data_5VA6 # _model_server_result.job_id DfSFxwdyIB8utRTEO5Zg1A _model_server_result.datetime_utc '2024-11-05 01:18:17' _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 5va6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 5VA6 # _exptl.entry_id 5VA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 127.83 _cell.angle_gamma 90 _cell.entry_id 5VA6 _cell.length_a 101.31 _cell.length_b 86.81 _cell.length_c 74.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VA6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,C,E,G 1 1 B,D,F,H,I 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 ? 3 E N N ? 3 F 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 covale ? covale1 C C ALA 7 C ALA 26 1_555 C N NMM 8 C NMM 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 C C NMM 8 C NMM 27 1_555 C N LYS 9 C LYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale3 D C ALA 7 D ALA 26 1_555 D N NMM 8 D NMM 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 D C NMM 8 D NMM 27 1_555 D N LYS 9 D LYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? # _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 305 n n N HN1 SAH sing 306 n n N HN2 SAH sing 307 n n CA CB SAH sing 308 n n CA C SAH sing 309 n n CA HA SAH sing 310 n n CB CG SAH sing 311 n n CB HB1 SAH sing 312 n n CB HB2 SAH sing 313 n n CG SD SAH sing 314 n n CG HG1 SAH sing 315 n n CG HG2 SAH sing 316 n n SD C5' SAH sing 317 n n C O SAH doub 318 n n C OXT SAH sing 319 n n OXT HXT SAH sing 320 n n C5' C4' SAH sing 321 n n C5' "H5'1" SAH sing 322 n n C5' "H5'2" SAH sing 323 n n C4' O4' SAH sing 324 n n C4' C3' SAH sing 325 n n C4' H4' SAH sing 326 n n O4' C1' SAH sing 327 n n C3' O3' SAH sing 328 n n C3' C2' SAH sing 329 n n C3' H3' SAH sing 330 n n O3' HO3' SAH sing 331 n n C2' O2' SAH sing 332 n n C2' C1' SAH sing 333 n n C2' H2' SAH sing 334 n n O2' HO2' SAH sing 335 n n C1' N9 SAH sing 336 n n C1' H1' SAH sing 337 n n N9 C8 SAH sing 338 n y N9 C4 SAH sing 339 n y C8 N7 SAH doub 340 n y C8 H8 SAH sing 341 n n N7 C5 SAH sing 342 n y C5 C6 SAH sing 343 n y C5 C4 SAH doub 344 n y C6 N6 SAH sing 345 n n C6 N1 SAH doub 346 n y N6 HN61 SAH sing 347 n n N6 HN62 SAH sing 348 n n N1 C2 SAH sing 349 n y C2 N3 SAH doub 350 n y C2 H2 SAH sing 351 n n N3 C4 SAH sing 352 n y # _atom_sites.entry_id 5VA6 _atom_sites.fract_transf_matrix[1][1] 0.009871 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007665 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011519 _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] 0.0171 _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 3 SAH A 1 401 120 SAH SAH . F 3 SAH B 1 401 120 SAH SAH . G 4 HOH A 1 501 57 HOH HOH . G 4 HOH A 2 502 24 HOH HOH . G 4 HOH A 3 503 194 HOH HOH . G 4 HOH A 4 504 23 HOH HOH . G 4 HOH A 5 505 30 HOH HOH . G 4 HOH A 6 506 9 HOH HOH . G 4 HOH A 7 507 8 HOH HOH . G 4 HOH A 8 508 6 HOH HOH . G 4 HOH A 9 509 39 HOH HOH . G 4 HOH A 10 510 134 HOH HOH . G 4 HOH A 11 511 52 HOH HOH . G 4 HOH A 12 512 1 HOH HOH . G 4 HOH A 13 513 3 HOH HOH . G 4 HOH A 14 514 97 HOH HOH . G 4 HOH A 15 515 142 HOH HOH . G 4 HOH A 16 516 160 HOH HOH . G 4 HOH A 17 517 112 HOH HOH . G 4 HOH A 18 518 86 HOH HOH . G 4 HOH A 19 519 156 HOH HOH . G 4 HOH A 20 520 109 HOH HOH . G 4 HOH A 21 521 10 HOH HOH . G 4 HOH A 22 522 48 HOH HOH . G 4 HOH A 23 523 171 HOH HOH . G 4 HOH A 24 524 68 HOH HOH . G 4 HOH A 25 525 94 HOH HOH . G 4 HOH A 26 526 183 HOH HOH . G 4 HOH A 27 527 63 HOH HOH . G 4 HOH A 28 528 45 HOH HOH . G 4 HOH A 29 529 32 HOH HOH . G 4 HOH A 30 530 29 HOH HOH . G 4 HOH A 31 531 42 HOH HOH . G 4 HOH A 32 532 102 HOH HOH . G 4 HOH A 33 533 21 HOH HOH . G 4 HOH A 34 534 135 HOH HOH . G 4 HOH A 35 535 166 HOH HOH . G 4 HOH A 36 536 202 HOH HOH . G 4 HOH A 37 537 27 HOH HOH . G 4 HOH A 38 538 127 HOH HOH . G 4 HOH A 39 539 207 HOH HOH . G 4 HOH A 40 540 124 HOH HOH . G 4 HOH A 41 541 60 HOH HOH . G 4 HOH A 42 542 46 HOH HOH . G 4 HOH A 43 543 51 HOH HOH . G 4 HOH A 44 544 203 HOH HOH . G 4 HOH A 45 545 103 HOH HOH . G 4 HOH A 46 546 96 HOH HOH . G 4 HOH A 47 547 69 HOH HOH . G 4 HOH A 48 548 77 HOH HOH . G 4 HOH A 49 549 165 HOH HOH . G 4 HOH A 50 550 106 HOH HOH . G 4 HOH A 51 551 185 HOH HOH . G 4 HOH A 52 552 145 HOH HOH . G 4 HOH A 53 553 70 HOH HOH . G 4 HOH A 54 554 125 HOH HOH . G 4 HOH A 55 555 89 HOH HOH . G 4 HOH A 56 556 28 HOH HOH . G 4 HOH A 57 557 170 HOH HOH . G 4 HOH A 58 558 43 HOH HOH . G 4 HOH A 59 559 158 HOH HOH . G 4 HOH A 60 560 122 HOH HOH . G 4 HOH A 61 561 35 HOH HOH . G 4 HOH A 62 562 72 HOH HOH . G 4 HOH A 63 563 146 HOH HOH . G 4 HOH A 64 564 79 HOH HOH . G 4 HOH A 65 565 184 HOH HOH . G 4 HOH A 66 566 82 HOH HOH . G 4 HOH A 67 567 105 HOH HOH . G 4 HOH A 68 568 85 HOH HOH . G 4 HOH A 69 569 41 HOH HOH . G 4 HOH A 70 570 129 HOH HOH . G 4 HOH A 71 571 36 HOH HOH . G 4 HOH A 72 572 19 HOH HOH . G 4 HOH A 73 573 67 HOH HOH . G 4 HOH A 74 574 213 HOH HOH . G 4 HOH A 75 575 187 HOH HOH . G 4 HOH A 76 576 95 HOH HOH . G 4 HOH A 77 577 162 HOH HOH . G 4 HOH A 78 578 206 HOH HOH . H 4 HOH B 1 501 15 HOH HOH . H 4 HOH B 2 502 161 HOH HOH . H 4 HOH B 3 503 18 HOH HOH . H 4 HOH B 4 504 141 HOH HOH . H 4 HOH B 5 505 188 HOH HOH . H 4 HOH B 6 506 111 HOH HOH . H 4 HOH B 7 507 113 HOH HOH . H 4 HOH B 8 508 121 HOH HOH . H 4 HOH B 9 509 53 HOH HOH . H 4 HOH B 10 510 132 HOH HOH . H 4 HOH B 11 511 5 HOH HOH . H 4 HOH B 12 512 62 HOH HOH . H 4 HOH B 13 513 163 HOH HOH . H 4 HOH B 14 514 4 HOH HOH . H 4 HOH B 15 515 17 HOH HOH . H 4 HOH B 16 516 54 HOH HOH . H 4 HOH B 17 517 7 HOH HOH . H 4 HOH B 18 518 59 HOH HOH . H 4 HOH B 19 519 99 HOH HOH . H 4 HOH B 20 520 20 HOH HOH . H 4 HOH B 21 521 159 HOH HOH . H 4 HOH B 22 522 164 HOH HOH . H 4 HOH B 23 523 90 HOH HOH . H 4 HOH B 24 524 16 HOH HOH . H 4 HOH B 25 525 110 HOH HOH . H 4 HOH B 26 526 66 HOH HOH . H 4 HOH B 27 527 115 HOH HOH . H 4 HOH B 28 528 50 HOH HOH . H 4 HOH B 29 529 130 HOH HOH . H 4 HOH B 30 530 78 HOH HOH . H 4 HOH B 31 531 195 HOH HOH . H 4 HOH B 32 532 47 HOH HOH . H 4 HOH B 33 533 139 HOH HOH . H 4 HOH B 34 534 38 HOH HOH . H 4 HOH B 35 535 22 HOH HOH . H 4 HOH B 36 536 172 HOH HOH . H 4 HOH B 37 537 64 HOH HOH . H 4 HOH B 38 538 193 HOH HOH . H 4 HOH B 39 539 101 HOH HOH . H 4 HOH B 40 540 138 HOH HOH . H 4 HOH B 41 541 104 HOH HOH . H 4 HOH B 42 542 33 HOH HOH . H 4 HOH B 43 543 49 HOH HOH . H 4 HOH B 44 544 155 HOH HOH . H 4 HOH B 45 545 180 HOH HOH . H 4 HOH B 46 546 75 HOH HOH . H 4 HOH B 47 547 154 HOH HOH . H 4 HOH B 48 548 13 HOH HOH . H 4 HOH B 49 549 148 HOH HOH . H 4 HOH B 50 550 143 HOH HOH . H 4 HOH B 51 551 87 HOH HOH . H 4 HOH B 52 552 191 HOH HOH . H 4 HOH B 53 553 199 HOH HOH . H 4 HOH B 54 554 71 HOH HOH . H 4 HOH B 55 555 61 HOH HOH . H 4 HOH B 56 556 128 HOH HOH . H 4 HOH B 57 557 118 HOH HOH . H 4 HOH B 58 558 91 HOH HOH . H 4 HOH B 59 559 200 HOH HOH . H 4 HOH B 60 560 168 HOH HOH . H 4 HOH B 61 561 190 HOH HOH . H 4 HOH B 62 562 84 HOH HOH . H 4 HOH B 63 563 196 HOH HOH . H 4 HOH B 64 564 76 HOH HOH . H 4 HOH B 65 565 176 HOH HOH . H 4 HOH B 66 566 100 HOH HOH . H 4 HOH B 67 567 40 HOH HOH . H 4 HOH B 68 568 73 HOH HOH . H 4 HOH B 69 569 81 HOH HOH . H 4 HOH B 70 570 167 HOH HOH . H 4 HOH B 71 571 58 HOH HOH . H 4 HOH B 72 572 126 HOH HOH . H 4 HOH B 73 573 208 HOH HOH . I 4 HOH D 1 101 192 HOH HOH . I 4 HOH D 2 102 2 HOH HOH . I 4 HOH D 3 103 25 HOH HOH . I 4 HOH D 4 104 151 HOH HOH . I 4 HOH D 5 105 179 HOH HOH . I 4 HOH D 6 106 34 HOH HOH . I 4 HOH D 7 107 117 HOH HOH . I 4 HOH D 8 108 56 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 . . . F 3 -0.55 -13.041 38.392 1 22.63 ? N SAH 401 B 1 HETATM 2 C CA SAH . . . F 3 -1.044 -11.743 38.852 1 24.45 ? CA SAH 401 B 1 HETATM 3 C CB SAH . . . F 3 -1.094 -10.654 37.747 1 26.98 ? CB SAH 401 B 1 HETATM 4 C CG SAH . . . F 3 0.296 -10.199 37.303 1 29.85 ? CG SAH 401 B 1 HETATM 5 S SD SAH . . . F 3 0.98 -9.014 38.51 1 30.45 ? SD SAH 401 B 1 HETATM 6 C C SAH . . . F 3 -2.346 -11.809 39.68 1 38.92 ? C SAH 401 B 1 HETATM 7 O O SAH . . . F 3 -2.743 -13.019 39.991 1 37.68 ? O SAH 401 B 1 HETATM 8 O OXT SAH . . . F 3 -2.919 -10.755 40.058 1 47.58 ? OXT SAH 401 B 1 HETATM 9 C C5' SAH . . . F 3 2.657 -9.639 38.815 1 32.73 ? C5' SAH 401 B 1 HETATM 10 C C4' SAH . . . F 3 2.671 -10.889 39.675 1 34.51 ? C4' SAH 401 B 1 HETATM 11 O O4' SAH . . . F 3 2.253 -12.032 38.89 1 34.45 ? O4' SAH 401 B 1 HETATM 12 C C3' SAH . . . F 3 4.038 -11.274 40.234 1 37.49 ? C3' SAH 401 B 1 HETATM 13 O O3' SAH . . . F 3 4.35 -10.637 41.466 1 40.26 ? O3' SAH 401 B 1 HETATM 14 C C2' SAH . . . F 3 3.903 -12.789 40.409 1 37.89 ? C2' SAH 401 B 1 HETATM 15 O O2' SAH . . . F 3 3.236 -13.167 41.612 1 36.18 ? O2' SAH 401 B 1 HETATM 16 C C1' SAH . . . F 3 3.063 -13.156 39.179 1 33.65 ? C1' SAH 401 B 1 HETATM 17 N N9 SAH . . . F 3 3.845 -13.496 37.99 1 29.12 ? N9 SAH 401 B 1 HETATM 18 C C8 SAH . . . F 3 3.94 -12.791 36.816 1 26.32 ? C8 SAH 401 B 1 HETATM 19 N N7 SAH . . . F 3 4.69 -13.365 35.908 1 26.74 ? N7 SAH 401 B 1 HETATM 20 C C5 SAH . . . F 3 5.113 -14.536 36.522 1 28.3 ? C5 SAH 401 B 1 HETATM 21 C C6 SAH . . . F 3 5.901 -15.619 36.072 1 31.43 ? C6 SAH 401 B 1 HETATM 22 N N6 SAH . . . F 3 6.46 -15.682 34.86 1 30.99 ? N6 SAH 401 B 1 HETATM 23 N N1 SAH . . . F 3 6.126 -16.636 36.938 1 30.65 ? N1 SAH 401 B 1 HETATM 24 C C2 SAH . . . F 3 5.606 -16.564 38.167 1 30.66 ? C2 SAH 401 B 1 HETATM 25 N N3 SAH . . . F 3 4.839 -15.605 38.695 1 30.33 ? N3 SAH 401 B 1 HETATM 26 C C4 SAH . . . F 3 4.617 -14.619 37.812 1 28.69 ? C4 SAH 401 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #