C5 C6 SAH sing 334 n y C5 C4 SAH doub 335 n y C6 N6 SAH sing 336 n n C6 N1 SAH doub 337 n y N6 HN61 SAH sing 338 n n N6 HN62 SAH sing 339 n n N1 C2 SAH sing 340 n y C2 N3 SAH doub 341 n y C2 H2 SAH sing 342 n n N3 C4 SAH sing 343 n y # _atom_sites.entry_id 5PA7 _atom_sites.fract_transf_matrix[1][1] 0.017487 _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] 0.016638 _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] 0.006774 _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 SAH A 1 300 300 SAH SAH . D 3 MG A 1 301 301 MG MG . E 4 7JX A 1 302 302 7JX LIG . F 5 NA A 1 303 303 NA NA . G 2 SAH B 1 301 300 SAH SAH . H 5 NA B 1 302 303 NA NA . I 6 HOH A 1 401 81 HOH HOH . I 6 HOH A 2 402 71 HOH HOH . I 6 HOH A 3 403 76 HOH HOH . I 6 HOH A 4 404 12 HOH HOH . I 6 HOH A 5 405 79 HOH HOH . I 6 HOH A 6 406 8 HOH HOH . I 6 HOH A 7 407 19 HOH HOH . I 6 HOH A 8 408 6 HOH HOH . I 6 HOH A 9 409 21 HOH HOH . I 6 HOH A 10 410 87 HOH HOH . I 6 HOH A 11 411 89 HOH HOH . I 6 HOH A 12 412 32 HOH HOH . I 6 HOH A 13 413 25 HOH HOH . I 6 HOH A 14 414 28 HOH HOH . I 6 HOH A 15 415 24 HOH HOH . I 6 HOH A 16 416 9 HOH HOH . I 6 HOH A 17 417 17 HOH HOH . I 6 HOH A 18 418 38 HOH HOH . I 6 HOH A 19 419 26 HOH HOH . I 6 HOH A 20 420 13 HOH HOH . I 6 HOH A 21 421 4 HOH HOH . I 6 HOH A 22 422 2 HOH HOH . I 6 HOH A 23 423 20 HOH HOH . I 6 HOH A 24 424 31 HOH HOH . I 6 HOH A 25 425 7 HOH HOH . I 6 HOH A 26 426 34 HOH HOH . I 6 HOH A 27 427 36 HOH HOH . I 6 HOH A 28 428 1 HOH HOH . I 6 HOH A 29 429 10 HOH HOH . I 6 HOH A 30 430 22 HOH HOH . I 6 HOH A 31 431 5 HOH HOH . I 6 HOH A 32 432 15 HOH HOH . I 6 HOH A 33 433 29 HOH HOH . I 6 HOH A 34 434 3 HOH HOH . I 6 HOH A 35 435 86 HOH HOH . I 6 HOH A 36 436 14 HOH HOH . I 6 HOH A 37 437 91 HOH HOH . I 6 HOH A 38 438 39 HOH HOH . I 6 HOH A 39 439 18 HOH HOH . I 6 HOH A 40 440 30 HOH HOH . I 6 HOH A 41 441 72 HOH HOH . I 6 HOH A 42 442 11 HOH HOH . I 6 HOH A 43 443 80 HOH HOH . I 6 HOH A 44 444 48 HOH HOH . I 6 HOH A 45 445 27 HOH HOH . J 6 HOH B 1 401 43 HOH HOH . J 6 HOH B 2 402 46 HOH HOH . J 6 HOH B 3 403 63 HOH HOH . J 6 HOH B 4 404 33 HOH HOH . J 6 HOH B 5 405 54 HOH HOH . J 6 HOH B 6 406 59 HOH HOH . J 6 HOH B 7 407 62 HOH HOH . J 6 HOH B 8 408 77 HOH HOH . J 6 HOH B 9 409 73 HOH HOH . J 6 HOH B 10 410 52 HOH HOH . J 6 HOH B 11 411 40 HOH HOH . J 6 HOH B 12 412 41 HOH HOH . J 6 HOH B 13 413 45 HOH HOH . J 6 HOH B 14 414 85 HOH HOH . J 6 HOH B 15 415 56 HOH HOH . J 6 HOH B 16 416 35 HOH HOH . J 6 HOH B 17 417 53 HOH HOH . J 6 HOH B 18 418 60 HOH HOH . J 6 HOH B 19 419 47 HOH HOH . J 6 HOH B 20 420 75 HOH HOH . J 6 HOH B 21 421 61 HOH HOH . J 6 HOH B 22 422 64 HOH HOH . J 6 HOH B 23 423 44 HOH HOH . J 6 HOH B 24 424 42 HOH HOH . J 6 HOH B 25 425 78 HOH HOH . J 6 HOH B 26 426 88 HOH HOH . J 6 HOH B 27 427 51 HOH HOH . J 6 HOH B 28 428 49 HOH HOH . J 6 HOH B 29 429 23 HOH HOH . J 6 HOH B 30 430 68 HOH HOH . J 6 HOH B 31 431 16 HOH HOH . J 6 HOH B 32 432 65 HOH HOH . J 6 HOH B 33 433 55 HOH HOH . J 6 HOH B 34 434 67 HOH HOH . J 6 HOH B 35 435 58 HOH HOH . J 6 HOH B 36 436 74 HOH HOH . J 6 HOH B 37 437 69 HOH HOH . J 6 HOH B 38 438 57 HOH HOH . J 6 HOH B 39 439 70 HOH HOH . J 6 HOH B 40 440 37 HOH HOH . J 6 HOH B 41 441 83 HOH HOH . J 6 HOH B 42 442 90 HOH HOH . J 6 HOH B 43 443 50 HOH HOH . J 6 HOH B 44 444 82 HOH HOH . J 6 HOH B 45 445 84 HOH HOH . J 6 HOH B 46 446 66 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 . . . G 2 -10.823 -29.493 31.198 1 42.98 ? N SAH 301 B 1 HETATM 2 C CA SAH . . . G 2 -11.664 -28.445 31.776 1 53.11 ? CA SAH 301 B 1 HETATM 3 C CB SAH . . . G 2 -11.049 -27.825 33.034 1 46.34 ? CB SAH 301 B 1 HETATM 4 C CG SAH . . . G 2 -10.43 -28.798 34.033 1 46.47 ? CG SAH 301 B 1 HETATM 5 S SD SAH . . . G 2 -10.157 -27.936 35.604 1 44.38 ? SD SAH 301 B 1 HETATM 6 C C SAH . . . G 2 -12.027 -27.342 30.774 1 59.17 ? C SAH 301 B 1 HETATM 7 O O SAH . . . G 2 -11.235 -26.97 29.902 1 59.73 -1 O SAH 301 B 1 HETATM 8 O OXT SAH . . . G 2 -13.131 -26.792 30.827 1 59.17 ? OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . G 2 -9.54 -29.428 36.422 1 36.92 ? C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . G 2 -10.616 -30.414 36.872 1 36.94 ? C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . G 2 -9.937 -31.567 37.256 1 36.4 ? O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . G 2 -11.427 -30.02 38.106 1 37.03 ? C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . G 2 -12.789 -30.213 37.813 1 41.04 ? O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . G 2 -11.048 -31.007 39.21 1 41.73 ? C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . G 2 -12.153 -31.447 39.966 1 41.45 ? O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . G 2 -10.535 -32.168 38.395 1 39.69 ? C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . G 2 -9.506 -33.013 39.02 1 35.57 ? N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . G 2 -8.441 -32.628 39.791 1 37.3 ? C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . G 2 -7.729 -33.735 40.098 1 39.09 ? N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . G 2 -8.307 -34.811 39.518 1 36.42 ? C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . G 2 -7.996 -36.163 39.494 1 35.06 ? C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . G 2 -6.946 -36.66 40.149 1 35.48 ? N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . G 2 -8.816 -37.019 38.803 1 38.69 ? N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . G 2 -9.918 -36.552 38.126 1 35.14 ? C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . G 2 -10.218 -35.22 38.158 1 35.51 ? N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . G 2 -9.427 -34.361 38.836 1 37.65 ? C4 SAH 301 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #