data_7PHF # _model_server_result.job_id Ydi8b6wdwF5rvXnMrHzORg _model_server_result.datetime_utc '2024-11-28 04:03:58' _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 7phf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 7PHF # _exptl.entry_id 7PHF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.303 _cell.angle_gamma 90 _cell.entry_id 7PHF _cell.length_a 60.007 _cell.length_b 102.415 _cell.length_c 122.193 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PHF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,L,M 1 1 C,D,H,I,J,K,N,O 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 E N N ? 2 F N N ? 2 H N N ? 2 J N N # _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 7PHF _atom_sites.fract_transf_matrix[1][1] 0.016665 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00273 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009764 _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] 0.008293 _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 E 2 SAH A 1 401 390 SAH SAH . F 2 SAH B 1 401 390 SAH SAH . G 3 VAK B 1 402 391 VAK VAK . H 2 SAH C 1 401 390 SAH SAH . I 3 VAK C 1 402 391 VAK VAK . J 2 SAH D 1 401 390 SAH SAH . K 3 VAK D 1 402 391 VAK VAK . L 4 HOH A 1 501 161 HOH HOH . L 4 HOH A 2 502 24 HOH HOH . L 4 HOH A 3 503 184 HOH HOH . L 4 HOH A 4 504 29 HOH HOH . L 4 HOH A 5 505 89 HOH HOH . L 4 HOH A 6 506 100 HOH HOH . L 4 HOH A 7 507 93 HOH HOH . L 4 HOH A 8 508 48 HOH HOH . L 4 HOH A 9 509 88 HOH HOH . L 4 HOH A 10 510 70 HOH HOH . L 4 HOH A 11 511 8 HOH HOH . L 4 HOH A 12 512 20 HOH HOH . L 4 HOH A 13 513 252 HOH HOH . L 4 HOH A 14 514 62 HOH HOH . L 4 HOH A 15 515 207 HOH HOH . L 4 HOH A 16 516 49 HOH HOH . L 4 HOH A 17 517 162 HOH HOH . L 4 HOH A 18 518 51 HOH HOH . L 4 HOH A 19 519 113 HOH HOH . L 4 HOH A 20 520 304 HOH HOH . L 4 HOH A 21 521 84 HOH HOH . L 4 HOH A 22 522 141 HOH HOH . L 4 HOH A 23 523 240 HOH HOH . L 4 HOH A 24 524 256 HOH HOH . L 4 HOH A 25 525 129 HOH HOH . L 4 HOH A 26 526 148 HOH HOH . L 4 HOH A 27 527 15 HOH HOH . L 4 HOH A 28 528 120 HOH HOH . L 4 HOH A 29 529 164 HOH HOH . L 4 HOH A 30 530 263 HOH HOH . L 4 HOH A 31 531 136 HOH HOH . L 4 HOH A 32 532 26 HOH HOH . L 4 HOH A 33 533 104 HOH HOH . L 4 HOH A 34 534 281 HOH HOH . L 4 HOH A 35 535 122 HOH HOH . L 4 HOH A 36 536 115 HOH HOH . L 4 HOH A 37 537 72 HOH HOH . L 4 HOH A 38 538 137 HOH HOH . L 4 HOH A 39 539 67 HOH HOH . L 4 HOH A 40 540 290 HOH HOH . L 4 HOH A 41 541 235 HOH HOH . L 4 HOH A 42 542 46 HOH HOH . L 4 HOH A 43 543 144 HOH HOH . L 4 HOH A 44 544 291 HOH HOH . L 4 HOH A 45 545 223 HOH HOH . L 4 HOH A 46 546 265 HOH HOH . L 4 HOH A 47 547 295 HOH HOH . L 4 HOH A 48 548 286 HOH HOH . L 4 HOH A 49 549 175 HOH HOH . L 4 HOH A 50 550 156 HOH HOH . L 4 HOH A 51 551 288 HOH HOH . M 4 HOH B 1 501 27 HOH HOH . M 4 HOH B 2 502 47 HOH HOH . M 4 HOH B 3 503 87 HOH HOH . M 4 HOH B 4 504 108 HOH HOH . M 4 HOH B 5 505 153 HOH HOH . M 4 HOH B 6 506 181 HOH HOH . M 4 HOH B 7 507 260 HOH HOH . M 4 HOH B 8 508 285 HOH HOH . M 4 HOH B 9 509 9 HOH HOH . M 4 HOH B 10 510 19 HOH HOH . M 4 HOH B 11 511 82 HOH HOH . M 4 HOH B 12 512 39 HOH HOH . M 4 HOH B 13 513 4 HOH HOH . M 4 HOH B 14 514 174 HOH HOH . M 4 HOH B 15 515 3 HOH HOH . M 4 HOH B 16 516 266 HOH HOH . M 4 HOH B 17 517 127 HOH HOH . M 4 HOH B 18 518 167 HOH HOH . M 4 HOH B 19 519 143 HOH HOH . M 4 HOH B 20 520 57 HOH HOH . M 4 HOH B 21 521 125 HOH HOH . M 4 HOH B 22 522 294 HOH HOH . M 4 HOH B 23 523 116 HOH HOH . M 4 HOH B 24 524 169 HOH HOH . M 4 HOH B 25 525 306 HOH HOH . M 4 HOH B 26 526 241 HOH HOH . M 4 HOH B 27 527 52 HOH HOH . M 4 HOH B 28 528 279 HOH HOH . M 4 HOH B 29 529 214 HOH HOH . M 4 HOH B 30 530 5 HOH HOH . M 4 HOH B 31 531 71 HOH HOH . M 4 HOH B 32 532 139 HOH HOH . M 4 HOH B 33 533 200 HOH HOH . M 4 HOH B 34 534 230 HOH HOH . M 4 HOH B 35 535 298 HOH HOH . M 4 HOH B 36 536 101 HOH HOH . M 4 HOH B 37 537 192 HOH HOH . M 4 HOH B 38 538 220 HOH HOH . M 4 HOH B 39 539 262 HOH HOH . M 4 HOH B 40 540 199 HOH HOH . N 4 HOH C 1 501 124 HOH HOH . N 4 HOH C 2 502 133 HOH HOH . N 4 HOH C 3 503 146 HOH HOH . N 4 HOH C 4 504 99 HOH HOH . N 4 HOH C 5 505 284 HOH HOH . N 4 HOH C 6 506 95 HOH HOH . N 4 HOH C 7 507 1 HOH HOH . N 4 HOH C 8 508 63 HOH HOH . N 4 HOH C 9 509 97 HOH HOH . N 4 HOH C 10 510 106 HOH HOH . N 4 HOH C 11 511 13 HOH HOH . N 4 HOH C 12 512 6 HOH HOH . N 4 HOH C 13 513 176 HOH HOH . N 4 HOH C 14 514 33 HOH HOH . N 4 HOH C 15 515 219 HOH HOH . N 4 HOH C 16 516 166 HOH HOH . N 4 HOH C 17 517 78 HOH HOH . N 4 HOH C 18 518 59 HOH HOH . N 4 HOH C 19 519 45 HOH HOH . N 4 HOH C 20 520 185 HOH HOH . N 4 HOH C 21 521 135 HOH HOH . N 4 HOH C 22 522 69 HOH HOH . N 4 HOH C 23 523 158 HOH HOH . N 4 HOH C 24 524 50 HOH HOH . N 4 HOH C 25 525 65 HOH HOH . N 4 HOH C 26 526 73 HOH HOH . N 4 HOH C 27 527 14 HOH HOH . N 4 HOH C 28 528 154 HOH HOH . N 4 HOH C 29 529 131 HOH HOH . N 4 HOH C 30 530 270 HOH HOH . N 4 HOH C 31 531 83 HOH HOH . N 4 HOH C 32 532 145 HOH HOH . N 4 HOH C 33 533 170 HOH HOH . N 4 HOH C 34 534 40 HOH HOH . N 4 HOH C 35 535 269 HOH HOH . N 4 HOH C 36 536 165 HOH HOH . N 4 HOH C 37 537 150 HOH HOH . N 4 HOH C 38 538 41 HOH HOH . N 4 HOH C 39 539 179 HOH HOH . N 4 HOH C 40 540 157 HOH HOH . N 4 HOH C 41 541 254 HOH HOH . N 4 HOH C 42 542 251 HOH HOH . N 4 HOH C 43 543 79 HOH HOH . N 4 HOH C 44 544 56 HOH HOH . N 4 HOH C 45 545 206 HOH HOH . N 4 HOH C 46 546 163 HOH HOH . N 4 HOH C 47 547 155 HOH HOH . N 4 HOH C 48 548 212 HOH HOH . N 4 HOH C 49 549 190 HOH HOH . N 4 HOH C 50 550 201 HOH HOH . N 4 HOH C 51 551 299 HOH HOH . N 4 HOH C 52 552 274 HOH HOH . N 4 HOH C 53 553 273 HOH HOH . N 4 HOH C 54 554 226 HOH HOH . N 4 HOH C 55 555 215 HOH HOH . N 4 HOH C 56 556 242 HOH HOH . N 4 HOH C 57 557 247 HOH HOH . N 4 HOH C 58 558 23 HOH HOH . N 4 HOH C 59 559 198 HOH HOH . N 4 HOH C 60 560 296 HOH HOH . N 4 HOH C 61 561 245 HOH HOH . O 4 HOH D 1 501 268 HOH HOH . O 4 HOH D 2 502 76 HOH HOH . O 4 HOH D 3 503 58 HOH HOH . O 4 HOH D 4 504 12 HOH HOH . O 4 HOH D 5 505 55 HOH HOH . O 4 HOH D 6 506 255 HOH HOH . O 4 HOH D 7 507 7 HOH HOH . O 4 HOH D 8 508 186 HOH HOH . O 4 HOH D 9 509 253 HOH HOH . O 4 HOH D 10 510 21 HOH HOH . O 4 HOH D 11 511 18 HOH HOH . O 4 HOH D 12 512 36 HOH HOH . O 4 HOH D 13 513 44 HOH HOH . O 4 HOH D 14 514 171 HOH HOH . O 4 HOH D 15 515 35 HOH HOH . O 4 HOH D 16 516 248 HOH HOH . O 4 HOH D 17 517 32 HOH HOH . O 4 HOH D 18 518 16 HOH HOH . O 4 HOH D 19 519 37 HOH HOH . O 4 HOH D 20 520 66 HOH HOH . O 4 HOH D 21 521 34 HOH HOH . O 4 HOH D 22 522 216 HOH HOH . O 4 HOH D 23 523 123 HOH HOH . O 4 HOH D 24 524 280 HOH HOH . O 4 HOH D 25 525 25 HOH HOH . O 4 HOH D 26 526 187 HOH HOH . O 4 HOH D 27 527 300 HOH HOH . O 4 HOH D 28 528 2 HOH HOH . O 4 HOH D 29 529 114 HOH HOH . O 4 HOH D 30 530 28 HOH HOH . O 4 HOH D 31 531 38 HOH HOH . O 4 HOH D 32 532 261 HOH HOH . O 4 HOH D 33 533 96 HOH HOH . O 4 HOH D 34 534 81 HOH HOH . O 4 HOH D 35 535 31 HOH HOH . O 4 HOH D 36 536 53 HOH HOH . O 4 HOH D 37 537 149 HOH HOH . O 4 HOH D 38 538 86 HOH HOH . O 4 HOH D 39 539 60 HOH HOH . O 4 HOH D 40 540 182 HOH HOH . O 4 HOH D 41 541 121 HOH HOH . O 4 HOH D 42 542 64 HOH HOH . O 4 HOH D 43 543 196 HOH HOH . O 4 HOH D 44 544 68 HOH HOH . O 4 HOH D 45 545 257 HOH HOH . O 4 HOH D 46 546 75 HOH HOH . O 4 HOH D 47 547 61 HOH HOH . O 4 HOH D 48 548 119 HOH HOH . O 4 HOH D 49 549 209 HOH HOH . O 4 HOH D 50 550 275 HOH HOH . O 4 HOH D 51 551 105 HOH HOH . O 4 HOH D 52 552 77 HOH HOH . O 4 HOH D 53 553 147 HOH HOH . O 4 HOH D 54 554 289 HOH HOH . O 4 HOH D 55 555 277 HOH HOH . O 4 HOH D 56 556 92 HOH HOH . O 4 HOH D 57 557 85 HOH HOH . O 4 HOH D 58 558 278 HOH HOH . O 4 HOH D 59 559 301 HOH HOH . O 4 HOH D 60 560 188 HOH HOH . O 4 HOH D 61 561 91 HOH HOH . O 4 HOH D 62 562 177 HOH HOH . O 4 HOH D 63 563 140 HOH HOH . O 4 HOH D 64 564 308 HOH HOH . O 4 HOH D 65 565 225 HOH HOH . O 4 HOH D 66 566 151 HOH HOH . O 4 HOH D 67 567 246 HOH HOH . O 4 HOH D 68 568 217 HOH HOH . O 4 HOH D 69 569 117 HOH HOH . O 4 HOH D 70 570 293 HOH HOH . O 4 HOH D 71 571 103 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 . . . H 2 21.802 72.464 48.465 1 29.45 ? N SAH 401 C 1 HETATM 2 C CA SAH . . . H 2 22.183 71.087 48.173 1 38.33 ? CA SAH 401 C 1 HETATM 3 C CB SAH . . . H 2 21.449 70.104 49.093 1 33.27 ? CB SAH 401 C 1 HETATM 4 C CG SAH . . . H 2 19.927 70.276 49.111 1 34.25 ? CG SAH 401 C 1 HETATM 5 S SD SAH . . . H 2 19.145 69.067 50.208 1 37.16 ? SD SAH 401 C 1 HETATM 6 C C SAH . . . H 2 21.913 70.739 46.707 1 42.9 ? C SAH 401 C 1 HETATM 7 O O SAH . . . H 2 22.156 69.614 46.277 1 44.13 ? O SAH 401 C 1 HETATM 8 O OXT SAH . . . H 2 21.453 71.556 45.907 1 39.72 ? OXT SAH 401 C 1 HETATM 9 C C5' SAH . . . H 2 18.503 70.413 51.259 1 31.72 ? C5' SAH 401 C 1 HETATM 10 C C4' SAH . . . H 2 19.557 70.731 52.324 1 35.74 ? C4' SAH 401 C 1 HETATM 11 O O4' SAH . . . H 2 19.16 71.671 53.311 1 35.06 ? O4' SAH 401 C 1 HETATM 12 C C3' SAH . . . H 2 19.959 69.478 53.083 1 37.64 ? C3' SAH 401 C 1 HETATM 13 O O3' SAH . . . H 2 21.329 69.276 52.873 1 40.98 ? O3' SAH 401 C 1 HETATM 14 C C2' SAH . . . H 2 19.764 69.833 54.547 1 39.53 ? C2' SAH 401 C 1 HETATM 15 O O2' SAH . . . H 2 20.799 69.33 55.35 1 41.38 ? O2' SAH 401 C 1 HETATM 16 C C1' SAH . . . H 2 19.75 71.353 54.554 1 32.98 ? C1' SAH 401 C 1 HETATM 17 N N9 SAH . . . H 2 18.967 71.895 55.671 1 31.74 ? N9 SAH 401 C 1 HETATM 18 C C8 SAH . . . H 2 17.738 71.44 56.067 1 37.66 ? C8 SAH 401 C 1 HETATM 19 N N7 SAH . . . H 2 17.328 72.174 57.124 1 36.99 ? N7 SAH 401 C 1 HETATM 20 C C5 SAH . . . H 2 18.256 73.101 57.424 1 38.72 ? C5 SAH 401 C 1 HETATM 21 C C6 SAH . . . H 2 18.328 74.099 58.408 1 44.47 ? C6 SAH 401 C 1 HETATM 22 N N6 SAH . . . H 2 17.355 74.323 59.303 1 33.09 ? N6 SAH 401 C 1 HETATM 23 N N1 SAH . . . H 2 19.451 74.895 58.452 1 38.36 ? N1 SAH 401 C 1 HETATM 24 C C2 SAH . . . H 2 20.46 74.698 57.541 1 39.36 ? C2 SAH 401 C 1 HETATM 25 N N3 SAH . . . H 2 20.383 73.728 56.575 1 38.31 ? N3 SAH 401 C 1 HETATM 26 C C4 SAH . . . H 2 19.301 72.922 56.517 1 37.85 ? C4 SAH 401 C 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #