data_4RVD # _model_server_result.job_id vI3rVhWv2H0B2fYh5g9ipA _model_server_result.datetime_utc '2025-01-15 14:15:48' _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 4rvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 4RVD # _exptl.entry_id 4RVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 4RVD _cell.length_a 134.767 _cell.length_b 134.767 _cell.length_c 129.705 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _struct_asym.id C _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 covale ? covale1 A C CYS 348 A CYS 348 1_555 A N CSO 349 A CSO 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C CSO 349 A CSO 349 1_555 A N ASP 350 A ASP 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A SG CYS 13 A CYS 13 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 A SG CYS 16 A CYS 16 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc3 A SG CYS 56 A CYS 56 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 A SG CYS 59 A CYS 59 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _chem_comp.type non-polymer _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 SAM sing 297 n n N HN1 SAM sing 298 n n N HN2 SAM sing 299 n n CA C SAM sing 300 n n CA CB SAM sing 301 n n CA HA SAM sing 302 n n C O SAM doub 303 n n C OXT SAM sing 304 n n CB CG SAM sing 305 n n CB HB1 SAM sing 306 n n CB HB2 SAM sing 307 n n CG SD SAM sing 308 n n CG HG1 SAM sing 309 n n CG HG2 SAM sing 310 n n SD CE SAM sing 311 n n SD C5' SAM sing 312 n n CE HE1 SAM sing 313 n n CE HE2 SAM sing 314 n n CE HE3 SAM sing 315 n n C5' C4' SAM sing 316 n n C5' "H5'1" SAM sing 317 n n C5' "H5'2" SAM sing 318 n n C4' O4' SAM sing 319 n n C4' C3' SAM sing 320 n n C4' H4' SAM sing 321 n n O4' C1' SAM sing 322 n n C3' O3' SAM sing 323 n n C3' C2' SAM sing 324 n n C3' H3' SAM sing 325 n n O3' HO3' SAM sing 326 n n C2' O2' SAM sing 327 n n C2' C1' SAM sing 328 n n C2' H2' SAM sing 329 n n O2' HO2' SAM sing 330 n n C1' N9 SAM sing 331 n n C1' H1' SAM sing 332 n n N9 C8 SAM sing 333 n y N9 C4 SAM sing 334 n y C8 N7 SAM doub 335 n y C8 H8 SAM sing 336 n n N7 C5 SAM sing 337 n y C5 C6 SAM sing 338 n y C5 C4 SAM doub 339 n y C6 N6 SAM sing 340 n n C6 N1 SAM doub 341 n y N6 HN61 SAM sing 342 n n N6 HN62 SAM sing 343 n n N1 C2 SAM sing 344 n y C2 N3 SAM doub 345 n y C2 H2 SAM sing 346 n n N3 C4 SAM sing 347 n y # _atom_sites.entry_id 4RVD _atom_sites.fract_transf_matrix[1][1] 0.00742 _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] 0.00742 _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] 0.00771 _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 B 2 ZN A 1 501 500 ZN ZN . C 3 SAM A 1 502 601 SAM SAM . D 4 ACT A 1 503 603 ACT ACT . E 5 HOH A 1 601 1 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 3 HOH HOH . E 5 HOH A 4 604 4 HOH HOH . E 5 HOH A 5 605 5 HOH HOH . E 5 HOH A 6 606 6 HOH HOH . E 5 HOH A 7 607 7 HOH HOH . E 5 HOH A 8 608 8 HOH HOH . E 5 HOH A 9 609 10 HOH HOH . E 5 HOH A 10 610 11 HOH HOH . E 5 HOH A 11 611 12 HOH HOH . E 5 HOH A 12 612 14 HOH HOH . E 5 HOH A 13 613 15 HOH HOH . E 5 HOH A 14 614 16 HOH HOH . E 5 HOH A 15 615 17 HOH HOH . E 5 HOH A 16 616 18 HOH HOH . E 5 HOH A 17 617 19 HOH HOH . E 5 HOH A 18 618 21 HOH HOH . E 5 HOH A 19 619 22 HOH HOH . E 5 HOH A 20 620 23 HOH HOH . E 5 HOH A 21 621 24 HOH HOH . E 5 HOH A 22 622 26 HOH HOH . E 5 HOH A 23 623 27 HOH HOH . E 5 HOH A 24 624 29 HOH HOH . E 5 HOH A 25 625 30 HOH HOH . E 5 HOH A 26 626 31 HOH HOH . E 5 HOH A 27 627 32 HOH HOH . E 5 HOH A 28 628 33 HOH HOH . E 5 HOH A 29 629 34 HOH HOH . E 5 HOH A 30 630 35 HOH HOH . E 5 HOH A 31 631 37 HOH HOH . E 5 HOH A 32 632 38 HOH HOH . E 5 HOH A 33 633 39 HOH HOH . E 5 HOH A 34 634 42 HOH HOH . E 5 HOH A 35 635 43 HOH HOH . E 5 HOH A 36 636 44 HOH HOH . E 5 HOH A 37 637 54 HOH HOH . E 5 HOH A 38 638 56 HOH HOH . E 5 HOH A 39 639 57 HOH HOH . E 5 HOH A 40 640 58 HOH HOH . E 5 HOH A 41 641 60 HOH HOH . E 5 HOH A 42 642 62 HOH HOH . E 5 HOH A 43 643 65 HOH HOH . E 5 HOH A 44 644 66 HOH HOH . E 5 HOH A 45 645 67 HOH HOH . E 5 HOH A 46 646 68 HOH HOH . E 5 HOH A 47 647 71 HOH HOH . E 5 HOH A 48 648 75 HOH HOH . E 5 HOH A 49 649 76 HOH HOH . E 5 HOH A 50 650 84 HOH HOH . E 5 HOH A 51 651 91 HOH HOH . E 5 HOH A 52 652 92 HOH HOH . E 5 HOH A 53 653 93 HOH HOH . E 5 HOH A 54 654 117 HOH HOH . E 5 HOH A 55 655 121 HOH HOH . E 5 HOH A 56 656 122 HOH HOH . E 5 HOH A 57 657 123 HOH HOH . E 5 HOH A 58 658 125 HOH HOH . E 5 HOH A 59 659 126 HOH HOH . E 5 HOH A 60 660 127 HOH HOH . E 5 HOH A 61 661 128 HOH HOH . E 5 HOH A 62 662 129 HOH HOH . E 5 HOH A 63 663 130 HOH HOH . E 5 HOH A 64 664 131 HOH HOH . E 5 HOH A 65 665 132 HOH HOH . E 5 HOH A 66 666 133 HOH HOH . E 5 HOH A 67 667 134 HOH HOH . E 5 HOH A 68 668 135 HOH HOH . E 5 HOH A 69 669 136 HOH HOH . E 5 HOH A 70 670 137 HOH HOH . E 5 HOH A 71 671 138 HOH HOH . E 5 HOH A 72 672 139 HOH HOH . E 5 HOH A 73 673 140 HOH HOH . E 5 HOH A 74 674 141 HOH HOH . E 5 HOH A 75 675 142 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 SAM . . . C 3 -26.74 -0.708 3.648 1 42.79 ? N SAM 502 A 1 HETATM 2 C CA SAM . . . C 3 -25.673 0.208 4.028 1 46.56 ? CA SAM 502 A 1 HETATM 3 C C SAM . . . C 3 -24.738 -0.407 5.046 1 46.47 ? C SAM 502 A 1 HETATM 4 O O SAM . . . C 3 -25.008 -1.515 5.562 1 46.78 ? O SAM 502 A 1 HETATM 5 O OXT SAM . . . C 3 -23.713 0.234 5.356 1 47.29 ? OXT SAM 502 A 1 HETATM 6 C CB SAM . . . C 3 -26.246 1.513 4.588 1 47.16 ? CB SAM 502 A 1 HETATM 7 C CG SAM . . . C 3 -27.181 1.298 5.784 1 50.12 ? CG SAM 502 A 1 HETATM 8 S SD SAM . . . C 3 -27.749 2.748 6.408 1 51.74 ? SD SAM 502 A 1 HETATM 9 C CE SAM . . . C 3 -27.471 2.74 8.056 1 50.75 ? CE SAM 502 A 1 HETATM 10 C C5' SAM . . . C 3 -29.394 2.933 6.106 1 45.46 ? C5' SAM 502 A 1 HETATM 11 C C4' SAM . . . C 3 -29.644 3.198 4.615 1 41.91 ? C4' SAM 502 A 1 HETATM 12 O O4' SAM . . . C 3 -30.956 2.757 4.239 1 40.78 ? O4' SAM 502 A 1 HETATM 13 C C3' SAM . . . C 3 -29.555 4.672 4.21 1 39.01 ? C3' SAM 502 A 1 HETATM 14 O O3' SAM . . . C 3 -28.779 4.819 3.006 1 34.89 ? O3' SAM 502 A 1 HETATM 15 C C2' SAM . . . C 3 -31.001 5.096 3.99 1 38.62 ? C2' SAM 502 A 1 HETATM 16 O O2' SAM . . . C 3 -31.153 6.124 3.006 1 35.53 ? O2' SAM 502 A 1 HETATM 17 C C1' SAM . . . C 3 -31.638 3.802 3.532 1 38.78 ? C1' SAM 502 A 1 HETATM 18 N N9 SAM . . . C 3 -33.078 3.642 3.825 1 38.85 ? N9 SAM 502 A 1 HETATM 19 C C8 SAM . . . C 3 -33.75 4.068 4.909 1 38.79 ? C8 SAM 502 A 1 HETATM 20 N N7 SAM . . . C 3 -35.045 3.696 4.833 1 36.91 ? N7 SAM 502 A 1 HETATM 21 C C5 SAM . . . C 3 -35.214 3.01 3.702 1 36.59 ? C5 SAM 502 A 1 HETATM 22 C C6 SAM . . . C 3 -36.342 2.339 3.032 1 37.09 ? C6 SAM 502 A 1 HETATM 23 N N6 SAM . . . C 3 -37.561 2.355 3.611 1 37.37 ? N6 SAM 502 A 1 HETATM 24 N N1 SAM . . . C 3 -36.111 1.733 1.845 1 35.98 ? N1 SAM 502 A 1 HETATM 25 C C2 SAM . . . C 3 -34.879 1.736 1.284 1 37.9 ? C2 SAM 502 A 1 HETATM 26 N N3 SAM . . . C 3 -33.803 2.331 1.849 1 36.52 ? N3 SAM 502 A 1 HETATM 27 C C4 SAM . . . C 3 -33.912 2.97 3.036 1 37.36 ? C4 SAM 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #