data_4R6X # _model_server_result.job_id v0pADQvmiNG_83_9ubW-yw _model_server_result.datetime_utc '2024-11-23 22:23:12' _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 4r6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 4R6X # _exptl.entry_id 4R6X _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 107.79 _cell.angle_gamma 90 _cell.entry_id 4R6X _cell.length_a 76.826 _cell.length_b 43.652 _cell.length_c 88.053 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R6X _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 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,G 1 1 B,E,F,H 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 D N N ? 3 F 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 292 n n N HN1 SAH sing 293 n n N HN2 SAH sing 294 n n CA CB SAH sing 295 n n CA C SAH sing 296 n n CA HA SAH sing 297 n n CB CG SAH sing 298 n n CB HB1 SAH sing 299 n n CB HB2 SAH sing 300 n n CG SD SAH sing 301 n n CG HG1 SAH sing 302 n n CG HG2 SAH sing 303 n n SD C5' SAH sing 304 n n C O SAH doub 305 n n C OXT SAH sing 306 n n OXT HXT SAH sing 307 n n C5' C4' SAH sing 308 n n C5' "H5'1" SAH sing 309 n n C5' "H5'2" SAH sing 310 n n C4' O4' SAH sing 311 n n C4' C3' SAH sing 312 n n C4' H4' SAH sing 313 n n O4' C1' SAH sing 314 n n C3' O3' SAH sing 315 n n C3' C2' SAH sing 316 n n C3' H3' SAH sing 317 n n O3' HO3' SAH sing 318 n n C2' O2' SAH sing 319 n n C2' C1' SAH sing 320 n n C2' H2' SAH sing 321 n n O2' HO2' SAH sing 322 n n C1' N9 SAH sing 323 n n C1' H1' SAH sing 324 n n N9 C8 SAH sing 325 n y N9 C4 SAH sing 326 n y C8 N7 SAH doub 327 n y C8 H8 SAH sing 328 n n N7 C5 SAH sing 329 n y C5 C6 SAH sing 330 n y C5 C4 SAH doub 331 n y C6 N6 SAH sing 332 n n C6 N1 SAH doub 333 n y N6 HN61 SAH sing 334 n n N6 HN62 SAH sing 335 n n N1 C2 SAH sing 336 n y C2 N3 SAH doub 337 n y C2 H2 SAH sing 338 n n N3 C4 SAH sing 339 n y # _atom_sites.entry_id 4R6X _atom_sites.fract_transf_matrix[1][1] 0.013016 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004177 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022908 _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] 0.011927 _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 OPE A 1 501 501 OPE OPE . D 3 SAH A 1 502 502 SAH SAH . E 2 OPE B 1 501 501 OPE OPE . F 3 SAH B 1 502 502 SAH SAH . G 4 HOH A 1 601 2 HOH HOH . G 4 HOH A 2 602 3 HOH HOH . G 4 HOH A 3 603 4 HOH HOH . G 4 HOH A 4 604 8 HOH HOH . G 4 HOH A 5 605 10 HOH HOH . G 4 HOH A 6 606 11 HOH HOH . G 4 HOH A 7 607 12 HOH HOH . G 4 HOH A 8 608 13 HOH HOH . G 4 HOH A 9 609 18 HOH HOH . G 4 HOH A 10 610 20 HOH HOH . G 4 HOH A 11 611 22 HOH HOH . G 4 HOH A 12 612 25 HOH HOH . G 4 HOH A 13 613 27 HOH HOH . G 4 HOH A 14 614 29 HOH HOH . G 4 HOH A 15 615 30 HOH HOH . G 4 HOH A 16 616 31 HOH HOH . G 4 HOH A 17 617 32 HOH HOH . G 4 HOH A 18 618 34 HOH HOH . G 4 HOH A 19 619 36 HOH HOH . G 4 HOH A 20 620 40 HOH HOH . G 4 HOH A 21 621 41 HOH HOH . G 4 HOH A 22 622 45 HOH HOH . G 4 HOH A 23 623 46 HOH HOH . G 4 HOH A 24 624 49 HOH HOH . G 4 HOH A 25 625 51 HOH HOH . G 4 HOH A 26 626 54 HOH HOH . G 4 HOH A 27 627 55 HOH HOH . G 4 HOH A 28 628 56 HOH HOH . G 4 HOH A 29 629 57 HOH HOH . G 4 HOH A 30 630 58 HOH HOH . G 4 HOH A 31 631 59 HOH HOH . G 4 HOH A 32 632 62 HOH HOH . G 4 HOH A 33 633 63 HOH HOH . G 4 HOH A 34 634 64 HOH HOH . G 4 HOH A 35 635 65 HOH HOH . G 4 HOH A 36 636 66 HOH HOH . G 4 HOH A 37 637 68 HOH HOH . G 4 HOH A 38 638 69 HOH HOH . G 4 HOH A 39 639 70 HOH HOH . G 4 HOH A 40 640 71 HOH HOH . G 4 HOH A 41 641 72 HOH HOH . G 4 HOH A 42 642 73 HOH HOH . G 4 HOH A 43 643 75 HOH HOH . G 4 HOH A 44 644 77 HOH HOH . G 4 HOH A 45 645 78 HOH HOH . G 4 HOH A 46 646 79 HOH HOH . G 4 HOH A 47 647 80 HOH HOH . G 4 HOH A 48 648 81 HOH HOH . G 4 HOH A 49 649 83 HOH HOH . G 4 HOH A 50 650 85 HOH HOH . G 4 HOH A 51 651 87 HOH HOH . G 4 HOH A 52 652 88 HOH HOH . G 4 HOH A 53 653 89 HOH HOH . G 4 HOH A 54 654 91 HOH HOH . G 4 HOH A 55 655 92 HOH HOH . G 4 HOH A 56 656 93 HOH HOH . G 4 HOH A 57 657 94 HOH HOH . G 4 HOH A 58 658 95 HOH HOH . G 4 HOH A 59 659 96 HOH HOH . G 4 HOH A 60 660 98 HOH HOH . G 4 HOH A 61 661 99 HOH HOH . G 4 HOH A 62 662 100 HOH HOH . G 4 HOH A 63 663 101 HOH HOH . G 4 HOH A 64 664 105 HOH HOH . G 4 HOH A 65 665 107 HOH HOH . G 4 HOH A 66 666 109 HOH HOH . G 4 HOH A 67 667 111 HOH HOH . G 4 HOH A 68 668 113 HOH HOH . G 4 HOH A 69 669 115 HOH HOH . G 4 HOH A 70 670 116 HOH HOH . G 4 HOH A 71 671 117 HOH HOH . G 4 HOH A 72 672 118 HOH HOH . G 4 HOH A 73 673 120 HOH HOH . G 4 HOH A 74 674 121 HOH HOH . G 4 HOH A 75 675 123 HOH HOH . G 4 HOH A 76 676 124 HOH HOH . G 4 HOH A 77 677 125 HOH HOH . G 4 HOH A 78 678 126 HOH HOH . G 4 HOH A 79 679 129 HOH HOH . G 4 HOH A 80 680 130 HOH HOH . G 4 HOH A 81 681 131 HOH HOH . G 4 HOH A 82 682 132 HOH HOH . G 4 HOH A 83 683 133 HOH HOH . G 4 HOH A 84 684 134 HOH HOH . G 4 HOH A 85 685 137 HOH HOH . G 4 HOH A 86 686 141 HOH HOH . G 4 HOH A 87 687 142 HOH HOH . H 4 HOH B 1 601 1 HOH HOH . H 4 HOH B 2 602 5 HOH HOH . H 4 HOH B 3 603 7 HOH HOH . H 4 HOH B 4 604 9 HOH HOH . H 4 HOH B 5 605 15 HOH HOH . H 4 HOH B 6 606 16 HOH HOH . H 4 HOH B 7 607 17 HOH HOH . H 4 HOH B 8 608 19 HOH HOH . H 4 HOH B 9 609 23 HOH HOH . H 4 HOH B 10 610 24 HOH HOH . H 4 HOH B 11 611 26 HOH HOH . H 4 HOH B 12 612 33 HOH HOH . H 4 HOH B 13 613 35 HOH HOH . H 4 HOH B 14 614 37 HOH HOH . H 4 HOH B 15 615 39 HOH HOH . H 4 HOH B 16 616 42 HOH HOH . H 4 HOH B 17 617 43 HOH HOH . H 4 HOH B 18 618 44 HOH HOH . H 4 HOH B 19 619 47 HOH HOH . H 4 HOH B 20 620 48 HOH HOH . H 4 HOH B 21 621 50 HOH HOH . H 4 HOH B 22 622 52 HOH HOH . H 4 HOH B 23 623 53 HOH HOH . H 4 HOH B 24 624 60 HOH HOH . H 4 HOH B 25 625 67 HOH HOH . H 4 HOH B 26 626 74 HOH HOH . H 4 HOH B 27 627 76 HOH HOH . H 4 HOH B 28 628 82 HOH HOH . H 4 HOH B 29 629 84 HOH HOH . H 4 HOH B 30 630 86 HOH HOH . H 4 HOH B 31 631 90 HOH HOH . H 4 HOH B 32 632 103 HOH HOH . H 4 HOH B 33 633 104 HOH HOH . H 4 HOH B 34 634 106 HOH HOH . H 4 HOH B 35 635 108 HOH HOH . H 4 HOH B 36 636 110 HOH HOH . H 4 HOH B 37 637 112 HOH HOH . H 4 HOH B 38 638 114 HOH HOH . H 4 HOH B 39 639 119 HOH HOH . H 4 HOH B 40 640 122 HOH HOH . H 4 HOH B 41 641 127 HOH HOH . H 4 HOH B 42 642 128 HOH HOH . H 4 HOH B 43 643 135 HOH HOH . H 4 HOH B 44 644 136 HOH HOH . H 4 HOH B 45 645 138 HOH HOH . H 4 HOH B 46 646 139 HOH HOH . H 4 HOH B 47 647 140 HOH HOH . H 4 HOH B 48 648 143 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 53.684 21.219 17.448 1 18.36 ? N SAH 502 B 1 HETATM 2 C CA SAH . . . F 3 54.455 22.192 18.252 1 15.05 ? CA SAH 502 B 1 HETATM 3 C CB SAH . . . F 3 54.37 23.64 17.613 1 17.52 ? CB SAH 502 B 1 HETATM 4 C CG SAH . . . F 3 53.281 24.581 18.142 1 17.02 ? CG SAH 502 B 1 HETATM 5 S SD SAH . . . F 3 53.186 26.25 17.414 1 22.78 ? SD SAH 502 B 1 HETATM 6 C C SAH . . . F 3 54.034 22.1 19.664 1 17.29 ? C SAH 502 B 1 HETATM 7 O O SAH . . . F 3 52.876 21.835 19.929 1 28.29 ? O SAH 502 B 1 HETATM 8 O OXT SAH . . . F 3 54.85 22.205 20.549 1 16.35 ? OXT SAH 502 B 1 HETATM 9 C C5' SAH . . . F 3 52.474 26.12 15.757 1 15.83 ? C5' SAH 502 B 1 HETATM 10 C C4' SAH . . . F 3 53.32 25.719 14.689 1 21.28 ? C4' SAH 502 B 1 HETATM 11 O O4' SAH . . . F 3 52.516 25.524 13.493 1 17.75 ? O4' SAH 502 B 1 HETATM 12 C C3' SAH . . . F 3 54.25 26.822 14.371 1 27.81 ? C3' SAH 502 B 1 HETATM 13 O O3' SAH . . . F 3 55.576 26.45 14.667 1 24.88 ? O3' SAH 502 B 1 HETATM 14 C C2' SAH . . . F 3 54.099 27.08 12.943 1 29.69 ? C2' SAH 502 B 1 HETATM 15 O O2' SAH . . . F 3 55.348 27.144 12.318 1 32.15 ? O2' SAH 502 B 1 HETATM 16 C C1' SAH . . . F 3 53.345 25.901 12.442 1 17.25 ? C1' SAH 502 B 1 HETATM 17 N N9 SAH . . . F 3 52.687 26.184 11.112 1 12.26 ? N9 SAH 502 B 1 HETATM 18 C C8 SAH . . . F 3 51.777 27.121 10.811 1 22.79 ? C8 SAH 502 B 1 HETATM 19 N N7 SAH . . . F 3 51.485 26.99 9.513 1 19.43 ? N7 SAH 502 B 1 HETATM 20 C C5 SAH . . . F 3 52.201 25.984 8.996 1 17.74 ? C5 SAH 502 B 1 HETATM 21 C C6 SAH . . . F 3 52.295 25.419 7.715 1 17.63 ? C6 SAH 502 B 1 HETATM 22 N N6 SAH . . . F 3 51.54 25.908 6.681 1 12.9 ? N6 SAH 502 B 1 HETATM 23 N N1 SAH . . . F 3 53.135 24.384 7.523 1 21.11 ? N1 SAH 502 B 1 HETATM 24 C C2 SAH . . . F 3 53.868 23.899 8.524 1 17.4 ? C2 SAH 502 B 1 HETATM 25 N N3 SAH . . . F 3 53.802 24.423 9.77 1 20.5 ? N3 SAH 502 B 1 HETATM 26 C C4 SAH . . . F 3 52.982 25.457 10.026 1 15.69 ? C4 SAH 502 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #