data_4RTN # _model_server_result.job_id a2joW4ZcQVbTjWqdUYt4GA _model_server_result.datetime_utc '2025-01-07 04:05:32' _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 4rtn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4RTN # _exptl.entry_id 4RTN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 90 _cell.entry_id 4RTN _cell.length_a 36.201 _cell.length_b 63.477 _cell.length_c 144.048 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RTN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 4 _struct_asym.id D _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 hydrog WATSON-CRICK hydrog1 B N3 DT 2 F DT 2 1_555 C N1 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 2 F DT 2 1_555 C N6 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 3 F DT 3 1_555 C N1 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 3 F DT 3 1_555 C N6 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog5 B N1 DA 4 F DA 4 1_555 C N3 DT 9 G DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog6 B N1 DA 5 F DA 5 1_555 C N3 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DA 6 F DA 6 1_555 C N3 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 DA 6 F DA 6 1_555 C O4 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DG 7 F DG 7 1_555 C N3 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 DG 7 F DG 7 1_555 C O2 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 DG 7 F DG 7 1_555 C N4 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 8 F DA 8 1_555 C N3 DT 5 G DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 8 F DA 8 1_555 C O4 DT 5 G DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 9 F DT 9 1_555 C N1 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 9 F DT 9 1_555 C N6 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 10 F DC 10 1_555 C N1 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 10 F DC 10 1_555 C O6 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 10 F DC 10 1_555 C N2 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 11 F DG 11 1_555 C N3 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 11 F DG 11 1_555 C O2 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 11 F DG 11 1_555 C N4 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 426 n n N HN1 SAH sing 427 n n N HN2 SAH sing 428 n n CA CB SAH sing 429 n n CA C SAH sing 430 n n CA HA SAH sing 431 n n CB CG SAH sing 432 n n CB HB1 SAH sing 433 n n CB HB2 SAH sing 434 n n CG SD SAH sing 435 n n CG HG1 SAH sing 436 n n CG HG2 SAH sing 437 n n SD C5' SAH sing 438 n n C O SAH doub 439 n n C OXT SAH sing 440 n n OXT HXT SAH sing 441 n n C5' C4' SAH sing 442 n n C5' "H5'1" SAH sing 443 n n C5' "H5'2" SAH sing 444 n n C4' O4' SAH sing 445 n n C4' C3' SAH sing 446 n n C4' H4' SAH sing 447 n n O4' C1' SAH sing 448 n n C3' O3' SAH sing 449 n n C3' C2' SAH sing 450 n n C3' H3' SAH sing 451 n n O3' HO3' SAH sing 452 n n C2' O2' SAH sing 453 n n C2' C1' SAH sing 454 n n C2' H2' SAH sing 455 n n O2' HO2' SAH sing 456 n n C1' N9 SAH sing 457 n n C1' H1' SAH sing 458 n n N9 C8 SAH sing 459 n y N9 C4 SAH sing 460 n y C8 N7 SAH doub 461 n y C8 H8 SAH sing 462 n n N7 C5 SAH sing 463 n y C5 C6 SAH sing 464 n y C5 C4 SAH doub 465 n y C6 N6 SAH sing 466 n n C6 N1 SAH doub 467 n y N6 HN61 SAH sing 468 n n N6 HN62 SAH sing 469 n n N1 C2 SAH sing 470 n y C2 N3 SAH doub 471 n y C2 H2 SAH sing 472 n n N3 C4 SAH sing 473 n y # _atom_sites.entry_id 4RTN _atom_sites.fract_transf_matrix[1][1] 0.027624 _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] 0.015754 _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] 0.006942 _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 D 4 SAH A 1 301 301 SAH SAH . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 3 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 6 HOH HOH . E 5 HOH A 6 406 7 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 9 HOH HOH . E 5 HOH A 9 409 10 HOH HOH . E 5 HOH A 10 410 11 HOH HOH . E 5 HOH A 11 411 12 HOH HOH . E 5 HOH A 12 412 13 HOH HOH . E 5 HOH A 13 413 14 HOH HOH . E 5 HOH A 14 414 15 HOH HOH . E 5 HOH A 15 415 16 HOH HOH . E 5 HOH A 16 416 17 HOH HOH . E 5 HOH A 17 417 18 HOH HOH . E 5 HOH A 18 418 19 HOH HOH . E 5 HOH A 19 419 20 HOH HOH . E 5 HOH A 20 420 21 HOH HOH . E 5 HOH A 21 421 23 HOH HOH . E 5 HOH A 22 422 24 HOH HOH . E 5 HOH A 23 423 25 HOH HOH . E 5 HOH A 24 424 26 HOH HOH . E 5 HOH A 25 425 28 HOH HOH . E 5 HOH A 26 426 29 HOH HOH . E 5 HOH A 27 427 35 HOH HOH . E 5 HOH A 28 428 37 HOH HOH . E 5 HOH A 29 429 38 HOH HOH . F 5 HOH F 1 101 36 HOH HOH . G 5 HOH G 1 101 27 HOH HOH . G 5 HOH G 2 102 32 HOH HOH . G 5 HOH G 3 103 33 HOH HOH . G 5 HOH G 4 104 34 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 . A . D 4 -4.364 0.985 83.767 0.5 29.03 ? N SAH 301 A 1 HETATM 2 N N SAH . B . D 4 -7.481 -1.456 88.35 0.5 25.85 ? N SAH 301 A 1 HETATM 3 C CA SAH . A . D 4 -5.019 1.965 84.622 0.5 27.44 ? CA SAH 301 A 1 HETATM 4 C CA SAH . B . D 4 -7.1 -1.008 89.684 0.5 26.8 ? CA SAH 301 A 1 HETATM 5 C CB SAH . A . D 4 -5.117 1.442 86.05 0.5 26.63 ? CB SAH 301 A 1 HETATM 6 C CB SAH . B . D 4 -5.757 -0.283 89.663 0.5 29.78 ? CB SAH 301 A 1 HETATM 7 C CG SAH . A . D 4 -3.813 1.501 86.834 0.5 26.52 ? CG SAH 301 A 1 HETATM 8 C CG SAH . B . D 4 -5.307 0.247 88.307 0.5 32.71 ? CG SAH 301 A 1 HETATM 9 S SD SAH . A . D 4 -4.025 0.959 88.548 0.5 35.44 ? SD SAH 301 A 1 HETATM 10 S SD SAH . B . D 4 -3.998 1.489 88.466 0.5 37.7 ? SD SAH 301 A 1 HETATM 11 C C SAH . A . D 4 -4.268 3.292 84.605 0.5 26.95 ? C SAH 301 A 1 HETATM 12 C C SAH . B . D 4 -8.179 -0.146 90.332 0.5 26.66 ? C SAH 301 A 1 HETATM 13 O O SAH . A . D 4 -3.107 3.356 84.202 0.5 26.36 ? O SAH 301 A 1 HETATM 14 O O SAH . B . D 4 -9.373 -0.419 90.198 0.5 29.21 ? O SAH 301 A 1 HETATM 15 O OXT SAH . A . D 4 -4.805 4.33 84.991 0.5 26.58 ? OXT SAH 301 A 1 HETATM 16 O OXT SAH . B . D 4 -7.885 0.835 91.015 0.5 23.68 ? OXT SAH 301 A 1 HETATM 17 C C5' SAH . A . D 4 -2.612 -0.158 88.373 0.5 33.43 ? C5' SAH 301 A 1 HETATM 18 C C5' SAH . B . D 4 -2.717 0.237 88.195 0.5 34.13 ? C5' SAH 301 A 1 HETATM 19 C C4' SAH . A . D 4 -1.99 -0.529 89.714 0.5 32.92 ? C4' SAH 301 A 1 HETATM 20 C C4' SAH . B . D 4 -2.099 -0.264 89.498 0.5 32.92 ? C4' SAH 301 A 1 HETATM 21 O O4' SAH . A . D 4 -0.984 -1.502 89.519 0.5 32.3 ? O4' SAH 301 A 1 HETATM 22 O O4' SAH . B . D 4 -1.117 -1.247 89.23 0.5 32.5 ? O4' SAH 301 A 1 HETATM 23 C C3' SAH . A . D 4 -1.333 0.657 90.404 0.5 32.23 ? C3' SAH 301 A 1 HETATM 24 C C3' SAH . B . D 4 -1.411 0.841 90.286 0.5 32.11 ? C3' SAH 301 A 1 HETATM 25 O O3' SAH . A . D 4 -2.009 0.937 91.608 0.5 31.91 ? O3' SAH 301 A 1 HETATM 26 O O3' SAH . B . D 4 -2.126 1.089 91.474 0.5 32.11 ? O3' SAH 301 A 1 HETATM 27 C C2' SAH . A . D 4 0.084 0.218 90.714 0.5 31.62 ? C2' SAH 301 A 1 HETATM 28 C C2' SAH . B . D 4 -0.036 0.302 90.625 0.5 32.01 ? C2' SAH 301 A 1 HETATM 29 O O2' SAH . A . D 4 0.374 0.421 92.077 0.5 31.64 ? O2' SAH 301 A 1 HETATM 30 O O2' SAH . B . D 4 0.195 0.38 92.011 0.5 31.74 ? O2' SAH 301 A 1 HETATM 31 C C1' SAH . A . D 4 0.113 -1.263 90.376 0.5 32.22 ? C1' SAH 301 A 1 HETATM 32 C C1' SAH . B . D 4 -0.068 -1.148 90.172 0.5 32.41 ? C1' SAH 301 A 1 HETATM 33 N N9 SAH . A . D 4 1.365 -1.632 89.695 0.5 31.55 ? N9 SAH 301 A 1 HETATM 34 N N9 SAH . B . D 4 1.217 -1.556 89.572 0.5 31.36 ? N9 SAH 301 A 1 HETATM 35 C C8 SAH . A . D 4 2.15 -0.818 88.921 0.5 31.32 ? C8 SAH 301 A 1 HETATM 36 C C8 SAH . B . D 4 2.048 -0.782 88.805 0.5 31.36 ? C8 SAH 301 A 1 HETATM 37 N N7 SAH . A . D 4 3.207 -1.538 88.479 0.5 31.14 ? N7 SAH 301 A 1 HETATM 38 N N7 SAH . B . D 4 3.123 -1.524 88.45 0.5 31.14 ? N7 SAH 301 A 1 HETATM 39 C C5 SAH . A . D 4 3.105 -2.797 88.958 0.5 31.56 ? C5 SAH 301 A 1 HETATM 40 C C5 SAH . B . D 4 2.99 -2.76 88.979 0.5 31.67 ? C5 SAH 301 A 1 HETATM 41 C C6 SAH . A . D 4 3.905 -3.924 88.813 0.5 32.61 ? C6 SAH 301 A 1 HETATM 42 C C6 SAH . B . D 4 3.793 -3.893 88.925 0.5 32.7 ? C6 SAH 301 A 1 HETATM 43 N N6 SAH . A . D 4 5.014 -3.869 88.082 0.5 32.49 ? N6 SAH 301 A 1 HETATM 44 N N6 SAH . B . D 4 4.94 -3.876 88.25 0.5 32.48 ? N6 SAH 301 A 1 HETATM 45 N N1 SAH . A . D 4 3.543 -5.102 89.432 0.5 31.87 ? N1 SAH 301 A 1 HETATM 46 N N1 SAH . B . D 4 3.392 -5.039 89.578 0.5 31.72 ? N1 SAH 301 A 1 HETATM 47 C C2 SAH . A . D 4 2.391 -5.155 90.19 0.5 31.86 ? C2 SAH 301 A 1 HETATM 48 C C2 SAH . B . D 4 2.201 -5.053 90.278 0.5 31.56 ? C2 SAH 301 A 1 HETATM 49 N N3 SAH . A . D 4 1.601 -4.032 90.33 0.5 31.55 ? N3 SAH 301 A 1 HETATM 50 N N3 SAH . B . D 4 1.409 -3.924 90.328 0.5 31.46 ? N3 SAH 301 A 1 HETATM 51 C C4 SAH . A . D 4 1.952 -2.871 89.725 0.5 31.3 ? C4 SAH 301 A 1 HETATM 52 C C4 SAH . B . D 4 1.797 -2.794 89.688 0.5 31.27 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 52 #